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Harrigan SP, Velásquez García HA, Abdia Y, Wilton J, Prystajecky N, Tyson J, Fjell C, Hoang L, Kwong JC, Mishra S, Wang L, Sander B, Janjua NZ, Sbihi H. The Clinical Severity of COVID-19 Variants of Concern: Retrospective Population-Based Analysis. JMIR Public Health Surveill 2024; 10:e45513. [PMID: 39190434 PMCID: PMC11387920 DOI: 10.2196/45513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND SARS-CoV-2 variants of concern (VOCs) emerged and rapidly replaced the original strain worldwide. The increased transmissibility of these new variants led to increases in infections, hospitalizations, and mortality. However, there is a scarcity of retrospective investigations examining the severity of all the main VOCs in presence of key public health measures and within various social determinants of health (SDOHs). OBJECTIVE This study aims to provide a retrospective assessment of the clinical severity of COVID-19 VOCs in the context of heterogenous SDOHs and vaccination rollout. METHODS We used a population-based retrospective cohort design with data from the British Columbia COVID-19 Cohort, a linked provincial surveillance platform. To assess the relative severity (hospitalizations, intensive care unit [ICU] admissions, and deaths) of Gamma, Delta, and Omicron infections during 2021 relative to Alpha, we used inverse probability treatment weighted Cox proportional hazard modeling. We also conducted a subanalysis among unvaccinated individuals, as assessed severity differed across VOCs and SDOHs. RESULTS We included 91,964 individuals infected with a SARS-CoV-2 VOC (Alpha: n=20,487, 22.28%; Gamma: n=15,223, 16.55%; Delta: n=49,161, 53.46%; and Omicron: n=7093, 7.71%). Delta was associated with the most severe disease in terms of hospitalization, ICU admissions, and deaths (hospitalization: adjusted hazard ratio [aHR] 2.00, 95% CI 1.92-2.08; ICU: aHR 2.05, 95% CI 1.91-2.20; death: aHR 3.70, 95% CI 3.23-4.25 relative to Alpha), followed generally by Gamma and then Omicron and Alpha. The relative severity by VOC remained similar in the unvaccinated individual subanalysis, although the proportion of individuals infected with Delta and Omicron who were hospitalized was 2 times higher in those unvaccinated than in those fully vaccinated. Regarding SDOHs, the proportion of hospitalized individuals was higher in areas with lower income across all VOCs, whereas among Alpha and Gamma infections, 2 VOCs that cocirculated, differential distributions of hospitalizations were found among racially minoritized groups. CONCLUSIONS Our study provides robust severity estimates for all VOCs during the COVID-19 pandemic in British Columbia, Canada. Relative to Alpha, we found Delta to be the most severe, followed by Gamma and Omicron. This study highlights the importance of targeted testing and sequencing to ensure timely detection and accurate estimation of severity in emerging variants. It further sheds light on the importance of vaccination coverage and SDOHs in the context of pandemic preparedness to support the prioritization of allocation for resource-constrained or minoritized groups.
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Affiliation(s)
- Sean P Harrigan
- BC Centre for Disease Control, Vancouver, BC, Canada
- University of British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | | | - Younathan Abdia
- University of British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - James Wilton
- BC Centre for Disease Control, Vancouver, BC, Canada
| | - Natalie Prystajecky
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - John Tyson
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chris Fjell
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Linda Hoang
- BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey C Kwong
- Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
- Public Health Ontario, Toronto, ON, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Sharmistha Mishra
- Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Linwei Wang
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, ON, Canada
| | - Beate Sander
- Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
- Public Health Ontario, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Toronto Health Economics and Technology Assessment Collaborative, University Health Network, Toronto, ON, Canada
| | - Naveed Z Janjua
- BC Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- Centre for Advancing Health Outcomes, St Paul's Hospital, Vancouver, BC, Canada
| | - Hind Sbihi
- BC Centre for Disease Control, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
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Xia Y, Sun R, Zhu Y, Wang J, Pang H, Chen M, Xu Z, Zhang Y. Moxibustion Treatment of COVID-19 and Rehabilitation Period of COVID-19: A Scoping Review. JOURNAL OF INTEGRATIVE AND COMPLEMENTARY MEDICINE 2023; 29:637-648. [PMID: 37159407 DOI: 10.1089/jicm.2022.0742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Objective: The aim of this study is to provide a scoping review of the clinical literature on moxibustion therapy for the treatment of Coronavirus disease 2019 (COVID-19). Design: The PubMed, Embase, Cochrane Library, MEDLINE, CNKI, Wanfang, and VIP databases were searched from January 1, 2020, to August 31, 2022. Essential data were extracted from each article, and the data were displayed using tables and graphs. The study did not require IRB approval. Results: This scoping review included 14 research articles: 8 observational studies, 5 randomized controlled trials, and 1 nonrandomized clinical trial. All the studies were published by Chinese scholars. The findings revealed that moxibustion can contribute to reducing the symptoms of patients with COVID-19, improving inflammation and immune indicators, and shortening the time of nucleic acid negative conversion. Moxibustion confers curative effects on patients of all ages and degrees of illness. In addition, moxibustion can optimize the prognosis of patients in the rehabilitation period. The most commonly chosen acupoints are ST36, RN4, RN8, and RN12. No side effect was mentioned in the included studies. Conclusion: Moxibustion can produce a good effect in the treatment and rehabilitation of patients with COVID-19. It is safe, effective, simple, and noninvasive and should be included as standard care.
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Affiliation(s)
- Yuge Xia
- The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Rui Sun
- School of Acupuncture-Moxibustion and Tuina, Anhui University of Chinese Medicine, Hefei, China
| | - Yunyi Zhu
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China
| | - Jing Wang
- The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hailin Pang
- Guangzhou Qinzheng Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Mingzhu Chen
- Guangzhou Zengcheng District Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Zhirui Xu
- Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yicong Zhang
- China Academy of Chinese Medical Sciences, Guang'anmen Hospital, Beijing, China
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3
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Yuan Z, Shao Z, Ma L, Guo R. Clinical Severity of SARS-CoV-2 Variants during COVID-19 Vaccination: A Systematic Review and Meta-Analysis. Viruses 2023; 15:1994. [PMID: 37896770 PMCID: PMC10611048 DOI: 10.3390/v15101994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Due to the variation in the SARS-CoV-2 virus, COVID-19 exhibits significant variability in severity. This presents challenges for governments in managing the allocation of healthcare resources and prioritizing health interventions. Clinical severity is also a critical statistical parameter for researchers to quantify the risks of infectious disease, model the transmission of COVID-19, and provide some targeted measures to control the pandemic. To obtain more accurate severity estimates, including confirmed case-hospitalization risk, confirmed case-fatality risk, hospitalization-fatality risk, and hospitalization-ICU risk, we conducted a systematic review and meta-analysis on the clinical severity (including hospitalization, ICU, and fatality risks) of different variants during the period of COVID-19 mass vaccination and provided pooled estimates for each clinical severity metric. All searches were carried out on 1 February 2022 in PubMed for articles published from 1 January 2020 to 1 February 2022. After identifying a total of 3536 studies and excluding 3523 irrelevant studies, 13 studies were included. The severity results show that the Delta and Omicron variants have the highest (6.56%, 0.46%, 19.63%, and 9.06%) and lowest severities (1.51%, 0.04%, 6.01%, and 3.18%), respectively, according to the four clinical severity metrics. Adults over 65 have higher severity levels for all four clinical severity metrics.
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Affiliation(s)
- Zhilu Yuan
- School of Architecture and Urban Planning, Research Institute for Smart Cities, Shenzhen University, Shenzhen 518060, China; (Z.Y.); (R.G.)
| | - Zengyang Shao
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Lijia Ma
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Renzhong Guo
- School of Architecture and Urban Planning, Research Institute for Smart Cities, Shenzhen University, Shenzhen 518060, China; (Z.Y.); (R.G.)
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Nyberg T, Bager P, Svalgaard IB, Bejko D, Bundle N, Evans J, Krause TG, McMenamin J, Mossong J, Mutch H, Omokanye A, Peralta-Santos A, Pinto-Leite P, Starrfelt J, Thelwall S, Veneti L, Whittaker R, Wood J, Pebody R, Presanis AM. A standardised protocol for relative SARS-CoV-2 variant severity assessment, applied to Omicron BA.1 and Delta in six European countries, October 2021 to February 2022. Euro Surveill 2023; 28:2300048. [PMID: 37676146 PMCID: PMC10486193 DOI: 10.2807/1560-7917.es.2023.28.36.2300048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/21/2023] [Indexed: 09/08/2023] Open
Abstract
Several SARS-CoV-2 variants that evolved during the COVID-19 pandemic have appeared to differ in severity, based on analyses of single-country datasets. With decreased testing and sequencing, international collaborative studies will become increasingly important for timely assessment of the severity of new variants. Therefore, a joint WHO Regional Office for Europe and ECDC working group was formed to produce and pilot a standardised study protocol to estimate relative case-severity of SARS-CoV-2 variants during periods when two variants were co-circulating. The study protocol and its associated statistical analysis code was applied by investigators in Denmark, England, Luxembourg, Norway, Portugal and Scotland to assess the severity of cases with the Omicron BA.1 virus variant relative to Delta. After pooling estimates using meta-analysis methods (random effects estimates), the risk of hospital admission (adjusted hazard ratio (aHR) = 0.41; 95% confidence interval (CI): 0.31-0.54), admission to intensive care unit (aHR = 0.12; 95% CI: 0.05-0.27) and death (aHR = 0.31; 95% CI: 0.28-0.35) was lower for Omicron BA.1 compared with Delta cases. The aHRs varied by age group and vaccination status. In conclusion, this study demonstrates the feasibility of conducting variant severity analyses in a multinational collaborative framework and adds evidence for the reduced severity of the Omicron BA.1 variant.
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Affiliation(s)
- Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | - Nick Bundle
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Josie Evans
- Public Health Scotland, Glasgow, Scotland, United Kingdom
| | | | - Jim McMenamin
- Public Health Scotland, Glasgow, Scotland, United Kingdom
| | | | - Heather Mutch
- Public Health Scotland, Glasgow, Scotland, United Kingdom
| | - Ajibola Omokanye
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | | | | | - Simon Thelwall
- COVID-19 Vaccines and Epidemiology Division, UK Health Security Agency, London, United Kingdom
| | | | | | - John Wood
- Public Health Scotland, Glasgow, Scotland, United Kingdom
| | - Richard Pebody
- These authors contributed equally to this work and share last authorship
- World Health Organization Regional Office for Europe, Copenhagen, Denmark
| | - Anne M Presanis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
- These authors contributed equally to this work and share last authorship
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5
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Cobat A, Zhang Q, Abel L, Casanova JL, Fellay J. Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants. Annu Rev Biomed Data Sci 2023; 6:465-486. [PMID: 37196358 PMCID: PMC10879986 DOI: 10.1146/annurev-biodatasci-020222-021705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is silent or benign in most infected individuals, but causes hypoxemic COVID-19 pneumonia in about 10% of cases. We review studies of the human genetics of life-threatening COVID-19 pneumonia, focusing on both rare and common variants. Large-scale genome-wide association studies have identified more than 20 common loci robustly associated with COVID-19 pneumonia with modest effect sizes, some implicating genes expressed in the lungs or leukocytes. The most robust association, on chromosome 3, concerns a haplotype inherited from Neanderthals. Sequencing studies focusing on rare variants with a strong effect have been particularly successful, identifying inborn errors of type I interferon (IFN) immunity in 1-5% of unvaccinated patients with critical pneumonia, and their autoimmune phenocopy, autoantibodies against type I IFN, in another 15-20% of cases. Our growing understanding of the impact of human genetic variation on immunity to SARS-CoV-2 is enabling health systems to improve protection for individuals and populations.
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Affiliation(s)
- Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Pascall DJ, Vink E, Blacow R, Bulteel N, Campbell A, Campbell R, Clifford S, Davis C, da Silva Filipe A, El Sakka N, Fjodorova L, Forrest R, Goldstein E, Gunson R, Haughney J, Holden MTG, Honour P, Hughes J, James E, Lewis T, MacLean O, McHugh M, Mollett G, Nyberg T, Onishi Y, Parcell B, Ray S, Robertson DL, Seaman SR, Shabaan S, Shepherd JG, Smollett K, Templeton K, Wastnedge E, Wilkie C, Williams T, Thomson EC. Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. J Infect 2023; 87:128-135. [PMID: 37270070 PMCID: PMC10234362 DOI: 10.1016/j.jinf.2023.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVES To determine how the intrinsic severity of successively dominant SARS-CoV-2 variants changed over the course of the pandemic. METHODS A retrospective cohort analysis in the NHS Greater Glasgow and Clyde (NHS GGC) Health Board. All sequenced non-nosocomial adult COVID-19 cases in NHS GGC with relevant SARS-CoV-2 lineages (B.1.177/Alpha, Alpha/Delta, AY.4.2 Delta/non-AY.4.2 Delta, non-AY.4.2 Delta/Omicron, and BA.1 Omicron/BA.2 Omicron) during analysis periods were included. Outcome measures were hospital admission, ICU admission, or death within 28 days of positive COVID-19 test. We report the cumulative odds ratio; the ratio of the odds that an individual experiences a severity event of a given level vs all lower severity levels for the resident and the replacement variant after adjustment. RESULTS After adjustment for covariates, the cumulative odds ratio was 1.51 (95% CI: 1.08-2.11) for Alpha versus B.1.177, 2.09 (95% CI: 1.42-3.08) for Delta versus Alpha, 0.99 (95% CI: 0.76-1.27) for AY.4.2 Delta versus non-AY.4.2 Delta, 0.49 (95% CI: 0.22-1.06) for Omicron versus non-AY.4.2 Delta, and 0.86 (95% CI: 0.68-1.09) for BA.2 Omicron versus BA.1 Omicron. CONCLUSIONS The direction of change in intrinsic severity between successively emerging SARS-CoV-2 variants was inconsistent, reminding us that the intrinsic severity of future SARS-CoV-2 variants remains uncertain.
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Affiliation(s)
- David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom; Joint Universities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom.
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Lothian, Edinburgh EH1 3EG, United Kingdom.
| | - Rachel Blacow
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | | | | | | | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | | | | | - Emily Goldstein
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Rory Gunson
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - John Haughney
- NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Matthew T G Holden
- Public Health Scotland, Edinburgh EH12 9EB, United Kingdom; School of Medicine, University of St Andrews, St Andrews KY16 9TF, United Kingdom.
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | - Tim Lewis
- NHS Lothian, Edinburgh EH1 3EG, United Kingdom.
| | - Oscar MacLean
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | - Guy Mollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom.
| | - Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom.
| | | | - Ben Parcell
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8TA, United Kingdom.
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Shaun R Seaman
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, United Kingdom.
| | - Sharif Shabaan
- Public Health Scotland, Edinburgh EH12 9EB, United Kingdom.
| | - James G Shepherd
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom.
| | | | | | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8TA, United Kingdom.
| | - Thomas Williams
- NHS Lothian, Edinburgh EH1 3EG, United Kingdom; Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom.
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, United Kingdom; NHS Greater Glasgow and Clyde, Glasgow G12 0XH, United Kingdom; London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.
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7
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Morales-Bayuelo A, Sánchez-Márquez J. Receptor-Based Pharmacophore Modelling of a series of ligands used as inhibitors of the SARS-CoV-2 virus by complementary theoretical approaches, molecular docking, and reactivity descriptors. F1000Res 2023; 12:749. [PMID: 39291142 PMCID: PMC11406136 DOI: 10.12688/f1000research.133426.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 09/19/2024] Open
Abstract
Background: A coronavirus identified in 2019, SARS- CoV- 2, has caused a pandemic of respiratory illness, called COVID- 19. Most people with COVID-19 experience mild to moderate symptoms and recover without the need for special treatments. The SARS‑CoV‑2 RNA‑dependent RNA polymerase (RdRp) plays a crucial role in the viral life cycle. The active site of the RdRp is a very accessible region, so targeting this region to study the inhibition of viral replication may be an effective therapeutic approach. For this reason, this study has selected and analysed a series of ligands used as SARS-CoV-2 virus inhibitors, namely: the Zidovudine, Tromantadine, Pyramidine, Oseltamivir, Hydroxychoroquine, Cobicistat, Doravirine (Pifeltro), Dolutegravir, Boceprevir, Indinavir, Truvada, Trizivir, Trifluridine, Sofosbuvir and Zalcitabine. Methods: These ligands were analyzed using molecular docking, Receptor-Based Pharmacophore Modelling. On the other hand, these outcomes were supported with chemical reactivity indices defined within a conceptual density functional theory framework. Results: The results show the conformations with the highest root-mean-square deviation (RMSD), have π-π stacking interaction with residue LEU141, GLN189, GLU166 and GLY143, HIE41, among others. Also was development an electrostatic potential comparison using the global and local reactivity indices. Conclusions: These studies allow the identification of the main stabilizing interactions using the crystal structure of SARS‑CoV‑2 RNA‑dependent RNA polymerase. In this order of ideas, this study provides new insights into these ligands that can be used in the design of new COVID-19 treatments. The studies allowed us to find an explanation supported in the Density Functional Theory about the chemical reactivity and the stabilization in the active site of the ligands.
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Gottlieb M, Wang RC, Yu H, Spatz ES, Montoy JCC, Rodriguez RM, Chang AM, Elmore JG, Hannikainen PA, Hill M, Huebinger RM, Idris AH, Lin Z, Koo K, McDonald S, O’Laughlin KN, Plumb ID, Santangelo M, Saydah S, Willis M, Wisk LE, Venkatesh A, Stephens KA, Weinstein RA. Severe Fatigue and Persistent Symptoms at 3 Months Following Severe Acute Respiratory Syndrome Coronavirus 2 Infections During the Pre-Delta, Delta, and Omicron Time Periods: A Multicenter Prospective Cohort Study. Clin Infect Dis 2023; 76:1930-1941. [PMID: 36705268 PMCID: PMC10249989 DOI: 10.1093/cid/ciad045] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/12/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Most research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants focuses on initial symptomatology with limited longer-term data. We characterized prevalences of prolonged symptoms 3 months post-SARS-CoV-2 infection across 3 variant time-periods (pre-Delta, Delta, and Omicron). METHODS This multicenter prospective cohort study of adults with acute illness tested for SARS-CoV-2 compared fatigue severity, fatigue symptoms, organ system-based symptoms, and ≥3 symptoms across variants among participants with a positive ("COVID-positive") or negative SARS-CoV-2 test ("COVID-negative") at 3 months after SARS-CoV-2 testing. Variant periods were defined by dates with ≥50% dominant strain. We performed multivariable logistic regression modeling to estimate independent effects of variants adjusting for sociodemographics, baseline health, and vaccine status. RESULTS The study included 2402 COVID-positive and 821 COVID-negative participants. Among COVID-positives, 463 (19.3%) were pre-Delta, 1198 (49.9%) Delta, and 741 (30.8%) Omicron. The pre-Delta COVID-positive cohort exhibited more prolonged severe fatigue (16.7% vs 11.5% vs 12.3%; P = .017) and presence of ≥3 prolonged symptoms (28.4% vs 21.7% vs 16.0%; P < .001) compared with the Delta and Omicron cohorts. No differences were seen in the COVID-negatives across time-periods. In multivariable models adjusted for vaccination, severe fatigue and odds of having ≥3 symptoms were no longer significant across variants. CONCLUSIONS Prolonged symptoms following SARS-CoV-2 infection were more common among participants infected during pre-Delta than with Delta and Omicron; however, these differences were no longer significant after adjusting for vaccination status, suggesting a beneficial effect of vaccination on risk of long-term symptoms. Clinical Trials Registration. NCT04610515.
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Affiliation(s)
- Michael Gottlieb
- Department of Emergency Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Ralph C Wang
- Department of Emergency Medicine, University of California, San Francisco, California, USA
| | - Huihui Yu
- Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, Connecticut, USA
- Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Erica S Spatz
- Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Juan Carlos C Montoy
- Department of Emergency Medicine, University of California, San Francisco, California, USA
| | - Robert M Rodriguez
- Department of Emergency Medicine, University of California – San Francisco School of Medicine, San Francisco, California, USA
| | - Anna Marie Chang
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joann G Elmore
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, USA
| | - Paavali A Hannikainen
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mandy Hill
- Department of Emergency Medicine, UTHealth Houston, Houston, Texas, USA
| | - Ryan M Huebinger
- Department of Emergency Medicine, UTHealth Houston, Houston, Texas, USA
| | - Ahamed H Idris
- Department of Emergency Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zhenqiu Lin
- Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, Connecticut, USA
- Section of Cardiovascular Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Katherine Koo
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
| | - Samuel McDonald
- Department of Emergency Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Clinical Informatics Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kelli N O’Laughlin
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ian D Plumb
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michelle Santangelo
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
| | - Sharon Saydah
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael Willis
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Lauren E Wisk
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, USA
| | - Arjun Venkatesh
- Center for Outcomes Research and Evaluation, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Emergency Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Kari A Stephens
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Robert A Weinstein
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
- Department of Medicine, Division of Infectious Diseases, Cook County Hospital, Chicago, Illinois, USA
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9
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Zajic P, Hiesmayr M, Bauer P, Baron DM, Gruber A, Joannidis M, Posch M, Metnitz PGH. Nationwide analysis of hospital admissions and outcomes of patients with SARS-CoV-2 infection in Austria in 2020 and 2021. Sci Rep 2023; 13:8548. [PMID: 37236991 DOI: 10.1038/s41598-023-35349-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
This retrospective study evaluated temporal and regional trends of patient admissions to hospitals, intensive care units (ICU), and intermediate care units (IMCU) as well as outcomes during the COVID-19 pandemic in Austria. We analysed anonymous data from patients admitted to Austrian hospitals with COVID-19 between January 1st, 2020 and December 31st, 2021. We performed descriptive analyses and logistic regression analyses for in-hospital mortality, IMCU or ICU admission, and in-hospital mortality following ICU admission. 68,193 patients were included, 8304 (12.3%) were primarily admitted to ICU, 3592 (5.3%) to IMCU. Hospital mortality was 17.3%; risk factors were male sex (OR 1.67, 95% CI 1.60-1.75, p < 0.001) and high age (OR 7.86, 95% CI 7.07-8.74, p < 0.001 for 90+ vs. 60-64 years). Mortality was higher in the first half of 2020 (OR 1.15, 95% CI 1.04-1.27, p = 0.01) and the second half of 2021 (OR 1.11, 95% CI 1.05-1.17, p < 0.001) compared to the second half of 2020 and differed regionally. ICU or IMCU admission was most likely between 55 and 74 years, and less likely in younger and older age groups. We find mortality in Austrian COVID-19-patients to be almost linearly associated with age, ICU admission to be less likely in older individuals, and outcomes to differ between regions and over time.
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Affiliation(s)
- Paul Zajic
- Division of General Anaesthesiology, Emergency- and Intensive Care Medicine, Medical University of Graz, Auenbruggerplatz 5, 8036, Graz, Austria.
| | - Michael Hiesmayr
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Peter Bauer
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - David M Baron
- Department of Anaesthesiology, General Intensive Care Medicine and Pain Medicine, Medical University of Vienna, Vienna, Austria
| | - Anastasiia Gruber
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Michael Joannidis
- Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Posch
- Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Philipp G H Metnitz
- Division of General Anaesthesiology, Emergency- and Intensive Care Medicine, Medical University of Graz, Auenbruggerplatz 5, 8036, Graz, Austria
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10
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Nitecki M, Savitsky B, Akavian I, Yakhin A, Narkiss T, Michael YB, Shapira S, Friedensohn L. B.1.1.7 Variant Outbreak in an Air Force Military Base-Real-World Data. Mil Med 2023; 188:e1293-e1299. [PMID: 34755833 PMCID: PMC8689938 DOI: 10.1093/milmed/usab451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/21/2021] [Accepted: 11/04/2021] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE To assess the clinical features and infectivity of variant B.1.1.7 among healthy young adults in a military setting. MATERIALS AND METHODS Positive cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a single military base (March 23, 2020 and February 16, 2021) were included. An epidemiological investigation conducted via phone included questions regarding symptoms, exposure history, smoking status, list of contacts, and recently visited places. Symptoms surveyed included fever, cough, shortness of breath, sore throat, loss of smell or taste, gastrointestinal symptoms (GI), headache, chest pain, and constitutional symptoms. Cases were divided before B.1.1.7 first reported case in Israel (December 23, 2020) (period 1) and after its identification (period 2). Symptom distribution and the risk of a contact to be infected were compared between the periods, using a chi-square test, and a negative binominal regression model, respectively. RESULTS Of 293 confirmed cases, 89 were reported in the first period and 204 in the second. 56.0% were men with a median age of 19.5 years (interquartile range 18.6-20.5). GI symptoms, loss of taste or smell, headache, fever, and chills were more prevalent in the first period (P < .001, P = .026, P = .034, P = .001, and P < .001, respectively), while fatigue was more common in the second period (P = .008). The risk of a contact to be infected was three times higher in the second period (relative risk = 3.562 [2.414-5.258]). CONCLUSION An outbreak of SARS-CoV-2 in young healthy adults, during a period with high national-wide B.1.1.7 variant prevalence, is characterized by decreased prevalence of fever, loss of taste or smell and GI symptoms, increased reports of fatigue, and more infected contacts for each index case.
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Affiliation(s)
- Maya Nitecki
- Israel Defense Forces, Medical Corps, Ramat Gan 02149, Israel
- Department of Military Medicine, Hebrew University, Jerusalem 9112102, Israel
| | - Bella Savitsky
- Department of Nursing, School of Health Science, Ashkelon Academic College, Ashkelon 78211, Israel
| | - Inbal Akavian
- Israel Defense Forces, Medical Corps, Ramat Gan 02149, Israel
| | - Alexey Yakhin
- Israel Defense Forces, Medical Corps, Ramat Gan 02149, Israel
| | - Tamar Narkiss
- Israel Defense Forces, Medical Corps, Ramat Gan 02149, Israel
| | | | - Shachar Shapira
- Israel Defense Forces, Medical Corps, Ramat Gan 02149, Israel
- Department of Military Medicine, Hebrew University, Jerusalem 9112102, Israel
| | - Limor Friedensohn
- Israel Defense Forces, Medical Corps, Ramat Gan 02149, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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11
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Toh KB, Runge M, Richardson RA, Hladish TJ, Gerardin J. Design of effective outpatient sentinel surveillance for COVID-19 decision-making: a modeling study. BMC Infect Dis 2023; 23:287. [PMID: 37142984 PMCID: PMC10158704 DOI: 10.1186/s12879-023-08261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/17/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Decision-makers impose COVID-19 mitigations based on public health indicators such as reported cases, which are sensitive to fluctuations in supply and demand for diagnostic testing, and hospital admissions, which lag infections by up to two weeks. Imposing mitigations too early has unnecessary economic costs while imposing too late leads to uncontrolled epidemics with unnecessary cases and deaths. Sentinel surveillance of recently-symptomatic individuals in outpatient testing sites may overcome biases and lags in conventional indicators, but the minimal outpatient sentinel surveillance system needed for reliable trend estimation remains unknown. METHODS We used a stochastic, compartmental transmission model to evaluate the performance of various surveillance indicators at reliably triggering an alarm in response to, but not before, a step increase in transmission of SARS-CoV-2. The surveillance indicators included hospital admissions, hospital occupancy, and sentinel cases with varying levels of sampling effort capturing 5, 10, 20, 50, or 100% of incident mild cases. We tested 3 levels of transmission increase, 3 population sizes, and conditions of either simultaneous transmission increase or lagged increase in the older population. We compared the indicators' performance at triggering alarm soon after, but not prior, to the transmission increase. RESULTS Compared to surveillance based on hospital admissions, outpatient sentinel surveillance that captured at least 20% of incident mild cases could trigger an alarm 2 to 5 days earlier for a mild increase in transmission and 6 days earlier for a moderate or strong increase. Sentinel surveillance triggered fewer false alarms and averted more deaths per day spent in mitigation. When transmission increase in older populations lagged the increase in younger populations by 14 days, sentinel surveillance extended its lead time over hospital admissions by an additional 2 days. CONCLUSIONS Sentinel surveillance of mild symptomatic cases can provide more timely and reliable information on changes in transmission to inform decision-makers in an epidemic like COVID-19.
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Affiliation(s)
- Kok Ben Toh
- Department of Preventive Medicine, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Manuela Runge
- Department of Preventive Medicine, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Reese Ak Richardson
- Department of Chemical and Biological Engineering, Northwestern University, Chicago, IL, USA
| | - Thomas J Hladish
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogen Institute, University of Florida, Gainesville, FL, USA
| | - Jaline Gerardin
- Department of Preventive Medicine, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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12
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Robinson ML, Morris CP, Betz JF, Zhang Y, Bollinger R, Wang N, Thiemann DR, Fall A, Eldesouki RE, Norton JM, Gaston DC, Forman M, Luo CH, Zeger SL, Gupta A, Garibaldi BT, Mostafa HH. Impact of Severe Acute Respiratory Syndrome Coronavirus 2 Variants on Inpatient Clinical Outcome. Clin Infect Dis 2023; 76:1539-1549. [PMID: 36528815 PMCID: PMC10411930 DOI: 10.1093/cid/ciac957] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/21/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Prior observation has shown differences in COVID-19 hospitalization risk between SARS-CoV-2 variants, but limited information describes hospitalization outcomes. METHODS Inpatients with COVID-19 at 5 hospitals in the eastern United States were included if they had hypoxia, tachypnea, tachycardia, or fever, and SARS-CoV-2 variant data, determined from whole-genome sequencing or local surveillance inference. Analyses were stratified by history of SARS-CoV-2 vaccination or infection. The average effect of SARS-CoV-2 variant on 28-day risk of severe disease, defined by advanced respiratory support needs, or death was evaluated using models weighted on propensity scores derived from baseline clinical features. RESULTS Severe disease or death within 28 days occurred for 977 (29%) of 3369 unvaccinated patients and 269 (22%) of 1230 patients with history of vaccination or prior SARS-CoV-2 infection. Among unvaccinated patients, the relative risk of severe disease or death for Delta variant compared with ancestral lineages was 1.30 (95% confidence interval [CI]: 1.11-1.49). Compared with Delta, the risk for Omicron patients was .72 (95% CI: .59-.88) and compared with ancestral lineages was .94 (.78-1.1). Among Omicron and Delta infections, patients with history of vaccination or prior SARS-CoV-2 infection had half the risk of severe disease or death (adjusted hazard ratio: .40; 95% CI: .30-.54), but no significant outcome difference by variant. CONCLUSIONS Although risk of severe disease or death for unvaccinated inpatients with Omicron was lower than with Delta, it was similar to ancestral lineages. Severe outcomes were less common in vaccinated inpatients, with no difference between Delta and Omicron infections.
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Affiliation(s)
- Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - C Paul Morris
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua F Betz
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Yifan Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Robert Bollinger
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natalie Wang
- Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - David R Thiemann
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amary Fall
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Raghda E Eldesouki
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julie M Norton
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David C Gaston
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Forman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amita Gupta
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brian T Garibaldi
- Division of Pulmonary and Critical Care, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Xie Y, Tian X, Zhang X, Yao H, Wu N. Immune interference in effectiveness of influenza and COVID-19 vaccination. Front Immunol 2023; 14:1167214. [PMID: 37153582 PMCID: PMC10154574 DOI: 10.3389/fimmu.2023.1167214] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
Vaccines are known to function as the most effective interventional therapeutics for controlling infectious diseases, including polio, smallpox, rabies, tuberculosis, influenza and SARS-CoV-2. Smallpox has been eliminated completely and polio is almost extinct because of vaccines. Rabies vaccines and Bacille Calmette-Guérin (BCG) vaccines could effectively protect humans against respective infections. However, both influenza vaccines and COVID-19 vaccines are unable to eliminate these two infectious diseases of their highly variable antigenic sites in viral proteins. Vaccine effectiveness (VE) could be negatively influenced (i.e., interfered with) by immune imprinting of previous infections or vaccinations, and repeated vaccinations could interfere with VE against infections due to mismatch between vaccine strains and endemic viral strains. Moreover, VE could also be interfered with when more than one kind of vaccine is administrated concomitantly (i.e., co-administrated), suggesting that the VE could be modulated by the vaccine-induced immunity. In this review, we revisit the evidence that support the interfered VE result from immune imprinting or repeated vaccinations in influenza and COVID-19 vaccine, and the interference in co-administration of these two types of vaccines is also discussed. Regarding the development of next-generation COVID-19 vaccines, the researchers should focus on the induction of cross-reactive T-cell responses and naive B-cell responses to overcome negative effects from the immune system itself. The strategy of co-administrating influenza and COVID-19 vaccine needs to be considered more carefully and more clinical data is needed to verify this strategy to be safe and immunogenic.
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Affiliation(s)
- Yiwen Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Xuebin Tian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Xiaodi Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
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14
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Pascall DJ, Vink E, Blacow R, Bulteel N, Campbell A, Campbell R, Clifford S, Davis C, da Silva Filipe A, El Sakka N, Fjodorova L, Forrest R, Goldstein E, Gunson R, Haughney J, Holden MTG, Honour P, Hughes J, James E, Lewis T, Lycett S, MacLean O, McHugh M, Mollett G, Onishi Y, Parcell B, Ray S, Robertson DL, Shabaan S, Shepherd JG, Smollett K, Templeton K, Wastnedge E, Wilkie C, Williams T, Thomson EC. The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis. PLoS One 2023; 18:e0284187. [PMID: 37053201 PMCID: PMC10101505 DOI: 10.1371/journal.pone.0284187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
OBJECTIVES The SARS-CoV-2 Alpha variant was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between Alpha variant infection and increased hospitalisation and 28-day mortality. However, none have addressed the impact on maximum severity of illness in the general population classified by the level of respiratory support required, or death. We aimed to do this. METHODS In this retrospective multi-centre clinical cohort sub-study of the COG-UK consortium, 1475 samples from Scottish hospitalised and community cases collected between 1st November 2020 and 30th January 2021 were sequenced. We matched sequence data to clinical outcomes as the Alpha variant became dominant in Scotland and modelled the association between Alpha variant infection and severe disease using a 4-point scale of maximum severity by 28 days: 1. no respiratory support, 2. supplemental oxygen, 3. ventilation and 4. death. RESULTS Our cumulative generalised linear mixed model analyses found evidence (cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93) of a positive association between increased clinical severity and lineage (Alpha variant versus pre-Alpha variants). CONCLUSIONS The Alpha variant was associated with more severe clinical disease in the Scottish population than co-circulating lineages.
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Affiliation(s)
- David J. Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom
| | - Elen Vink
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Lothian, Edinburgh, United Kingdom
| | - Rachel Blacow
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | | | | | | | | | - Chris Davis
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | | | | | | | - Rory Gunson
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - John Haughney
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Matthew T. G. Holden
- Public Health Scotland, Edinburgh, United Kingdom
- School of Medicine, University of St Andrews, St Andrews, Fife, United Kingdom
| | | | - Joseph Hughes
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Edward James
- NHS Borders, Melrose, Scottish Borders, United Kingdom
| | - Tim Lewis
- NHS Lothian, Edinburgh, United Kingdom
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Oscar MacLean
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - Guy Mollett
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | | | - Ben Parcell
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Surajit Ray
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - James G. Shepherd
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Katherine Smollett
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | | | - Craig Wilkie
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Thomas Williams
- NHS Lothian, Edinburgh, United Kingdom
- Royal Hospital for Children and Young People, University of Edinburgh, Edinburgh, United Kingdom
| | - Emma C. Thomson
- MRC–University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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15
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Clinical outcomes of COVID-19 caused by the Alpha variant compared with one by wild type in Kobe, Japan. A multi-center nested case-control study. J Infect Chemother 2023; 29:289-293. [PMID: 36494058 PMCID: PMC9722619 DOI: 10.1016/j.jiac.2022.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/02/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The emergence of the Alpha variant of novel coronavirus 2019 (SARS-CoV-2) is a concerning issue but their clinical implications have not been investigated fully. METHODS We conducted a nested case-control study to compare severity and mortality caused by the Alpha variant (B.1.1.7) with the one caused by the wild type as a control from December 2020 to March 2021, using whole-genome sequencing. 28-day mortality and other clinically important outcomes were evaluated. RESULTS Infections caused by the Alpha variant were associated with an increase in the use of oxygen (43.4% vs 26.3%. p = 0.017), high flow nasal cannula (21.2% vs 4.0%, p = 0.0007), mechanical ventilation (16.2% vs 6.1%, p = 0.049), ICU care (30.3% vs 14.1%, p = 0.01) and the length of hospital stay (17 vs 10 days, p = 0.031). More patients with the Alpha variant received medications such as dexamethasone. However, the duration of each modality did not differ between the 2 groups. Likewise, there was no difference in 28-day mortality between the 2 groups (12% vs 8%, p = 0.48), even after multiple sensitivity analyses, including propensity score analysis. CONCLUSION The Alpha variant was associated with a severe form of COVID-19, compared with the non-Alpha wild type, but might not be associated with higher mortality.
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16
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Velásquez García HA, Adu PA, Harrigan S, Wilton J, Rasali D, Binka M, Sbihi H, Smolina K, Janjua NZ. Risk factors for COVID-19 hospitalization after COVID-19 vaccination: a population-based cohort study in Canada. Int J Infect Dis 2023; 127:116-123. [PMID: 36503044 PMCID: PMC9731811 DOI: 10.1016/j.ijid.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/10/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES With the uptake of COVID-19 vaccines, there is a need for population-based studies to assess risk factors for COVID-19-related hospitalization after vaccination and how they differ from unvaccinated individuals. METHODS We used data from the British Columbia COVID-19 Cohort, a population-based cohort that includes all individuals (aged ≥18 years) who tested positive for SARS-CoV-2 by real-time reverse transcription-polymerase chain reaction from January 1, 2021 (after the start of vaccination program) to December 31, 2021. We used multivariable logistic regression models to assess COVID-19-related hospitalization risk by vaccination status and age group among confirmed COVID-19 cases. RESULTS Of the 162,509 COVID-19 cases included in the analysis, 8,546 (5.3%) required hospitalization. Among vaccinated individuals, an increased odds of hospitalization with increasing age was observed for older age groups, namely those aged 50-59 years (odds ratio [OR] = 2.95, 95% confidence interval [CI]: 2.01-4.33), 60-69 years (OR = 4.82, 95% CI: 3.29, 7.07), 70-79 years (OR = 11.92, 95% CI: 8.02, 17.71), and ≥80 years (OR = 24.25, 95% CI: 16.02, 36.71). However, among unvaccinated individuals, there was a graded increase in odds of hospitalization with increasing age, starting at age group 30-39 years (OR = 2.14, 95% CI: 1.90, 2.41) to ≥80 years (OR = 41.95, 95% CI: 35.43, 49.67). Also, comparing all the age groups to the youngest, the observed magnitude of association was much higher among unvaccinated individuals than vaccinated ones. CONCLUSION Alongside a number of comorbidities, our findings showed a strong association between age and COVID-19-related hospitalization, regardless of vaccination status. However, age-related hospitalization risk was reduced two-fold by vaccination, highlighting the need for vaccination in reducing the risk of severe disease and subsequent COVID-19-related hospitalization across all population groups.
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Affiliation(s)
- Héctor A. Velásquez García
- Data and Analytic Services, British Columbia Centre for Disease Control, Vancouver, Canada,School of Population and Public Health, University of British Columbia, Vancouver, Canada,Corresponding authors
| | - Prince A. Adu
- Data and Analytic Services, British Columbia Centre for Disease Control, Vancouver, Canada,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Sean Harrigan
- Data and Analytic Services, British Columbia Centre for Disease Control, Vancouver, Canada
| | - James Wilton
- Data and Analytic Services, British Columbia Centre for Disease Control, Vancouver, Canada
| | - Drona Rasali
- Data and Analytic Services, British Columbia Centre for Disease Control, Vancouver, Canada
| | - Mawuena Binka
- School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Hind Sbihi
- Data and Analytic Services, British Columbia Centre for Disease Control, Vancouver, Canada
| | - Kate Smolina
- Data and Analytic Services, British Columbia Centre for Disease Control, Vancouver, Canada,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Naveed Z. Janjua
- Data and Analytic Services, British Columbia Centre for Disease Control, Vancouver, Canada,School of Population and Public Health, University of British Columbia, Vancouver, Canada,Centre for Health Evaluation & Outcome Sciences, St. Paul's Hospital, Vancouver, Canada,Corresponding authors
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Sala I, Jarach CM, Bagnardi V, Cattaruzza MS, Morri M, Ottogalli P, Zagà V, Gallus S, Boschini A. SARS-CoV-2 Infection in San Patrignano, the Largest European Drug Rehabilitation Community. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2136. [PMID: 36767503 PMCID: PMC9916305 DOI: 10.3390/ijerph20032136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Studies on SARS-CoV-2 conducted in confined settings for prolonged times allow researchers to assess how the coronavirus spreads. San Patrignano (SP), Italy, is the largest European drug rehabilitation facility. METHODS Between 15 October and 31 December 2020, all SP residents were tested for SARS-CoV-2. We analyzed the relationships between individual characteristics and being SARS-CoV-2-positive. Three selected predictive models were used to calculate the number of expected hospitalizations. For each model, we summed the estimated individual risks to obtain the expected number of hospitalizations in our sample, and we tested whether the observed and expected numbers differed. RESULTS Of 807 residents, 529 (65.6%) were SARS-CoV-2-positive. Of these 323 (61.1%) were symptomatic. A strong relationship was found between being positive and living connections (p-value < 0.001). No statistically significant relationship was found with age, sex, smoking history, or comorbidities. Although 9 to 17 hospitalizations were expected, no hospitalizations were observed (p-value < 0.001). No one died of COVID-19. CONCLUSIONS The peculiar characteristics of SP residents or the SP environment might at least partially explain the null hospitalization rates. Despite the extreme uniqueness of our population and despite the protected environment and all precautions that were taken, the fact that the virus was able to circulate and infect a large portion of the population highlights the fundamental role of social interactions in the spread of the disease.
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Affiliation(s)
- Isabella Sala
- Department of Statistics and Quantitative Methods, University of Milan-Bicocca, 20126 Milan, Italy
- Department of Medicine and Surgery, University of Milan-Bicocca, 20126 Milan, Italy
| | - Carlotta Micaela Jarach
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Vincenzo Bagnardi
- Department of Statistics and Quantitative Methods, University of Milan-Bicocca, 20126 Milan, Italy
| | - Maria Sofia Cattaruzza
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy
- Società Italiana di Tabaccologia (SITAB), 00136 Rome, Italy
| | - Michela Morri
- Hygiene and Public Health Unit, AUSL della Romagna, 47924 Rimini, Italy
| | | | - Vincenzo Zagà
- Società Italiana di Tabaccologia (SITAB), 00136 Rome, Italy
| | - Silvano Gallus
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
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Swann OV, Pollock L, Holden KA, Munro APS, Bennett A, Williams TC, Turtle L, Fairfield CJ, Drake TM, Faust SN, Sinha IP, Roland D, Whittaker E, Ladhani SN, Nguyen-Van-Tam JS, Girvan M, Donohue C, Donegan C, Spencer RG, Hardwick HE, Openshaw PJM, Baillie JK, Harrison EM, Docherty AB, Semple MG. Comparison of UK paediatric SARS-CoV-2 admissions across the first and second pandemic waves. Pediatr Res 2023; 93:207-216. [PMID: 35449394 PMCID: PMC9876790 DOI: 10.1038/s41390-022-02052-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 01/29/2023]
Abstract
BACKGROUND We hypothesised that the clinical characteristics of hospitalised children and young people (CYP) with SARS-CoV-2 in the UK second wave (W2) would differ from the first wave (W1) due to the alpha variant (B.1.1.7), school reopening and relaxation of shielding. METHODS Prospective multicentre observational cohort study of patients <19 years hospitalised in the UK with SARS-CoV-2 between 17/01/20 and 31/01/21. Clinical characteristics were compared between W1 and W2 (W1 = 17/01/20-31/07/20,W2 = 01/08/20-31/01/21). RESULTS 2044 CYP < 19 years from 187 hospitals. 427/2044 (20.6%) with asymptomatic/incidental SARS-CoV-2 were excluded from main analysis. 16.0% (248/1548) of symptomatic CYP were admitted to critical care and 0.8% (12/1504) died. 5.6% (91/1617) of symptomatic CYP had Multisystem Inflammatory Syndrome in Children (MIS-C). After excluding CYP with MIS-C, patients in W2 had lower Paediatric Early Warning Scores (PEWS, composite vital sign score), lower antibiotic use and less respiratory and cardiovascular support than W1. The proportion of CYP admitted to critical care was unchanged. 58.0% (938/1617) of symptomatic CYP had no reported comorbidity. Patients without co-morbidities were younger (42.4%, 398/938, <1 year), had lower PEWS, shorter length of stay and less respiratory support. CONCLUSIONS We found no evidence of increased disease severity in W2 vs W1. A large proportion of hospitalised CYP had no comorbidity. IMPACT No evidence of increased severity of COVID-19 admissions amongst children and young people (CYP) in the second vs first wave in the UK, despite changes in variant, relaxation of shielding and return to face-to-face schooling. CYP with no comorbidities made up a significant proportion of those admitted. However, they had shorter length of stays and lower treatment requirements than CYP with comorbidities once those with MIS-C were excluded. At least 20% of CYP admitted in this cohort had asymptomatic/incidental SARS-CoV-2 infection. This paper was presented to SAGE to inform CYP vaccination policy in the UK.
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Affiliation(s)
- Olivia V Swann
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
- Paediatric Infectious Diseases, Royal Hospital for Children, Glasgow, UK
| | - Louisa Pollock
- Paediatric Infectious Diseases, Royal Hospital for Children, Glasgow, UK
- Child Health, School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow, UK
| | - Karl A Holden
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- Respiratory Medicine, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Alasdair P S Munro
- NIHR Southampton Clinical Research Facility and NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Aisleen Bennett
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | - Thomas C Williams
- Department of Child Life and Health, University of Edinburgh, Edinburgh, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
- Tropical and Infectious Diseases Unit, Liverpool University Hospitals NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool, UK
| | - Cameron J Fairfield
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Thomas M Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Saul N Faust
- NIHR Southampton Clinical Research Facility and NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Ian P Sinha
- Respiratory Medicine, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
- Women's and Children's Health, Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Damian Roland
- Paediatric Emergency Medicine Leicester Academic (PEMLA) Group, University Hospitals of Leicester NHS Trust, Leicester, UK
- SAPPHIRE Group, Health Sciences, Leicester University, Leicester, UK
| | - Elizabeth Whittaker
- Section of Paediatric Infectious Diseases, Imperial College London, London, UK
- Paediatric Infectious Diseases, Imperial College Healthcare National Health System Trust, London, UK
| | - Shamez N Ladhani
- Immunisation and Countermeasures Division, Public Health England Colindale, London, UK
- Paediatric Infectious Disease, St. George's Hospital London, London, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK
| | - Michelle Girvan
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Chloe Donohue
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Cara Donegan
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Rebecca G Spencer
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | - Hayley E Hardwick
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7BE, UK.
- Respiratory Medicine, Alder Hey Children's NHS Foundation Trust, Liverpool, UK.
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Wolf JM, Wolf LM, Bello GL, Maccari JG, Nasi LA. Molecular evolution of SARS-CoV-2 from December 2019 to August 2022. J Med Virol 2023; 95:e28366. [PMID: 36458547 PMCID: PMC9877913 DOI: 10.1002/jmv.28366] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/24/2022] [Accepted: 11/20/2022] [Indexed: 12/04/2022]
Abstract
Severe acute respiratorysyndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning worldwide, presenting more than 590 million coronavirus disease 2019 cases and 6.4 million deaths. The emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide during the pandemic. The present study review and summarizes the temporal spreading and molecular evolution of SARS-CoV-2 clades and variants worldwide. The evaluation of these data is important for understanding the evolutionary histories of SARSCoV-2 lineages, allowing us to identify the origins of each lineage of this virus responsible for one of the biggest pandemics in history. A total of 2897 SARS-CoV-2 whole-genome sequences with available information from the country and sampling date (December 2019 to August 2022), were obtained and were evaluated by Bayesian approach. The results demonstrated that the SARS-CoV-2 the time to the most recent common ancestor (tMRCA) in Asia was 2019-12-26 (highest posterior density 95% [HPD95%]: 2019-12-18; 2019-12-29), in Oceania 2020-01-24 (HPD95%: 2020-01-15; 2020-01-30), in Africa 2020-02-27 (HPD95%: 2020-02-21; 2020-03-04), in Europe 2020-02-27 (HPD95%: 2020-02-20; 2020-03-06), in North America 2020-03-12 (HPD95%: 2020-03-05; 2020-03-18), and in South America 2020-03-15 (HPD95%: 2020-03-09; 2020-03-28). Between December 2019 and June 2020, 11 clades were detected (20I [Alpha] and 19A, 19B, 20B, 20C, 20A, 20D, 20E [EU1], 20F, 20H [Beta]). From July to December 2020, 4 clades were identified (20J [Gamma, V3], 21 C [Epsilon], 21D [Eta], and 21G [Lambda]). Between January and June 2021, 3 clades of the Delta variant were detected (21A, 21I, and 21J). Between July and December 2021, two variants were detected, Delta (21A, 21I, and 21J) and Omicron (21K, 21L, 22B, and 22C). Between January and June 2022, the Delta (21I and 21J) and Omicron (21K, 21L, and 22A) variants were detected. Finally, between July and August 2022, 3 clades of Omicron were detected (22B, 22C, and 22D). Clade 19A was first detected in the SARS-CoV-2 pandemic (Wuhan strain) with origin in 2019-12-16 (HPD95%: 2019-12-15; 2019-12-25); 20I (Alpha) in 2020-11-24 (HPD95%: 2020-11-15; 2021-12-02); 20H (Beta) in 2020-11-25 (HPD95%: 2020-11-13; 2020-11-29); 20J (Gamma) was 2020-12-21 (HPD95%: 2020-11-05; 2021-01-15); 21A (Delta) in 2020-09-20 (HPD95%: 2020-05-17; 2021-02-03); 21J (Delta) in 2021-02-26 (2020-11-02; 2021-04-24); 21M (Omicron) in 2021-01-25 (HPD95%: 2020-09-16; 2021-08-08); 21K (Omicron) in 2021-07-30 (HPD95%: 2021-05-30; 2021-10-19); 21L (Omicron) in 2021-10-03 (HPD95%: 2021-04-16; 2021-12-23); 22B (Omicron) in 2022-01-25 (HPD95%: 2022-01-10; 2022-02-05); 21L in 2021-12-20 (HPD95%: 2021-05-16; 2021-12-31). Currently, the Omicron variant predominates worldwide, with the 21L clade branching into 3 (22A, 22B, and 22C). Phylogeographic data showed that Alpha variant originated in the United Kingdom, Beta in South Africa, Gamma in Brazil, Delta in India, Omicron in South Africa, Mu in Colombia, Epsilon in the United States of America, and Lambda in Peru. The COVID-19 pandemic has had a significant impact on global health worldwide and the present study provides an overview of the molecular evolution of SARS-CoV-2 lineage clades (from the Wuhan strain to the currently circulating lineages of the Omicron).
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Affiliation(s)
| | - Lucas Michel Wolf
- Veterinary MedicineUFRGS (Universidade Federal do Rio Grande do Sul)Porto AlegreRio Grande do SulBrasil
| | - Graziele Lima Bello
- Programa Institutos Nacionais de Ciência e TecnologiaInstituto Nacional de Ciência e Tecnologia em Tuberculose (INCT‐TB)Porto AlegreRio Grande do SulBrasil
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20
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Minchella PA, Chanda D, Hines JZ, Fwoloshi S, Itoh M, Kampamba D, Chirwa R, Sivile S, Zyambo KD, Agolory S, Mulenga LB. Clinical Characteristics and Outcomes of Patients Hospitalized With COVID-19 During the First 4 Waves in Zambia. JAMA Netw Open 2022; 5:e2246152. [PMID: 36512359 PMCID: PMC9856263 DOI: 10.1001/jamanetworkopen.2022.46152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/26/2022] [Indexed: 12/15/2022] Open
Abstract
Importance Few epidemiologic studies related to COVID-19 have emerged from countries in Africa, where demographic characteristics, epidemiology, and health system capacity differ from other parts of the world. Objectives To describe the characteristics and outcomes of patients admitted to COVID-19 treatment centers, assess risk factors for in-hospital death, and explore how treatment center admissions were affected by COVID-19 waves in Zambia. Design, Setting, and Participants This retrospective cohort study assessed patients admitted to COVID-19 treatment centers in 5 Zambian cities between March 1, 2020, and February 28, 2022. Exposures Risk factors for in-hospital mortality, including patient age and severity of COVID-19, at treatment center admission. Main Outcomes and Measures Patient information was collected, including inpatient disposition (discharged or died). Differences across and within COVID-19 waves were assessed. Mixed-effects logistic regression models were used to assess associations between risk factors and in-hospital mortality as well as between characteristics of admitted patients and timing of admission. Results A total of 3876 patients were admitted during 4 COVID-19 waves (mean [SD] age, 50.6 [19.5] years; 2103 male [54.3%]). Compared with the first 3 waves (pooled), the proportion of patients who were 60 years or older admitted during wave 4, when the Omicron variant was circulating, was significantly lower (250 of 1009 [24.8%] vs 1116 of 2837 [39.3%]; P < .001). Factors associated with in-hospital mortality included older age (≥60 vs <30 years; adjusted odds ratio [aOR], 3.55; 95% CI, 2.34-5.52) and HIV infection (aOR, 1.39; 95% CI, 1.07-1.79). Within waves, patients who were admitted during weeks 5 to 9 had significantly higher odds of being 60 years or older (aOR, 2.09; 95% CI, 1.79-2.45) or having severe COVID-19 at admission (aOR, 2.49; 95% CI, 2.14-2.90) than those admitted during the first 4 weeks. Conclusions and Relevance The characteristics of admitted patients during the Omicron wave and risk factors for in-hospital mortality in Zambia reflect data reported elsewhere. Within-wave analyses revealed a pattern in which it appeared that admission of higher-risk patients was prioritized during periods when there were surges in demand for health services during COVID-19 waves. These findings support the need to expand health system capacity and improve health system resiliency in Zambia and other countries with resource-limited health systems.
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Affiliation(s)
| | | | - Jonas Z. Hines
- Centers for Disease Control and Prevention–Zambia, Lusaka, Zambia
| | | | - Megumi Itoh
- Centers for Disease Control and Prevention–Zambia, Lusaka, Zambia
| | | | | | | | | | - Simon Agolory
- Centers for Disease Control and Prevention–Zambia, Lusaka, Zambia
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21
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Cai J, Yang J, Deng X, Peng C, Chen X, Wu Q, Liu H, Zhang J, Zheng W, Zou J, Zhao Z, Ajelli M, Yu H. Assessing the transition of COVID-19 burden towards the young population while vaccines are rolled out in China. Emerg Microbes Infect 2022; 11:1205-1214. [PMID: 35380100 PMCID: PMC9045766 DOI: 10.1080/22221751.2022.2063073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/03/2022] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 infection causes most cases of severe illness and fatality in older age groups. Over 92% of the Chinese population aged ≥12 years has been fully vaccinated against COVID-19 (albeit with vaccines developed against historical lineages). At the end of October 2021, the vaccination programme has been extended to children aged 3-11 years. Here, we aim to assess whether, in this vaccination landscape, the importation of Delta variant infections could shift COVID-19 burden from adults to children. We developed an age-structured susceptible-infectious-removed model of SARS-CoV-2 transmission to simulate epidemics triggered by the importation of Delta variant infections and project the age-specific incidence of SARS-CoV-2 infections, cases, hospitalizations, intensive care unit admissions, and deaths. In the context of the vaccination programme targeting individuals aged ≥12 years, and in the absence of non-pharmaceutical interventions, the importation of Delta variant infections could have led to widespread transmission and substantial disease burden in mainland China, even with vaccination coverage as high as 89% across the eligible age groups. Extending the vaccination roll-out to include children aged 3-11 years (as it was the case since the end of October 2021) is estimated to dramatically decrease the burden of symptomatic infections and hospitalizations within this age group (39% and 68%, respectively, when considering a vaccination coverage of 87%), but would have a low impact on protecting infants. Our findings highlight the importance of including children among the target population and the need to strengthen vaccination efforts by increasing vaccine effectiveness.
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Affiliation(s)
- Jun Cai
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
- Department of Infectious Diseases, Huashan Hospital, School of Public Health, Fudan University, Shanghai, People's Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Cheng Peng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Qianhui Wu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Hengcong Liu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
- Department of Infectious Diseases, Huashan Hospital, School of Public Health, Fudan University, Shanghai, People's Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
| | - Wen Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Junyi Zou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Zeyao Zhao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
- Department of Infectious Diseases, Huashan Hospital, School of Public Health, Fudan University, Shanghai, People's Republic of China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, People’s Republic of China
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22
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Muacevic A, Adler JR, Ibrahim EA, Ibrahim AS, Raza T. Clinical Outcomes of COVID-19-Induced Acute Respiratory Distress Syndrome in Patients With Three Different Respiratory Support Modalities: A Retrospective Cohort Study. Cureus 2022; 14:e31991. [PMID: 36589198 PMCID: PMC9797753 DOI: 10.7759/cureus.31991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced acute respiratory failure and acute respiratory distress syndrome (ARDS) had a considerable impact on intensive care utilization and resource optimization. Multiple modalities for respiratory support were implemented during the COVID-19 pandemic with the main concern of being able to identify those patients at high risk of rapidly progressive respiratory failure, whom the early initiation of invasive respiratory support would, in particular, affect the outcome in comparison to the noninvasive management strategy. Objectives In our cohort study, we describe demographic characteristics, respiratory support modalities, and their relation to patient outcomes. Method Patients 18 years of age and older who were admitted to a tertiary center COVID-19-dedicated medical intensive care unit (MICU) in Qatar between March 2020 and May 2020 with a confirmed diagnosis of COVID-19 pneumonia were included in this study. Patients were divided into invasive or noninvasive, and those who required invasive strategy were subdivided into the early intubation group (patients who were intubated within 72 hours of intensive care unit (ICU) admission) and the late intubation group (patients who were intubated after 72 hours from ICU admission). The primary outcome was ICU and hospital mortality, and the secondary effects were the length of stay and mortality determinants. Results A total of 686 patients were admitted to the medical intensive care unit (MICU) during the study period. There were 222 (32.4%), 131 (19.1%), and 333 (48.5%) patients in the early, late, and not intubated groups, respectively. Compared to the late intubated group, the early intubated group had a higher proportion of males. Diabetes (39.8%) was the most common comorbidity, followed by hypertension (HTN) (36%) and heart disease (9.8%). The 30-day ICU and hospital mortality were significantly higher in the late intubated group compared to the early intubated group (30.5% versus 15.8%, and 30% versus 16.2%). The median ICU and hospital stay days in the total sample were 8 (interquartile range (IQR): 5-14) and 19 (IQR: 14-25), respectively. The mean estimates of 30-day ICU survival times for early intubated, late intubated, and not intubated groups were 25.14 (95% confidence interval (CI): 23.71, 26.57), 23.35 (95% CI: 21.63, 25.07), and 29.91 (95% CI: 29.74, 30.09) respectively. Conclusions In our study, the COVID-19 ARDS patients who required early invasive ventilatory support and in whom the physiological parameter was more severe (Acute Physiology and Chronic Health Evaluation II (APACHE II) and Sequential Organ Failure Assessment (SOFA) scores) had a better outcome than the late intubation group. Age more than 60 years old, diabetes, hypertension, chronic kidney disease (CKD), and chronic liver disease (CLD) were the main predictor of mortality in total.
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23
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Cherrie M, Rhodes S, Wilkinson J, Mueller W, Nafilyan V, Tongeren MV, Pearce N. Longitudinal changes in proportionate mortality due to COVID-19 by occupation in England and Wales. Scand J Work Environ Health 2022; 48:611-620. [PMID: 35770926 PMCID: PMC10546610 DOI: 10.5271/sjweh.4048] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE This study aimed to understand whether the proportionate mortality of COVID-19 for various occupational groups has varied over the pandemic. METHODS We used the Office for National Statistics (ONS) mortality data for England and Wales. The deaths (20-64 years) were classified as either COVID-19-related using ICD-10 codes (U07.1, U07.2), or from other causes. Occupational data recorded at the time of death was coded using the SOC10 coding system into 13 groups. Three time periods (TP) were used: (i) January 2020 to September 2020; (ii) October 2020-May 2021; and (iii) June 2021-October 2021. We analyzed the data with logistic regression and compared odds of death by COVID-19 to other causes, adjusting for age, sex, deprivation, region, urban/rural and population density. RESULTS Healthcare professionals and associates had a higher proportionate odds of COVID-19 death in TP1 compared to non-essential workers but were not observed to have increased odds thereafter. Medical support staff had increased odds of death from COVID-19 during both TP1 and TP2, but this had reduced by TP3. This latter pattern was also seen for social care, food retail and distribution, and bus and coach drivers. Taxi and cab drivers were the only group that had higher odds of death from COVID-19 compared to other causes throughout the whole period under study [TP1: odds ratio (OR) 2.42, 95% confidence interval (CI) 1.99-2.93; TP2: OR 3.15, 95% CI 2.63-3.78; TP3: OR 1.7, 95% CI 1.26-2.29]. CONCLUSION Differences in the odds of death from COVID-19 between occupational groups has declined over the course of the pandemic, although some occupations have remained relatively high throughout.
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Affiliation(s)
- Mark Cherrie
- Institute of Occupational Medicine, Edinburgh, UK
| | - Sarah Rhodes
- Centre for Biostatistics, School of Health Sciences, Faculty of Biology, Medicine and Health, School of Health Sciences, The University of Manchester, Manchester, Manchester, UK
| | - Jack Wilkinson
- Centre for Biostatistics, School of Health Sciences, Faculty of Biology, Medicine and Health, School of Health Sciences, The University of Manchester, Manchester, Manchester, UK
| | | | - Vahe Nafilyan
- Health Analysis Division, Office for National Statistics, Newport, UK
| | - Martie Van Tongeren
- Centre for Occupational and Environmental Health, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, Greater Manchester, UK
| | - Neil Pearce
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
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Chi WY, Li YD, Huang HC, Chan TEH, Chow SY, Su JH, Ferrall L, Hung CF, Wu TC. COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection. J Biomed Sci 2022; 29:82. [PMID: 36243868 PMCID: PMC9569411 DOI: 10.1186/s12929-022-00853-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/01/2022] [Indexed: 12/23/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) has been the most severe public health challenge in this century. Two years after its emergence, the rapid development and deployment of effective COVID-19 vaccines have successfully controlled this pandemic and greatly reduced the risk of severe illness and death associated with COVID-19. However, due to its ability to rapidly evolve, the SARS-CoV-2 virus may never be eradicated, and there are many important new topics to work on if we need to live with this virus for a long time. To this end, we hope to provide essential knowledge for researchers who work on the improvement of future COVID-19 vaccines. In this review, we provided an up-to-date summary for current COVID-19 vaccines, discussed the biological basis and clinical impact of SARS-CoV-2 variants and subvariants, and analyzed the effectiveness of various vaccine booster regimens against different SARS-CoV-2 strains. Additionally, we reviewed potential mechanisms of vaccine-induced severe adverse events, summarized current studies regarding immune correlates of protection, and finally, discussed the development of next-generation vaccines.
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Affiliation(s)
- Wei-Yu Chi
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Hsin-Che Huang
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy En Haw Chan
- International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Department of Urology, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sih-Yao Chow
- Downstream Process Science, EirGenix Inc., Zhubei, Hsinchu, Taiwan R.O.C
| | - Jun-Han Su
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Louise Ferrall
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Chien-Fu Hung
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
- Department of Obstetrics and Gynecology, Johns Hopkins University, Baltimore, MD, USA
| | - T-C Wu
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Obstetrics and Gynecology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA.
- The Johns Hopkins Medical Institutions, CRB II Room 309, 1550 Orleans St, MD, 21231, Baltimore, USA.
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25
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Seaman SR, Nyberg T, Overton CE, Pascall DJ, Presanis AM, De Angelis D. Adjusting for time of infection or positive test when estimating the risk of a post-infection outcome in an epidemic. Stat Methods Med Res 2022; 31:1942-1958. [PMID: 35695245 PMCID: PMC7613654 DOI: 10.1177/09622802221107105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
When comparing the risk of a post-infection binary outcome, for example, hospitalisation, for two variants of an infectious pathogen, it is important to adjust for calendar time of infection. Typically, the infection time is unknown and positive test time used as a proxy for it. Positive test time may also be used when assessing how risk of the outcome changes over calendar time. We show that if time from infection to positive test is correlated with the outcome, the risk conditional on positive test time is a function of the trajectory of infection incidence. Hence, a risk ratio adjusted for positive test time can be quite different from the risk ratio adjusted for infection time. We propose a simple sensitivity analysis that indicates how risk ratios adjusted for positive test time and infection time may differ. This involves adjusting for a shifted positive test time, shifted to make the difference between it and infection time uncorrelated with the outcome. We illustrate this method by reanalysing published results on the relative risk of hospitalisation following infection with the Alpha versus pre-existing variants of SARS-CoV-2. Results indicate the relative risk adjusted for infection time may be lower than that adjusted for positive test time.
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Affiliation(s)
- Shaun R Seaman
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Shaun Seaman, MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK.
| | - Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Christopher E Overton
- Department of Mathematics, University of Manchester, UK
- Clinical Data Science Unit, Manchester University NHS Foundation Trust, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) consortium, Cambridge, UK
| | - David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) consortium, Cambridge, UK
| | - Anne M Presanis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Daniela De Angelis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Joint Universities Pandemic and Epidemiological Research (JUNIPER) consortium, Cambridge, UK
- Statistics, Modelling and Economics Department, UKHSA, London, UK
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26
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Harrigan SP, Wilton J, Chong M, Abdia Y, Garcia HV, Rose C, Taylor M, Mishra S, Sander B, Hoang L, Tyson J, Krajden M, Prystajecky N, Janjua NZ, Sbihi H. Clinical Severity of Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Relative to Delta in British Columbia, Canada: A Retrospective Analysis of Whole-Genome Sequenced Cases. Clin Infect Dis 2022; 76:e18-e25. [PMID: 36041009 PMCID: PMC9452171 DOI: 10.1093/cid/ciac705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/18/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND In late 2021, the Omicron severe acute respiratory syndrome coronavirus 2 variant emerged and rapidly replaced Delta as the dominant variant. The increased transmissibility of Omicron led to surges in case rates and hospitalizations; however, the true severity of the variant remained unclear. We aimed to provide robust estimates of Omicron severity relative to Delta. METHODS This retrospective cohort study was conducted with data from the British Columbia COVID-19 Cohort, a large provincial surveillance platform with linkage to administrative datasets. To capture the time of cocirculation with Omicron and Delta, December 2021 was chosen as the study period. Whole-genome sequencing was used to determine Omicron and Delta variants. To assess the severity (hospitalization, intensive care unit [ICU] admission, length of stay), we conducted adjusted Cox proportional hazard models, weighted by inverse probability of treatment weights (IPTW). RESULTS The cohort was composed of 13 128 individuals (7729 Omicron and 5399 Delta). There were 419 coronavirus disease 2019 hospitalizations, with 118 (22%) among people diagnosed with Omicron (crude rate = 1.5% Omicron, 5.6% Delta). In multivariable IPTW analysis, Omicron was associated with a 50% lower risk of hospitalization compared with Delta (adjusted hazard ratio [aHR] = 0.50, 95% confidence interval [CI] = 0.43 to 0.59), a 73% lower risk of ICU admission (aHR = 0.27, 95% CI = 0.19 to 0.38), and a 5-day shorter hospital stay (aß = -5.03, 95% CI = -8.01 to -2.05). CONCLUSIONS Our analysis supports findings from other studies that have demonstrated lower risk of severe outcomes in Omicron-infected individuals relative to Delta.
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Affiliation(s)
| | | | - Mei Chong
- British Columbia Centre for Disease Control, British Columbia (BC), Canada
| | - Younathan Abdia
- British Columbia Centre for Disease Control, British Columbia (BC), Canada
| | | | - Caren Rose
- British Columbia Centre for Disease Control, British Columbia (BC), Canada,University of British Columbia, School of Population and Public Health, BC, Canada
| | - Marsha Taylor
- British Columbia Centre for Disease Control, British Columbia (BC), Canada
| | - Sharmistha Mishra
- Department of Medicine, University of Toronto, Toronto, Canada,MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Canada,Division of Epidemiology and Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada,Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Beate Sander
- Toronto Health Economics and Technology Assessment (THETA) collaborative, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada,Institute of Health Policy, Management and Evaluation (IHPME), Dalla Lana School of Public Health, University of Toronto, Toronto, Canada,Public Health Ontario Toronto, Canada,ICES, Toronto, Canada
| | - Linda Hoang
- British Columbia Centre for Disease Control, British Columbia (BC), Canada,University of British Columbia, Pathology and Laboratory Medicine, BC, Canada
| | - John Tyson
- British Columbia Centre for Disease Control, British Columbia (BC), Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control, British Columbia (BC), Canada,University of British Columbia, Pathology and Laboratory Medicine, BC, Canada
| | - Natalie Prystajecky
- British Columbia Centre for Disease Control, British Columbia (BC), Canada,University of British Columbia, Pathology and Laboratory Medicine, BC, Canada
| | - Naveed Z Janjua
- British Columbia Centre for Disease Control, British Columbia (BC), Canada,University of British Columbia, School of Population and Public Health, BC, Canada,Centre for Health Evaluation and Outcome Sciences, St. Paul's Hospital, Vancouver, BC, Canada
| | - Hind Sbihi
- Corresponding author: Hind Sbihi (, 1-604-707-2662), Vancouver, BC. Canada
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27
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Alsafar H, Albreiki M, Mousa M, Azman SK, Vurivi H, Waasia F, Ruta D, Alhosani F, Almazrouei S, Abuyadek R, Selvaraj F, Chaves-Coira I, Zvereff V, Abdel-Malek MAY, Alkaabi N, Uddin M, Al Awadhi T, Al Marzouqi N, Al Attar F, Al Shamsi S, Al Shehhi F, Alteneiji H, Mohamed K, Al Muhairi N, AlRand H, Fikri A, Henschel A. Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates. Sci Rep 2022; 12:14669. [PMID: 36038563 PMCID: PMC9421632 DOI: 10.1038/s41598-022-16967-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Since the declaration of SARS-CoV-2 outbreak as a pandemic, the United Arab Emirates (UAE) public health authorities have adopted strict measures to reduce transmission as early as March 2020. As a result of these measures, flight suspension, nationwide RT-PCR and surveillance of viral sequences were extensively implemented. This study aims to characterize the epidemiology, transmission pattern, and emergence of variants of concerns (VOCs) and variants of interests (VOIs) of SARS-CoV-2 in the UAE, followed by the investigation of mutations associated with hospitalized cases. A total of 1274 samples were collected and sequenced from all seven emirates between the period of 25 April 2020 to 15 February 2021. Phylogenetic analysis demonstrated multiple introductions of SARS-CoV-2 into the UAE in the early pandemic, followed by a local spread of root clades (A, B, B.1 and B.1.1). As the international flight resumed, the frequencies of VOCs surged indicating the January peak of positive cases. We observed that the hospitalized cases were significantly associated with the presence of B.1.1.7 (p < 0.001), B.1.351 (p < 0.001) and A.23.1 (p = 0.009). Deceased cases are more likely to occur in the presence of B.1.351 (p < 0.001) and A.23.1 (p = 0.022). Logistic and ridge regression showed that 51 mutations are significantly associated with hospitalized cases with the highest proportion originated from S and ORF1a genes (31% and 29% respectively). Our study provides an epidemiological insight of the emergence of VOCs and VOIs following the borders reopening and worldwide travels. It provides reassurance that hospitalization is markedly more associated with the presence of VOCs. This study can contribute to understand the global transmission of SARS-CoV-2 variants.
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Affiliation(s)
- Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Mohammed Albreiki
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates.,Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, UK
| | - Syafiq Kamarul Azman
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hema Vurivi
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Fathimathuz Waasia
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates
| | - Dymitr Ruta
- Emirates ICT Innovation Center (EBTIC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Farida Alhosani
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates
| | - Shereena Almazrouei
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates
| | - Rowan Abuyadek
- Abu Dhabi Public Health Center, Abu Dhabi Department of Health, Abu Dhabi, United Arab Emirates.,High Institute of Public Health, Alexandria University, Alexandria, Egypt
| | - Francis Selvaraj
- Department Laboratory Medicine Services, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Irene Chaves-Coira
- Molecular and Genetics Department, UniLabs, Abu Dhabi, United Arab Emirates
| | - Val Zvereff
- Department of Molecular Diagnostics, National Reference Laboratory, Abu Dhabi, United Arab Emirates.,Department of Pathology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mohamed A Y Abdel-Malek
- Molecular Biology Laboratory, Mediclinic Alnoor Hospital, Abu Dhabi, United Arab Emirates.,Clinical Pathology Department, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Nawal Alkaabi
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Maimunah Uddin
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Tayba Al Awadhi
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | - Fatma Al Attar
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | | | - Hala Alteneiji
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | | | - Noor Al Muhairi
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Hussain AlRand
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Asma Fikri
- Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Andreas Henschel
- Center for Biotechnology, Khalifa University of Science and Technology, PO BOX, 127788, Abu Dhabi, United Arab Emirates. .,Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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28
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Clinical and demographic characteristics of COVID-19 cases in Brunei Darussalam: comparison between the first and second waves, 2020 and 2021. Western Pac Surveill Response J 2022; 13:1-7. [PMID: 36688183 PMCID: PMC9831597 DOI: 10.5365/wpsar.2022.13.3.925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Objective Differences in clinical manifestations between strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported. This retrospective descriptive study compares the clinical and demographic characteristics of all confirmed coronavirus disease (COVID-19) cases admitted to the National Isolation Centre (NIC) in the first wave and at the beginning of the second wave of the pandemic in Brunei Darussalam. Methods All COVID-19 cases admitted to the NIC between 9 March and 6 May 2020 (first wave) and 7-17 August 2021 (second wave) were included. Data were obtained from NIC databases and case characteristics compared using Student's t-tests and χ2 tests, as appropriate. Results Cases from the first wave were significantly older than those from the second wave (mean 37.2 vs 29.7 years, P < 0.001), and a higher proportion reported comorbidities (30.5% vs 20.3%, P = 0.019). Cases from the second wave were more likely to be symptomatic at admission (77.7% vs 63.1%, P < 0.001), with a higher proportion reporting cough, anosmia, sore throat and ageusia/dysgeusia; however, myalgia and nausea/vomiting were more common among symptomatic first wave cases (all P < 0.05). There was no difference in the mean number of reported symptoms (2.6 vs 2.4, P = 0.890). Discussion Our study showed clear differences in the profile of COVID-19 cases in Brunei Darussalam between the first and second waves, reflecting a shift in the predominating SARS-CoV-2 strain. Awareness of changes in COVID-19 disease manifestation can help guide adjustments to management policies such as duration of isolation, testing strategies, and criteria for admission and treatment.
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29
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Grint DJ, Wing K, Houlihan C, Gibbs HP, Evans SJW, Williamson E, McDonald HI, Bhaskaran K, Evans D, Walker AJ, Hickman G, Nightingale E, Schultze A, Rentsch CT, Bates C, Cockburn J, Curtis HJ, Morton CE, Bacon S, Davy S, Wong AYS, Mehrkar A, Tomlinson L, Douglas IJ, Mathur R, MacKenna B, Ingelsby P, Croker R, Parry J, Hester F, Harper S, DeVito NJ, Hulme W, Tazare J, Smeeth L, Goldacre B, Eggo RM. Severity of Severe Acute Respiratory System Coronavirus 2 (SARS-CoV-2) Alpha Variant (B.1.1.7) in England. Clin Infect Dis 2022; 75:e1120-e1127. [PMID: 34487522 PMCID: PMC8522415 DOI: 10.1093/cid/ciab754] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) alpha variant (B.1.1.7) is associated with higher transmissibility than wild-type virus, becoming the dominant variant in England by January 2021. We aimed to describe the severity of the alpha variant in terms of the pathway of disease from testing positive to hospital admission and death. METHODS With the approval of NHS England, we linked individual-level data from primary care with SARS-CoV-2 community testing, hospital admission, and Office for National Statistics all-cause death data. We used testing data with S-gene target failure as a proxy for distinguishing alpha and wild-type cases, and stratified Cox proportional hazards regression to compare the relative severity of alpha cases with wild-type diagnosed from 16 November 2020 to 11 January 2021. RESULTS Using data from 185 234 people who tested positive for SARS-CoV-2 in the community (alpha = 93 153; wild-type = 92 081), in fully adjusted analysis accounting for individual-level demographics and comorbidities as well as regional variation in infection incidence, we found alpha associated with 73% higher hazards of all-cause death (adjusted hazard ratio [aHR]: 1.73; 95% confidence interval [CI]: 1.41-2.13; P < .0001) and 62% higher hazards of hospital admission (1.62; 1.48-1.78; P < .0001) compared with wild-type virus. Among patients already admitted to the intensive care unit, the association between alpha and increased all-cause mortality was smaller and the CI included the null (aHR: 1.20; 95% CI: .74-1.95; P = .45). CONCLUSIONS The SARS-CoV-2 alpha variant is associated with an increased risk of both hospitalization and mortality than wild-type virus.
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Affiliation(s)
- Daniel J Grint
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kevin Wing
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Catherine Houlihan
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Hamish P Gibbs
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Stephen J W Evans
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Elizabeth Williamson
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Helen I McDonald
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Krishnan Bhaskaran
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David Evans
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Alex J Walker
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - George Hickman
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Emily Nightingale
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Anna Schultze
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher T Rentsch
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Helen J Curtis
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Caroline E Morton
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Sebastian Bacon
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Simon Davy
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Angel Y S Wong
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Amir Mehrkar
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Laurie Tomlinson
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ian J Douglas
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rohini Mathur
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brian MacKenna
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Peter Ingelsby
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Richard Croker
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | | | - Nicholas J DeVito
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Will Hulme
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - John Tazare
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Liam Smeeth
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ben Goldacre
- The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Rosalind M Eggo
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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30
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COVID-19 Severity and Mortality in Two Pandemic Waves in Poland and Predictors of Poor Outcomes of SARS-CoV-2 Infection in Hospitalized Young Adults. Viruses 2022; 14:v14081700. [PMID: 36016322 PMCID: PMC9413321 DOI: 10.3390/v14081700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 variants pose a significant threat to global public health. However, their influence on disease severity, especially among young adults who may exhibit different clinical characteristics, is debatable. In this retrospective study of 229 young adults hospitalized with COVID-19, we investigated the differences between Poland's second and third waves of the pandemic. To identify potential predictors of severe COVID-19 in young adults, we analyzed patient characteristics and laboratory findings between survivors and non-survivors and we performed logistic regression to assess the risk of death, mechanical ventilation, and intensive care unit treatment. We found no increase in COVID-19 severity comparing the third and second waves of the pandemic, indicating that the alpha variant had no influence on disease severity. In addition, we found that factors, such as obesity, comorbidities, lung involvement, leukocytosis, neutrophilia, lymphopenia, higher IG count, the neutrophil-to-lymphocyte ratio, C-reactive protein, procalcitonin, interleukin-6, D-Dimer, lactate dehydrogenase, high-sensitive troponin I, creatine kinase-myocardial band, myoglobin, N-terminal-pro-B-type natriuretic peptide, creatinine, urea and gamma-glutamyl transferase, lower estimated glomerular filtration rate, albumin, calcium and vitamin D3, possibly a decrease in red blood cell counts, hemoglobin and hematocrit, and an increase in creatine kinase during hospitalization may be associated with poor outcomes of COVID-19.
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31
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da Silva ES, Kohnen M, Gilson G, Staub T, Arendt V, Hilger C, Servais JY, Charpentier E, Domingues O, Snoeck CJ, Ollert M, Seguin-Devaux C, Perez-Bercoff D. Pre-Omicron Vaccine Breakthrough Infection Induces Superior Cross-Neutralization against SARS-CoV-2 Omicron BA.1 Compared to Infection Alone. Int J Mol Sci 2022; 23:7675. [PMID: 35887023 PMCID: PMC9320437 DOI: 10.3390/ijms23147675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 variants raise concern because of their high transmissibility and their ability to evade neutralizing antibodies elicited by prior infection or by vaccination. Here, we compared the neutralizing abilities of sera from 70 unvaccinated COVID-19 patients infected before the emergence of variants of concern (VOCs) and of 16 vaccine breakthrough infection (BTI) cases infected with Gamma or Delta against the ancestral B.1 strain, the Gamma, Delta and Omicron BA.1 VOCs using live virus. We further determined antibody levels against the Nucleocapsid (N) and full Spike proteins, the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the Spike protein. Convalescent sera featured considerable variability in the neutralization of B.1 and in the cross-neutralization of different strains. Their neutralizing capacity moderately correlated with antibody levels against the Spike protein and the RBD. All but one convalescent serum failed to neutralize Omicron BA.1. Overall, convalescent sera from patients with moderate disease had higher antibody levels and displayed a higher neutralizing ability against all strains than patients with mild or severe forms of the disease. The sera from BTI cases fell into one of two categories: half the sera had a high neutralizing activity against the ancestral B.1 strain as well as against the infecting strain, while the other half had no or a very low neutralizing activity against all strains. Although antibody levels against the spike protein and the RBD were lower in BTI sera than in unvaccinated convalescent sera, most neutralizing sera also retained partial neutralizing activity against Omicron BA.1, suggestive of a better cross-neutralization and higher affinity of vaccine-elicited antibodies over virus-induced antibodies. Accordingly, the IC50: antibody level ratios were comparable for BTI and convalescent sera, but remained lower in the neutralizing convalescent sera from patients with moderate disease than in BTI sera. The neutralizing activity of BTI sera was strongly correlated with antibodies against the Spike protein and the RBD. Together, these findings highlight qualitative differences in antibody responses elicited by infection in vaccinated and unvaccinated individuals. They further indicate that breakthrough infection with a pre-Omicron variant boosts immunity and induces cross-neutralizing antibodies against different strains, including Omicron BA.1.
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Affiliation(s)
- Eveline Santos da Silva
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (C.S.-D.)
| | - Michel Kohnen
- Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (G.G.); (T.S.); (V.A.)
| | - Georges Gilson
- Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (G.G.); (T.S.); (V.A.)
| | - Therese Staub
- Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (G.G.); (T.S.); (V.A.)
| | - Victor Arendt
- Centre Hospitalier de Luxembourg, 4 rue Ernest Barblé, L-1210 Luxembourg, Luxembourg; (M.K.); (G.G.); (T.S.); (V.A.)
| | - Christiane Hilger
- Molecular and Translational Allergology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg;
| | - Jean-Yves Servais
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (C.S.-D.)
| | - Emilie Charpentier
- Clinical and Applied Virology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.C.); (C.J.S.)
| | - Olivia Domingues
- Allergy and Clinical Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (O.D.); (M.O.)
| | - Chantal J. Snoeck
- Clinical and Applied Virology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.C.); (C.J.S.)
| | - Markus Ollert
- Allergy and Clinical Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (O.D.); (M.O.)
| | - Carole Seguin-Devaux
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (C.S.-D.)
| | - Danielle Perez-Bercoff
- HIV Clinical and Translational Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.S.d.S.); (J.-Y.S.); (C.S.-D.)
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Zachreson C, Chang S, Harding N, Prokopenko M. The effects of local homogeneity assumptions in metapopulation models of infectious disease. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211919. [PMID: 35845852 PMCID: PMC9277238 DOI: 10.1098/rsos.211919] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 06/23/2022] [Indexed: 05/10/2023]
Abstract
Computational models of infectious disease can be broadly categorized into two types: individual-based (agent-based) or compartmental models. While there are clear conceptual distinctions between these methodologies, a fair comparison of the approaches is difficult to achieve. Here, we carry out such a comparison by building a set of compartmental metapopulation models from an agent-based representation of a real population. By adjusting the compartmental model to approximately match the dynamics of the agent-based model, we identify two key qualitative properties of the individual-based dynamics which are lost upon aggregation into metapopulations. These are (i) the local depletion of susceptibility to infection and (ii) decoupling of different regional groups due to correlation between commuting behaviours and contact rates. The first of these effects is a general consequence of aggregating small, closely connected groups (i.e. families) into larger homogeneous metapopulations. The second can be interpreted as a consequence of aggregating two distinct types of individuals: school children, who travel short distances but have many potentially infectious contacts, and adults, who travel further but tend to have fewer contacts capable of transmitting infection. Our results could be generalized to other types of correlations between the characteristics of individuals and the behaviours that distinguish them.
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Affiliation(s)
- Cameron Zachreson
- School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sheryl Chang
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nathan Harding
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mikhail Prokopenko
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales 2145, Australia
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Zachreson C, Chang S, Harding N, Prokopenko M. The effects of local homogeneity assumptions in metapopulation models of infectious disease. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211919. [PMID: 35845852 DOI: 10.5281/zenodo.6486795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 06/23/2022] [Indexed: 05/25/2023]
Abstract
Computational models of infectious disease can be broadly categorized into two types: individual-based (agent-based) or compartmental models. While there are clear conceptual distinctions between these methodologies, a fair comparison of the approaches is difficult to achieve. Here, we carry out such a comparison by building a set of compartmental metapopulation models from an agent-based representation of a real population. By adjusting the compartmental model to approximately match the dynamics of the agent-based model, we identify two key qualitative properties of the individual-based dynamics which are lost upon aggregation into metapopulations. These are (i) the local depletion of susceptibility to infection and (ii) decoupling of different regional groups due to correlation between commuting behaviours and contact rates. The first of these effects is a general consequence of aggregating small, closely connected groups (i.e. families) into larger homogeneous metapopulations. The second can be interpreted as a consequence of aggregating two distinct types of individuals: school children, who travel short distances but have many potentially infectious contacts, and adults, who travel further but tend to have fewer contacts capable of transmitting infection. Our results could be generalized to other types of correlations between the characteristics of individuals and the behaviours that distinguish them.
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Affiliation(s)
- Cameron Zachreson
- School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sheryl Chang
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nathan Harding
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mikhail Prokopenko
- Centre for Complex Systems, Faculty of Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales 2145, Australia
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Balloux F, Tan C, Swadling L, Richard D, Jenner C, Maini M, van Dorp L. The past, current and future epidemiological dynamic of SARS-CoV-2. OXFORD OPEN IMMUNOLOGY 2022; 3:iqac003. [PMID: 35872966 PMCID: PMC9278178 DOI: 10.1093/oxfimm/iqac003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.
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Affiliation(s)
- François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 138672 Singapore, Singapore
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Charlotte Jenner
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Mala Maini
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
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Van Goethem N, Chung PYJ, Meurisse M, Vandromme M, De Mot L, Brondeel R, Stouten V, Klamer S, Cuypers L, Braeye T, Catteau L, Nevejan L, van Loenhout JAF, Blot K. Clinical Severity of SARS-CoV-2 Omicron Variant Compared with Delta among Hospitalized COVID-19 Patients in Belgium during Autumn and Winter Season 2021-2022. Viruses 2022; 14:1297. [PMID: 35746768 PMCID: PMC9227815 DOI: 10.3390/v14061297] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 01/08/2023] Open
Abstract
This retrospective multi-center matched cohort study assessed the risk for severe COVID-19 (combination of severity indicators), intensive care unit (ICU) admission, and in-hospital mortality in hospitalized patients when infected with the Omicron variant compared to when infected with the Delta variant. The study is based on a causal framework using individually-linked data from national COVID-19 registries. The study population consisted of 954 COVID-19 patients (of which, 445 were infected with Omicron) above 18 years old admitted to a Belgian hospital during the autumn and winter season 2021-2022, and with available viral genomic data. Patients were matched based on the hospital, whereas other possible confounders (demographics, comorbidities, vaccination status, socio-economic status, and ICU occupancy) were adjusted for by using a multivariable logistic regression analysis. The estimated standardized risk for severe COVID-19 and ICU admission in hospitalized patients was significantly lower (RR = 0.63; 95% CI (0.30; 0.97) and RR = 0.56; 95% CI (0.14; 0.99), respectively) when infected with the Omicron variant, whereas in-hospital mortality was not significantly different according to the SARS-CoV-2 variant (RR = 0.78, 95% CI (0.28-1.29)). This study demonstrates the added value of integrated genomic and clinical surveillance to recognize the multifactorial nature of COVID-19 pathogenesis.
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Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Pui Yan Jenny Chung
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Marjan Meurisse
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Mathil Vandromme
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Laurane De Mot
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Ruben Brondeel
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Veerle Stouten
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Sofieke Klamer
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Lize Cuypers
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium; (L.C.); (L.N.)
| | - Toon Braeye
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Lucy Catteau
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Louis Nevejan
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, 3000 Leuven, Belgium; (L.C.); (L.N.)
| | - Joris A. F. van Loenhout
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
| | - Koen Blot
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (P.Y.J.C.); (M.M.); (M.V.); (L.D.M.); (R.B.); (V.S.); (S.K.); (T.B.); (L.C.); (J.A.F.v.L.); (K.B.)
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Martin-Blondel G, Lescure FX, Assoumou L, Charpentier C, Chapplain JM, Perpoint T, Grouteau G, Cordel H, Pialoux G, Pacanowski J, Thy M, Bauvois A, Laureillard D, Hamrouni F, Algarte-Genin M, Poissy J, Descamps D, Costagliola D. Increased risk of severe COVID-19 in hospitalized patients with SARS-CoV-2 Alpha variant infection: a multicentre matched cohort study. BMC Infect Dis 2022; 22:540. [PMID: 35698029 PMCID: PMC9189443 DOI: 10.1186/s12879-022-07508-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The impact of the variant of concern (VOC) Alpha on the severity of COVID-19 has been debated. We report our analysis in France. METHODS We conducted an exposed/unexposed cohort study with retrospective data collection, comparing patients infected by VOC Alpha to contemporaneous patients infected by historical lineages. Participants were matched on age (± 2.5 years), sex and region of hospitalization. The primary endpoint was the proportion of hospitalized participants with severe COVID-19, defined as a WHO-scale > 5 or by the need of a non-rebreather mask, occurring up to day 29 after admission. We used a logistic regression model stratified on each matched pair and accounting for factors known to be associated with the severity of the disease. RESULTS We included 650 pairs of patients hospitalized between Jan 1, 2021, and Feb 28, 2021, in 47 hospitals. Median age was 70 years and 61.3% of participants were male. The proportion of participants with comorbidities was high in both groups (85.0% vs 90%, p = 0.004). Infection by VOC Alpha was associated with a higher odds of severe COVID-19 (41.7% vs 38.5%-aOR = 1.33 95% CI [1.03-1.72]). CONCLUSION Infection by the VOC Alpha was associated with a higher odds of severe COVID-19.
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Affiliation(s)
- Guillaume Martin-Blondel
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Toulouse, Toulouse, France. .,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291, CNRS UMR5051, Université Toulouse III, Toulouse, France.
| | - François-Xavier Lescure
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude-Bernard, APHP, Paris, France
| | - Lambert Assoumou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Charlotte Charpentier
- Service de Virologie, Université de Paris, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, 75018, Paris, France
| | - Jean-Marc Chapplain
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Thomas Perpoint
- Service des Maladies Infectieuses et Tropicales, Hospices Civils de Lyon, Lyon, France
| | - Gaspard Grouteau
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Hugues Cordel
- Service des Maladies Infectieuses et Tropicales, Hôpital Avicenne, AP-HP, Bobigny, France
| | - Gilles Pialoux
- Service des Maladies Infectieuses et Tropicales, Hôpital Tenon, APHP, Paris, France
| | - Jérome Pacanowski
- Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, APHP, Paris, France
| | - Michael Thy
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude-Bernard, APHP, Paris, France
| | - Adeline Bauvois
- Service de Médecine Interne, Hôpital Ambroise Paré, APHP, Boulogne-Billancourt, France
| | - Didier Laureillard
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
| | - Fadia Hamrouni
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Michèle Algarte-Genin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Julien Poissy
- University of Lille, Inserm U1285, CHU Lille, Pôle de Médecine Intensive Réanimation, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Diane Descamps
- Service de Virologie, Université de Paris, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, 75018, Paris, France
| | - Dominique Costagliola
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
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Santolino M, Alcañiz M, Bolancé C. Hospitalizations from covid-19: a health planning tool. Rev Saude Publica 2022; 56:51. [PMID: 35703605 PMCID: PMC9239335 DOI: 10.11606/s1518-8787.2022056004315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Estimate the future number of hospitalizations from Covid-19 based on the number of diagnosed positive cases. METHOD Using the covid-19 Panel data recorded in Spain at the Red Nacional de Vigilancia Epidemiológica, Renave (Epidemiological Surveillance Network), a regression model with multiplicative structure is adjusted to explain and predict the number of hospitalizations from the lagged series of positive cases diagnosed from May 11, 2020 to September 20, 2021. The effect of the time elapsed since the vaccination program starting on the number of hospitalizations is reviewed. RESULTS Nine days is the number of lags in the positive cases series with greatest explanatory power on the number of hospitalizations. The variability of the number of hospitalizations explained by the model is high (adjusted R2: 96.6%). Before the vaccination program starting, the expected number of hospitalizations on day t was 20.2% of the positive cases on day t-9 raised to 0.906. After the vaccination program started, this percentage was reduced by 0.3% a day. Using the same model, we find that in the first pandemic wave the number of positive cases was more than six times that reported on official records. CONCLUSIONS Starting from the covid-19 cases detected up to a given date, the proposed model allows estimating the number of hospitalizations nine days in advance. Thus, it is a useful tool for forecasting the hospital pressure that health systems shall bear as a consequence of the disease.
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Affiliation(s)
- Miguel Santolino
- Universitat de BarcelonaInstitut de Recerca en Economia AplicadaResearch Group on Risk in Insurance and FinanceBarcelonaEspaña Universitat de Barcelona. Institut de Recerca en Economia Aplicada. Research Group on Risk in Insurance and Finance. Barcelona, España
| | - Manuela Alcañiz
- Universitat de BarcelonaInstitut de Recerca en Economia AplicadaResearch Group on Risk in Insurance and FinanceBarcelonaEspaña Universitat de Barcelona. Institut de Recerca en Economia Aplicada. Research Group on Risk in Insurance and Finance. Barcelona, España
| | - Catalina Bolancé
- Universitat de BarcelonaInstitut de Recerca en Economia AplicadaResearch Group on Risk in Insurance and FinanceBarcelonaEspaña Universitat de Barcelona. Institut de Recerca en Economia Aplicada. Research Group on Risk in Insurance and Finance. Barcelona, España
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Van Goethem N, Vandromme M, Van Oyen H, Haarhuis F, Brondeel R, Catteau L, André E, Cuypers L, Blot K, Serrien B. Severity of infection with the SARS-CoV-2 B.1.1.7 lineage among hospitalized COVID-19 patients in Belgium. PLoS One 2022; 17:e0269138. [PMID: 35657787 PMCID: PMC9165825 DOI: 10.1371/journal.pone.0269138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/13/2022] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION The pathogenesis of COVID-19 depends on the interplay between host characteristics, viral characteristics and contextual factors. Here, we compare COVID-19 disease severity between hospitalized patients in Belgium infected with the SARS-CoV-2 variant B.1.1.7 and those infected with previously circulating strains. METHODS The study is conducted within a causal framework to study the severity of SARS-CoV-2 variants by merging surveillance registries in Belgium. Infection with SARS-CoV-2 B.1.1.7 ('exposed') was compared to infection with previously circulating strains ('unexposed') in terms of the manifestation of severe COVID-19, intensive care unit (ICU) admission, or in-hospital mortality. The exposed and unexposed group were matched based on the hospital and the mean ICU occupancy rate during the patient's hospital stay. Other variables identified as confounders in a Directed Acyclic Graph (DAG) were adjusted for using regression analysis. Sensitivity analyses were performed to assess the influence of selection bias, vaccination rollout, and unmeasured confounding. RESULTS We observed no difference between the exposed and unexposed group in severe COVID-19 disease or in-hospital mortality (RR = 1.15, 95% CI [0.93-1.38] and RR = 0.92, 95% CI [0.62-1.23], respectively). The estimated standardized risk to be admitted in ICU was significantly higher (RR = 1.36, 95% CI [1.03-1.68]) when infected with the B.1.1.7 variant. An age-stratified analysis showed that among the younger age group (≤65 years), the SARS-CoV-2 variant B.1.1.7 was significantly associated with both severe COVID-19 progression and ICU admission. CONCLUSION This matched observational cohort study did not find an overall increased risk of severe COVID-19 or death associated with B.1.1.7 infection among patients already hospitalized. There was a significant increased risk to be transferred to ICU when infected with the B.1.1.7 variant, especially among the younger age group. However, potential selection biases advocate for more systematic sequencing of samples from hospitalized COVID-19 patients.
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Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Woluwe-Saint-Lambert, Belgium
| | - Mathil Vandromme
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Herman Van Oyen
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Freek Haarhuis
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Ruben Brondeel
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Lucy Catteau
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Emmanuel André
- University Hospitals Leuven, Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, Leuven, Belgium
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory Clinical Bacteriology and Mycology, Rega Institute for Medical Research, Leuven, Belgium
| | - Lize Cuypers
- University Hospitals Leuven, Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, Leuven, Belgium
| | | | | | - Koen Blot
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Ben Serrien
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
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Dol J, Boulos L, Somerville M, Saxinger L, Doroshenko A, Hastings S, Reynolds B, Gallant A, Shin HD, Wong H, Crowther D, Macdonald M, Martin-Misener R, McCulloch H, Tricco AC, Curran JA. Health system impacts of SARS-CoV - 2 variants of concern: a rapid review. BMC Health Serv Res 2022; 22:544. [PMID: 35461246 PMCID: PMC9034743 DOI: 10.1186/s12913-022-07847-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 03/21/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND As of November 25th 2021, four SARS-CoV - 2 variants of concern (VOC: Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2)) have been detected. Variable degrees of increased transmissibility of the VOC have been documented, with potential implications for hospital and health system capacity and control measures. This rapid review aimed to provide a synthesis of evidence related to health system responses to the emergence of VOC worldwide. METHODS Seven databases were searched up to September 27, 2021, for terms related to VOC. Titles, abstracts, and full-text documents were screened independently by two reviewers. Data were extracted independently by two reviewers using a standardized form. Studies were included if they reported on at least one of the VOC and health system outcomes. RESULTS Of the 4877 articles retrieved, 59 studies were included, which used a wide range of designs and methods. Most of the studies reported on Alpha, and all except two reported on impacts for capacity planning related to hospitalization, intensive care admissions, and mortality. Most studies (73.4%) observed an increase in hospitalization, but findings on increased admission to intensive care units were mixed (50%). Most studies (63.4%) that reported mortality data found an increased risk of death due to VOC, although health system capacity may influence this. No studies reported on screening staff and visitors or cohorting patients based on VOC. CONCLUSION While the findings should be interpreted with caution as most of the sources identified were preprints, evidence is trending towards an increased risk of hospitalization and, potentially, mortality due to VOC compared to wild-type SARS-CoV - 2. There is little evidence on the need for, and the effect of, changes to health system arrangements in response to VOC transmission.
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Affiliation(s)
- Justine Dol
- Faculty of Health, Dalhousie University, Halifax, NS, Canada
| | - Leah Boulos
- Maritime SPOR SUPPORT Unit, Halifax, NS, Canada
| | - Mari Somerville
- School of Nursing, Dalhousie University, Halifax, NS, Canada
| | - Lynora Saxinger
- Division of Infectious Diseases, Departments of Medicine and Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Alexander Doroshenko
- Division of Preventive Medicine, Faculty of Medicine and Dentistry, University of Alberta, Calgary, AB, Canada
| | | | | | - Allyson Gallant
- Faculty of Health, Dalhousie University, Halifax, NS, Canada
| | | | - Helen Wong
- Faculty of Health, Dalhousie University, Halifax, NS, Canada
| | - Daniel Crowther
- School of Nursing, Dalhousie University, Halifax, NS, Canada
| | | | | | | | - Andrea C Tricco
- Knowledge Translation Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health, Toronto, ON, Canada
- Epidemiology Division and Institute for Health Policy, Management, and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Queen's Collaboration for Health Care Quality Joanna Briggs Institute Centre of Excellence, School of Nursing, Queen's University, Toronto, ON, Canada
| | - Janet A Curran
- School of Nursing, Dalhousie University, Halifax, NS, Canada.
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Njoh AA, Mboke E, Ndoula ST, Bachir HB, Nembot R, Chebo C, Aman A, Saidu Y. COVID-19 in a region of Cameroon hit by armed conflict. Pan Afr Med J 2022; 41:32. [PMID: 35382043 PMCID: PMC8956904 DOI: 10.11604/pamj.2022.41.32.32587] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 12/14/2021] [Indexed: 12/16/2022] Open
Abstract
Introduction the emergence of more transmissible SARS-CoV-2 variants like Delta and Omicron have triggered the next wave of COVID-19 in many parts of the world. Here we report a surge in COVID-19 cases and deaths in the Northwest (NW) Region of Cameroon, which is plagued with low immunization coverage and armed conflict. Methods a cross-sectional study was conducted in September 2021 and data on COVID-19 cases and vaccination were reviewed from the Ministry of Health database from January 1st, 2020 to September 4th, 2021. The security situation of the region was obtained from the districts and regional health managers. Data were analyzed with MS Excel and results presented as trends and proportions. Results since the onset of COVID-19 pandemic, there is an increasing prevalence in cases in the NW. Between epidemiological week 34-35 of 2021, there was a surge in COVID-19 cases in the NW. More than 70% of all COVID-19 related deaths reported in the country during epidemiological week-35 were recorded in this region. Despite this high mortality, COVID-19 vaccine uptake remains very low in the region. Indeed, just 0.6% of the 962,036-target population 18-years and above are fully immunized after 6-months of vaccination. Conclusion though the country´s epi-curve does not suggest a third wave currently, the NW is experiencing a steady COVID-19 case surge amid insecurity and the circulation of the Delta variant. There is therefore a need to adopt innovative strategies to improve immunization and strengthen other SARS-CoV-2 preventive measures in this region.
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Affiliation(s)
- Andreas Ateke Njoh
- Expanded Program on Immunization, Ministry of Public Health, Yaounde, Cameroon.,Faculty of Science, University of Buea, Buea, Cameroon
| | - Eric Mboke
- Expanded Program on Immunization, Ministry of Public Health, Yaounde, Cameroon
| | | | - Hassan Ben Bachir
- Department of Family Health, Ministry of Public Health, Yaounde, Cameroon
| | - Raoul Nembot
- Expanded Program on Immunization, Ministry of Public Health, Yaounde, Cameroon
| | - Cornelius Chebo
- Regional Delegation of Public Health for the Northwest Region, Bamenda, Cameroon
| | - Adidja Aman
- Department of Family Health, Ministry of Public Health, Yaounde, Cameroon.,Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
| | - Yauba Saidu
- Clinton Health Access Initiative, Yaounde, Cameroon.,Institute for Global Health, University of Siena, Siena, Italy
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41
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Gupta AK, Leslie A, Hewitt JN, Kovoor JG, Ovenden CD, Edwards S, Chan JCY, Worthington MG. Cardiac surgery on patients with COVID-19: a systematic review and meta-analysis. ANZ J Surg 2022; 92:1007-1014. [PMID: 35373439 PMCID: PMC9111466 DOI: 10.1111/ans.17667] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 12/15/2022]
Abstract
Introduction The COVID‐19 pandemic has had a significant impact on global surgery. In particular, deleterious effects of SARS‐CoV‐2 infection on the heart and cardiovascular system have been described. To inform surgical patients, we performed a systematic review and meta‐analysis aiming to characterize outcomes of COVID‐19 positive patients undergoing cardiac surgery. Methods The study protocol was registered with PROSPERO (CRD42021228533) and conformed with PRISMA 2020 and MOOSE guidelines. PubMed, Ovid MEDLINE and Web of Science were searched between 1 January 2019 to 24 February 2022 for studies reporting outcomes on COVID‐19 positive patients undergoing cardiac surgery. Study screening, data extraction and risk of bias assessment were conducted in duplicate. Meta‐analysis was conducted using a random‐effects model where at least two studies had sufficient data for that variable. Results Searches identified 4223 articles of which 18 studies were included with a total 44 patients undergoing cardiac surgery. Within these studies, 12 (66.7%) reported populations undergoing coronary artery bypass graft (CABG) surgery, three (16.7%) aortic valve replacements (AVR) and three (16.7%) aortic dissection repairs. Overall mean postoperative length of ICU stay was 3.39 (95% confidence interval (CI): 0.38, 6.39) and mean postoperative length of hospital stay was 17.88 (95% CI: 14.57, 21.19). Conclusion This systematic review and meta‐analysis investigated studies of limited quality which characterized cardiac surgery in COVID‐19 positive patients and demonstrates that these patients have poor outcomes. Further issues to be explored are effects of COVID‐19 on decision‐making in cardiac surgery, and effects of COVID‐19 on the cardiovascular system at a cellular level.
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Affiliation(s)
- Aashray K Gupta
- Department of Surgery, University of Sydney, Sydney, New South Wales, Australia.,Department of Cardiothoracic Surgery, Royal Adelaide Hospital, Adelaide, Australia.,University of Adelaide, Discipline of Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Alasdair Leslie
- University of Adelaide, Discipline of Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Joseph N Hewitt
- University of Adelaide, Discipline of Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Joshua G Kovoor
- University of Adelaide, Discipline of Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Christopher D Ovenden
- University of Adelaide, Discipline of Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Suzanne Edwards
- Adelaide Health Technology Assessment, School of Public Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Justin C Y Chan
- University of Adelaide, Discipline of Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
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Dugani SB, Fischer KM, Schroeder DR, Geyer HL, Maniaci MJ, Croghan IT, Kashani D, Burton MC. Wellness of hospitalists and hospital medicine advanced practice providers during the COVID-19 pandemic, 2020-2021. J Hosp Med 2022; 17:259-267. [PMID: 35535916 PMCID: PMC9088352 DOI: 10.1002/jhm.12812] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND The early phase of the coronavirus disease 2019 (COVID-19) pandemic had a negative impact on the wellness of hospitalists and hospital medicine advanced practice providers (APPs). However, the burden of the pandemic has evolved and the change in hospitalist and hospital medicine APP wellness is unknown. OBJECTIVE To evaluate the longitudinal trend in wellness of hospitalists and hospital medicine APPs during the COVID-19 pandemic and guide wellness interventions. DESIGN, SETTING AND PARTICIPANTS Between May 4, 2020, and June 6, 2021, we administered three surveys to Internal Medicine hospitalists (physicians) and hospital medicine APPs (nurse practitioners and physician assistants) at 16 Mayo Clinic hospitals in four U.S. states. MEASUREMENTS We evaluated the association of hospitalist and hospital medicine APP characteristics with PROMIS® measures of global wellbeing-mental health, global wellbeing-social activities and relationships, anxiety, social isolation, and emotional support, using logistic and linear regression models. RESULTS The response rates were 52.2% (n=154/295; May 2020), 37.1% (n=111/299; October 2020) and 35.5% (n=114/321; May 2021). In mixed models that included hospitalist and hospital medicine APP characteristics and survey period, APPs, compared with physicians, had lower odds of top global wellbeing-social activities and relationships (adjusted odds ratio 0.42 [0.22-0.82]; p = .01), whereas survey period showed no association. The survey period showed an independent association with higher anxiety (May 2020 vs. others) and higher social isolation (October 2020 vs. others), whereas profession showed no association. Concern about contracting COVID-19 at work was significantly associated with lower odds of top global wellbeing-mental health and global wellbeing-social activities and relationships, and with higher anxiety and social isolation. Hospitalist and hospital medicine APP characteristics showed no association with levels of emotional support. CONCLUSIONS In this longitudinal assessment of hospitalists and hospital medicine APPs, concern about contracting COVID-19 at work remained a determinant of wellness. The trend for global wellbeing, anxiety, and social isolation may guide wellness interventions.
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Affiliation(s)
- Sagar B. Dugani
- Division of Hospital Internal MedicineMayo ClinicRochesterMinnesotaUSA
- Kern Center for the Science of Health Care DeliveryMayo ClinicRochesterMinnesotaUSA
- Knowledge and Evaluation Research UnitMayo ClinicRochesterMinnesotaUSA
| | - Karen M. Fischer
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | | | - Holly L. Geyer
- Division of Hospital Internal MedicineMayo ClinicScottsdaleArizonaUSA
| | | | - Ivana T. Croghan
- Kern Center for the Science of Health Care DeliveryMayo ClinicRochesterMinnesotaUSA
- Knowledge and Evaluation Research UnitMayo ClinicRochesterMinnesotaUSA
- Department of Medicine, Division of General Internal MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Medicine, Research HubMayo ClinicRochesterMinnesotaUSA
| | - Daniel Kashani
- Division of Hospital Internal MedicineMayo ClinicRochesterMinnesotaUSA
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McAlister FA, Nabipoor M, Chu A, Lee DS, Saxinger L, Bakal JA. The impact of shifting demographics, variants of concern and vaccination on outcomes during the first 3 COVID-19 waves in Alberta and Ontario: a retrospective cohort study. CMAJ Open 2022; 10:E400-E408. [PMID: 35473827 PMCID: PMC9121845 DOI: 10.9778/cmajo.20210323] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In Canada, published outcome data for COVID-19 come largely from the first 2 waves of the pandemic. We examined changes in demographics and 30-day outcomes after SARS-CoV-2 infection during the first 3 pandemic waves in Alberta and Ontario; for wave 3, we compared outcomes between those infected with a variant of concern and those infected with the original "wild-type" SARS-CoV-2. METHODS We conducted a population-based retrospective cohort study using linked health care data sets in Alberta and Ontario. We identified all-cause hospitalizations or deaths within 30 days after a positive result on a reverse transcription polymerase chain reaction test for SARS-CoV-2 in individuals of any age between Mar. 1, 2020, and June 30, 2021, with genomic confirmation of variants of concern. We compared outcomes in wave 3 (February 2021 to June 2021) with outcomes in waves 1 and 2 combined (March 2020 to January 2021) after adjusting for age, sex and Charlson Comorbidity Index score. Using wave 3 data only, we compared outcomes by vaccination status and whether or not the individual was infected with a variant of concern. RESULTS Compared to those infected with SARS-CoV-2 during waves 1 and 2 (n = 372 070), we found a shift toward a younger and healthier demographic in those infected during wave 3 (n = 359 079). In wave 3, patients were more likely to be hospitalized (adjusted odds ratio [aOR] 1.57, 95% confidence interval [CI] 1.46-1.70) but had a shorter length of hospital stay (median 6 days v. 7 days, p < 0.001) and lower 30-day mortality (aOR 0.73, 95% CI 0.65-0.81). The 217 892 patients in wave 3 who were infected with a variant of concern (83.5% confirmed to have the Alpha variant, 1.7% confirmed to have the Delta variant) had a higher risk of death (Alpha: aOR 1.29, 95% CI 1.16-1.44; Delta: aOR 2.05, 95% CI 1.49-2.82) and hospitalization (Alpha: aOR 1.59, 95% CI 1.53-1.66; Delta: aOR 1.88, 95% CI 1.64-2.15) than those infected with wild-type SARS-CoV-2. INTERPRETATION We observed a shift among those infected with SARS-CoV-2 toward younger patients with fewer comorbidities, a shorter length of hospital stay and lower mortality risk as the pandemic evolved in Alberta and Ontario; however, infection with a variant of concern was associated with a substantially higher risk of hospitalization or death. As variants of concern emerge, ongoing monitoring of disease expression and outcomes among vaccinated and unvaccinated individuals is important to understand the phenotypes of COVID-19 and the anticipated burdens for the health care system.
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Affiliation(s)
- Finlay A McAlister
- The Department of Medicine, Faculty of Medicine and Dentistry (McAlister, Saxinger, Bakal), University of Alberta, Edmonton, Alta.; The Alberta Strategy for Patient Oriented Research Support Unit (McAlister, Nabipoor, Bakal); The Canadian VIGOUR Centre (McAlister), University of Alberta, Edmonton, Alta.; ICES (Chu, Lee); University of Toronto (Chu, Lee); University Health Network (Lee), Toronto, Ont.
| | - Majid Nabipoor
- The Department of Medicine, Faculty of Medicine and Dentistry (McAlister, Saxinger, Bakal), University of Alberta, Edmonton, Alta.; The Alberta Strategy for Patient Oriented Research Support Unit (McAlister, Nabipoor, Bakal); The Canadian VIGOUR Centre (McAlister), University of Alberta, Edmonton, Alta.; ICES (Chu, Lee); University of Toronto (Chu, Lee); University Health Network (Lee), Toronto, Ont
| | - Anna Chu
- The Department of Medicine, Faculty of Medicine and Dentistry (McAlister, Saxinger, Bakal), University of Alberta, Edmonton, Alta.; The Alberta Strategy for Patient Oriented Research Support Unit (McAlister, Nabipoor, Bakal); The Canadian VIGOUR Centre (McAlister), University of Alberta, Edmonton, Alta.; ICES (Chu, Lee); University of Toronto (Chu, Lee); University Health Network (Lee), Toronto, Ont
| | - Douglas S Lee
- The Department of Medicine, Faculty of Medicine and Dentistry (McAlister, Saxinger, Bakal), University of Alberta, Edmonton, Alta.; The Alberta Strategy for Patient Oriented Research Support Unit (McAlister, Nabipoor, Bakal); The Canadian VIGOUR Centre (McAlister), University of Alberta, Edmonton, Alta.; ICES (Chu, Lee); University of Toronto (Chu, Lee); University Health Network (Lee), Toronto, Ont
| | - Lynora Saxinger
- The Department of Medicine, Faculty of Medicine and Dentistry (McAlister, Saxinger, Bakal), University of Alberta, Edmonton, Alta.; The Alberta Strategy for Patient Oriented Research Support Unit (McAlister, Nabipoor, Bakal); The Canadian VIGOUR Centre (McAlister), University of Alberta, Edmonton, Alta.; ICES (Chu, Lee); University of Toronto (Chu, Lee); University Health Network (Lee), Toronto, Ont
| | - Jeffrey A Bakal
- The Department of Medicine, Faculty of Medicine and Dentistry (McAlister, Saxinger, Bakal), University of Alberta, Edmonton, Alta.; The Alberta Strategy for Patient Oriented Research Support Unit (McAlister, Nabipoor, Bakal); The Canadian VIGOUR Centre (McAlister), University of Alberta, Edmonton, Alta.; ICES (Chu, Lee); University of Toronto (Chu, Lee); University Health Network (Lee), Toronto, Ont
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Abas AH, Marfuah S, Idroes R, Kusumawaty D, Fatimawali, Park MN, Siyadatpanah A, Alhumaydhi FA, Mahmud S, Tallei TE, Emran TB, Kim B. Can the SARS-CoV-2 Omicron Variant Confer Natural Immunity against COVID-19? Molecules 2022; 27:2221. [PMID: 35408618 PMCID: PMC9000495 DOI: 10.3390/molecules27072221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with no signs of abatement in sight. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of this pandemic and has claimed over 5 million lives, is still mutating, resulting in numerous variants. One of the newest variants is Omicron, which shows an increase in its transmissibility, but also reportedly reduces hospitalization rates and shows milder symptoms, such as in those who have been vaccinated. As a result, many believe that Omicron provides a natural vaccination, which is the first step toward ending the COVID-19 pandemic. Based on published research and scientific evidence, we review and discuss how the end of this pandemic is predicted to occur as a result of Omicron variants being surpassed in the community. In light of the findings of our research, we believe that it is most likely true that the Omicron variant is a natural way of vaccinating the masses and slowing the spread of this deadly pandemic. While the mutation that causes the Omicron variant is encouraging, subsequent mutations do not guarantee that the disease it causes will be less severe. As the virus continues to evolve, humans must constantly adapt by increasing their immunity through vaccination.
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Affiliation(s)
- Abdul Hawil Abas
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Siti Marfuah
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Aceh, Indonesia;
| | - Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung 40154, West Java, Indonesia;
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia;
| | - Moon Nyeo Park
- College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea;
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 97178-53577, Iran;
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Shafi Mahmud
- Department of Genome Science, John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia;
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia; (A.H.A.); (S.M.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Bonglee Kim
- College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea;
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Jackson CH, Grosso F, Kunzmann K, Corbella A, Gramegna M, Tirani M, Castaldi S, Cereda D, De Angelis D, Presanis A. Trends in outcomes following COVID-19 symptom onset in Milan: a cohort study. BMJ Open 2022; 12:e054859. [PMID: 35332039 PMCID: PMC8948075 DOI: 10.1136/bmjopen-2021-054859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND For people with symptomatic COVID-19, the relative risks of hospital admission, death without hospital admission and recovery without admission, and the times to those events, are not well understood. We describe how these quantities varied with individual characteristics, and through the first wave of the pandemic, in Milan, Italy. METHODS A cohort study of 27 598 people with known COVID-19 symptom onset date in Milan, Italy, testing positive between February and June 2020 and followed up until 17 July 2020. The probabilities of different events, and the times to events, were estimated using a mixture multistate model. RESULTS The risk of death without hospital admission was higher in March and April (for non-care home residents, 6%-8% compared with 2%-3% in other months) and substantially higher for care home residents (22%-29% in March). For all groups, the probabilities of hospitalisation decreased from February to June. The probabilities of hospitalisation also increased with age, and were higher for men, substantially lower for healthcare workers and care home residents, and higher for people with comorbidities. Times to hospitalisation and confirmed recovery also decreased throughout the first wave. Combining these results with our previously developed model for events following hospitalisation, the overall symptomatic case fatality risk was 15.8% (15.4%-16.2%). CONCLUSIONS The highest risks of death before hospital admission coincided with periods of severe burden on the healthcare system in Lombardy. Outcomes for care home residents were particularly poor. Outcomes improved as the first wave waned, community healthcare resources were reinforced and testing became more widely available.
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Affiliation(s)
| | - Francesca Grosso
- Postgraduate School of Public Health, Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Kevin Kunzmann
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Alice Corbella
- Department of Statistics, University of Warwick, Coventry, UK
| | - Maria Gramegna
- Welfare General Directorate, Regione Lombardia, Milan, Italy
| | - Marcello Tirani
- Welfare General Directorate, Regione Lombardia, Milan, Italy
| | - Silvana Castaldi
- Post-graduate School of Hygiene and Preventive Medicine, University of Milan, Milan, Italy
| | - Danilo Cereda
- Welfare General Directorate, Regione Lombardia, Milan, Italy
| | | | - Anne Presanis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
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Fisman DN, Tuite AR. Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. Clin Infect Dis 2022; 75:e69-e75. [PMID: 35234859 PMCID: PMC9047153 DOI: 10.1093/cid/ciac174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 12/15/2022] Open
Abstract
Background Novel variants of concern (VOCs) have been associated with both increased infectivity and virulence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virulence of SARS-CoV-2 is closely linked to age. Whether relative increases in virulence of novel VOCs are similar across the age spectrum or are limited to some age groups is unknown. Methods We created a retrospective cohort of people in Ontario, Canada, who tested positive for SARS-CoV-2 and were screened for VOCs (n = 259 984) between 7 February 2021 and 31 October 2021. Cases were classified as N501Y-positive VOC, probable Delta VOC, or VOC undetected. We constructed age-specific logistic regression models to evaluate associations between N501Y-postive or Delta VOC infections and infection severity using hospitalization, intensive care unit (ICU) admission, and death as outcome variables. Models were adjusted for sex, comorbidity, vaccination status, and temporal trends. Results Infection with either N501Y-positive or Delta VOCs was associated with significant elevations in risk of hospitalization, ICU admission, and death across age groups compared with infections where a VOC was not detected. The Delta VOC increased hospitalization risk in children aged <10 years by a factor of 2.5 (adjusted odds ratio; 95% confidence interval, 1.3 to 5.0) compared with non-VOCs. There was a significant inverse relationship between age and relative increase in risk of death with the Delta VOC, with younger age groups showing a greater relative increase in risk of death than older individuals. Conclusions SARS-CoV-2 VOCs appear to be associated with increased relative virulence of infection in all age groups, though low absolute numbers of outcomes in younger individuals make estimates in these groups imprecise.
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Affiliation(s)
- David N Fisman
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Ashleigh R Tuite
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Centre for Immunization Readiness, Public Health Agency of Canada, Ottawa, Ontario, Canada
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Tian D, Sun Y, Zhou J, Ye Q. The global epidemic of SARS-CoV-2 variants and their mutational immune escape. J Med Virol 2022; 94:847-857. [PMID: 34609003 PMCID: PMC8661756 DOI: 10.1002/jmv.27376] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/23/2021] [Accepted: 10/01/2021] [Indexed: 12/16/2022]
Abstract
During the COVID-19 pandemic, genetic variants of SARS-CoV-2 have been emerging and spreading around the world. Several SARS-CoV-2 endemic variants were found in United Kingdom, South Africa, Japan, and India between 2020 and April 2021. Studies have shown that many SARS-CoV-2 variants are more infectious than early wild strain and produce immune escape. These SARS-CoV-2 variants have brought new challenges to the prevention and control of COVID-19. This review summarizes and analyzes the biological characteristics of different amino acid mutations and the epidemic characteristics and immune escape of different SARS-CoV-2 variants. We hope to provide scientific reference for the monitoring, prevention, and control measures of new SARS-CoV-2 variants and the development strategy of the second-generation vaccine.
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Affiliation(s)
- Dandan Tian
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - YanHong Sun
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - JianMing Zhou
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - Qing Ye
- Department of Clinical Laboratory, National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's HospitalZhejiang University School of MedicineHangzhouChina
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48
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Angulo J, Martinez-Valdebenito C, Pardo-Roa C, Almonacid LI, Fuentes-Luppichini E, Contreras AM, Maldonado C, Le Corre N, Melo F, Medina RA, Ferrés M. Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021. Front Med (Lausanne) 2022; 9:841073. [PMID: 35280916 PMCID: PMC8914012 DOI: 10.3389/fmed.2022.841073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/02/2022] [Indexed: 11/13/2022] Open
Abstract
Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance.
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Affiliation(s)
- Jenniffer Angulo
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Constanza Martinez-Valdebenito
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Catalina Pardo-Roa
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Leonardo I. Almonacid
- Molecular Bioinformatics Laboratory, Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Ana Maria Contreras
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Constanza Maldonado
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Nicole Le Corre
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Francisco Melo
- Molecular Bioinformatics Laboratory, Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael A. Medina
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marcela Ferrés
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
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49
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Nyberg T, Harman K, Zaidi A, Seaman SR, Andrews N, Nash SG, Charlett A, Lopez Bernal J, Myers R, Groves N, Gallagher E, Gharbia S, Chand M, Thelwall S, De Angelis D, Dabrera G, Presanis AM. Hospitalisation and mortality risk for COVID-19 cases with SARS-CoV-2 AY.4.2 (VUI-21OCT-01) compared to non-AY.4.2 Delta variant sub-lineages. J Infect Dis 2022; 226:808-811. [PMID: 35184201 PMCID: PMC8903446 DOI: 10.1093/infdis/jiac063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/16/2022] [Indexed: 11/28/2022] Open
Abstract
To investigate if the AY.4.2 sublineage of the SARS-CoV-2 delta variant is associated with hospitalization and mortality risks that differ from non-AY.4.2 delta risks, we performed a retrospective cohort study of sequencing-confirmed COVID-19 cases in England based on linkage of routine health care datasets. Using stratified Cox regression, we estimated adjusted hazard ratios (aHR) of hospital admission (aHR = 0.85; 95% confidence interval [CI], .77–.94), hospital admission or emergency care attendance (aHR = 0.87; 95% CI, .81–.94), and COVID-19 mortality (aHR = 0.85; 95% CI, .71–1.03). The results indicate that the risks of hospitalization and mortality are similar or lower for AY.4.2 compared to cases with other delta sublineages.
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Affiliation(s)
- Tommy Nyberg
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, CB2 0SR, United Kingdom
| | - Katie Harman
- COVID-19 National Epidemiology Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Asad Zaidi
- COVID-19 National Epidemiology Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Shaun R Seaman
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, CB2 0SR, United Kingdom
| | - Nick Andrews
- Immunisation and Countermeasures Division, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Sophie G Nash
- COVID-19 National Epidemiology Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Andre Charlett
- National Infection Service, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Jamie Lopez Bernal
- Immunisation and Countermeasures Division, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Richard Myers
- Genomics Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Natalie Groves
- Genomics Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Eileen Gallagher
- Genomics Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Saheer Gharbia
- Genomics Programme, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Meera Chand
- Genomics Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Simon Thelwall
- COVID-19 National Epidemiology Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Daniela De Angelis
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, CB2 0SR, United Kingdom
| | - Gavin Dabrera
- COVID-19 National Epidemiology Cell, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Anne M Presanis
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge Biomedical Campus, Cambridge, CB2 0SR, United Kingdom
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50
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García YE, Mery G, Vásquez P, Calvo JG, Barboza LA, Rivas T, Sanchez F. Projecting the impact of Covid-19 variants and vaccination strategies in disease transmission using a multilayer network model in Costa Rica. Sci Rep 2022; 12:2279. [PMID: 35145180 PMCID: PMC8831570 DOI: 10.1038/s41598-022-06236-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/17/2022] [Indexed: 12/21/2022] Open
Abstract
For countries starting to receive steady supplies of vaccines against SARS-CoV-2, the course of Covid-19 for the following months will be determined by the emergence of new variants and successful roll-out of vaccination campaigns. To anticipate this scenario, we used a multilayer network model developed to forecast the transmission dynamics of Covid-19 in Costa Rica, and to estimate the impact of the introduction of the Delta variant in the country, under two plausible vaccination scenarios, one sustaining Costa Rica's July 2021 vaccination pace of 30,000 doses per day and with high acceptance from the population and another with declining vaccination pace to 13,000 doses per day and with lower acceptance. Results suggest that the introduction and gradual dominance of the Delta variant would increase Covid-19 hospitalizations and ICU admissions by [Formula: see text] and [Formula: see text], respectively, from August 2021 to December 2021, depending on vaccine administration and acceptance. In the presence of the Delta variant, new Covid-19 hospitalizations and ICU admissions are estimated to increase around [Formula: see text] and [Formula: see text], respectively, in the same period if the vaccination pace drops. Our results can help decision-makers better prepare for the Covid-19 pandemic in the months to come.
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Affiliation(s)
- Yury E García
- Department of Public Health Sciences, University of California Davis, Davis, CA, 95616, USA.
- Centro de Investigación en Matemática Pura y Aplicada, Universidad de Costa Rica, San José, 11501, Costa Rica.
| | - Gustavo Mery
- Pan American Health Organization, World Health Organization, San José, 10102, Costa Rica
| | - Paola Vásquez
- Centro de Investigación en Matemática Pura y Aplicada, Universidad de Costa Rica, San José, 11501, Costa Rica
| | - Juan G Calvo
- Centro de Investigación en Matemática Pura y Aplicada-Escuela de Matemática, Universidad de Costa Rica, San José, 11501, Costa Rica
| | - Luis A Barboza
- Centro de Investigación en Matemática Pura y Aplicada-Escuela de Matemática, Universidad de Costa Rica, San José, 11501, Costa Rica
| | - Tania Rivas
- Ministry of Health, San José, 10102, Costa Rica
| | - Fabio Sanchez
- Centro de Investigación en Matemática Pura y Aplicada-Escuela de Matemática, Universidad de Costa Rica, San José, 11501, Costa Rica
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