The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis

Pascall, D. J. et al. (2023) 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, 18(4), e0284187. (doi: 10.1371/journal.pone.0284187) (PMID:37053201) (PMCID:PMC10101505)

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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.

Item Type:Articles
Additional Information:COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. Funding was also provided by UKRI through the JUNIPER consortium (MR/V038613/1). Sequencing, bioinformatics and statistical support was funded by the Medical Research Council (MRC) core awards for the MRC-University of Glasgow Centre for Virus Research (MC UU 1201412) and MRC Biostatistics Unit (MC UU 00002/11).
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Robertson, Professor David and Thomson, Professor Emma and Haughney, Dr John and Davis, Dr Chris and Vink, Elen and MacLean, Dr Oscar and Lycett, Dr Samantha and Blacow, Dr Rachel and Da Silva Filipe, Dr Ana and Gunson, Dr Rory and Shepherd, Dr James and Pascall, Dr David and Ray, Professor Surajit and Bulteel, Dr Naomi and Smollett, Dr Katherine and Wilkie, Dr Craig and Hughes, Dr Joseph and Mollett, Mr Guy and Campbell, Dr Alasdair
Authors: Pascall, D. J., 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, M. T.G., Honour, P., Hughes, J., James, E., Lewis, T., Lycett, S., MacLean, O., McHugh, M., Mollett, G., Onishi, Y., Parcell, B., Ray, S., Robertson, D. L., Shabaan, S., Shepherd, J. G., Smollett, K., Templeton, K., Wastnedge, E., Wilkie, C., Williams, T., and Thomson, E. C.
College/School:College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
College of Medical Veterinary and Life Sciences > School of Infection & Immunity
College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing
College of Science and Engineering > School of Mathematics and Statistics > Statistics
Journal Name:PLoS ONE
Publisher:Public Library of Science
ISSN:1932-6203
ISSN (Online):1932-6203
Copyright Holders:Copyright © 2023 Pascall et al.
First Published:First published in PLoS ONE 18(4): e0284187
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
172630014Cross-Cutting Programme – Viral Genomics and Bioinformatics (Programme 9)David RobertsonMedical Research Council (MRC)MC_UU_12014/12III - Centre for Virus Research