Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer

Wright, D. W. et al. (2022) Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus Evolution, 8(1), veac023. (doi: 10.1093/ve/veac023) (PMID:35502202) (PMCID:PMC9037374)

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Abstract

COG-UK Mutation Explorer (COG-UK-ME, https://sars2.cvr.gla.ac.uk/cog-uk/-last accessed date 16 March 2022) is a web resource that displays knowledge and analyses on SARS-CoV-2 virus genome mutations and variants circulating in the UK, with a focus on the observed amino acid replacements that have an antigenic role in the context of the human humoral and cellular immune response. This analysis is based on more than 2 million genome sequences (as of March 2022) for UK SARS-CoV-2 data held in the CLIMB-COVID centralised data environment. COG-UK-ME curates these data and displays analyses that are cross-referenced to experimental data collated from the primary literature. The aim is to track mutations of immunological importance that are accumulating in current variants of concern and variants of interest that could alter the neutralising activity of monoclonal antibodies (mAbs), convalescent sera, and vaccines. Changes in epitopes recognised by T cells, including those where reduced T cell binding has been demonstrated, are reported. Mutations that have been shown to confer SARS-CoV-2 resistance to antiviral drugs are also included. Using visualisation tools, COG-UK-ME also allows users to identify the emergence of variants carrying mutations that could decrease the neutralising activity of both mAbs present in therapeutic cocktails, e.g. Ronapreve. COG-UK-ME tracks changes in the frequency of combinations of mutations and brings together the curated literature on the impact of those mutations on various functional aspects of the virus and therapeutics. Given the unpredictable nature of SARS-CoV-2 as exemplified by yet another variant of concern, Omicron, continued surveillance of SARS-CoV-2 remains imperative to monitor virus evolution linked to the efficacy of therapeutics.

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) (MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute. W.T.H. and T.P.P. are supported by the G2P-UK National Virology Consortium (MR/W005611/1) and W.T.H. by the MRC (MR/R024758/1). D.L.R., D.W., and J.H. are funded by the MRC (MC_UU_12014/12) and D.L.R. by the Wellcome Trust (220977/Z/20/Z).
Keywords:Fitness, variants of concern, evasion, spike, protein structure, virus, antibody escape, SARS-CoV-2, COVID-19, evolution, mutation, resistance, amino acid replacements, antigenic variation.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Wright, Mr Derek and Robertson, Professor David and Harvey, Dr William and Orton, Dr Richard and Hughes, Dr Joseph
Authors: Wright, D. W., Harvey, W. T., Hughes, J., Cox, M., Peacock, T. P., Colquhoun, R., Jackson, B., Orton, R., Nielsen, M., Hsu, N. S., Harrison, E. M., de Silva, T. I., Rambaut, A., Peacock, S. J., Robertson, D. L., and Carabelli, A. M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation > Centre for Virus Research
Journal Name:Virus Evolution
Publisher:Oxford University Press
ISSN:2057-1577
ISSN (Online):2057-1577
Published Online:18 March 2022
Copyright Holders:Copyright © 2022 The Authors
First Published:First published in Virus Evolution 8(1): veac023
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
302632Using a comparative One Health approach to investigate the structural basis of antigenic variation among human and avian influenza virusesJill PellMedical Research Council (MRC)MR/R024758/1Institute of Biodiversity, Animal Health and Comparative Medicine
172630014Cross-Cutting Programme – Viral Genomics and Bioinformatics (Programme 9)David RobertsonMedical Research Council (MRC)MC_UU_12014/12III - Centre for Virus Research