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Wright DW, Harvey WT, Hughes J, Cox M, Peacock TP, Colquhoun R, Jackson B, Orton R, Nielsen M, Hsu NS, Harrison EM, de Silva TI, Rambaut A, Peacock SJ, Robertson DL, Carabelli AM. Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus Evol 2022; 8:veac023. [PMID: 35502202 PMCID: PMC9037374 DOI: 10.1093/ve/veac023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Derek W Wright
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | - MacGregor Cox
- Department of Medicine, University of
Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ,
UK
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary’s
Medical School, Imperial College London, Praed Street, London,
Westminster W2 1NY, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of
Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | - Ben Jackson
- Institute of Evolutionary Biology, University of
Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | - Morten Nielsen
- Department of Health Technology, Technical
University of Denmark, Lyngby DK-2800, Denmark
| | - Nienyun Sharon Hsu
- The Florey Institute for Host-Pathogen
Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical
School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX,
UK
| | | | - Ewan M Harrison
- Department of Medicine, University of
Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ,
UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton
CB10 1SA, UK
- Department of Public Health and Primary Care,
University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Thushan I de Silva
- The Florey Institute for Host-Pathogen
Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical
School, University of Sheffield, Beech Hill Road, Sheffield S10 2RX,
UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of
Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Sharon J Peacock
- Department of Medicine, University of
Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ,
UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Garscube Campus, 464 Bearsden Road,
Glasgow G61 1QH, UK
| | - Alessandro M Carabelli
- Department of Medicine, University of
Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ,
UK
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