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

Derek W Wright; William T Harvey; Joseph Hughes; MacGregor Cox; Thomas P Peacock; Rachel Colquhoun; Ben Jackson; Richard Orton; Morten Nielsen; Nienyun Sharon Hsu; COVID-19 Genomics UK (COG-UK) consortium; Ewan M Harrison; Thushan I de Silva; Andrew Rambaut; Sharon J Peacock; David L Robertson; Alessandro M Carabelli

doi:10.1093/ve/veac023

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

Virus Evol. 2022 Mar 18;8(1):veac023. doi: 10.1093/ve/veac023. eCollection 2022.

Authors

Derek W Wright¹, William T Harvey, Joseph Hughes¹, MacGregor Cox², Thomas P Peacock³, Rachel Colquhoun⁴, Ben Jackson⁴, Richard Orton¹, Morten Nielsen⁵, Nienyun Sharon Hsu⁶; COVID-19 Genomics UK (COG-UK) consortium; Ewan M Harrison², Thushan I de Silva⁶, Andrew Rambaut⁴, Sharon J Peacock², David L Robertson¹, Alessandro M Carabelli²

Affiliations

¹ MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK.
² Department of Medicine, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK.
³ Department of Infectious Disease, St Mary's Medical School, Imperial College London, Praed Street, London, Westminster W2 1NY, UK.
⁴ Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
⁵ Department of Health Technology, Technical University of Denmark, Lyngby DK-2800, Denmark.
⁶ 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.

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.

Keywords: COVID-19; SARS-CoV-2; amino acid replacements; antibody escape; antigenic variation; evasion; evolution; fitness; mutation; protein structure; resistance; spike; variants of concern; virus.

Abstract

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