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

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Wright, Derek W 
Harvey, William T 
Cox, MacGregor 
Peacock, Thomas P 

COG-UK Mutation Explorer (COG-UK-ME, 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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Virus Evol
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Oxford University Press (OUP)
MRC (MC_PC_19027)
Medical Research Council (MC_PC_19027)
MRC (via Imperial College London) (MR/W005611/1)
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. WTH and TPP are supported by the G2P-UK National Virology Consortium (MR/W005611/1) and WTH by the MRC (MR/R024758/1). DLR, DW and JH are funded by the MRC (MC_UU_12014/12) and DLR by the Wellcome Trust (220977/Z/20/Z).