The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Martin, D. P. et al. (2021) The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell, 184(20), 5189-5200.e7. (doi: 10.1016/j.cell.2021.09.003) (PMID:34537136) (PMCID:PMC8421097)

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The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three “501Y lineages” coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.

Item Type:Articles
Additional Information:The Wellcome Trust funded D.P.M. (222574/Z/21/Z), D.L.R. (220977/Z/20/Z), P.L. (2206298/Z/17/Z), and O.A.M. (206369/Z/17/Z). The US National Institutes of Health funded S.L.K.P. (R01 AI134384 and AI140970), J.O.W. (R01 AI13599), G.W.H. (1U01Al152151-01), and J.E.S. and H.T. (via H3ABioNet U24HG006941). The US National Science Foundation funded S.L.K.P. (RAPID 2027196 NSF/DBI,BIO), The UK Medical Research Council funded D.L.R. (MC_UU_1201412) and COG-UK (via UK Research & Innovation, the National Institute of Health Research, and Genome Research Limited operating as the Wellcome Sanger Institute). The European Research Council funded P.L. (725422-ReservoirDOCS and 874850-MOOD). The South African Medical Research Council funded NGS-SA via the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council and Department of Science and Innovation.
Keywords:COVID 19, evolutionary adaptation, positive selection, directional selection, recurrent mutations, convergent mutations, diversifying selection, immune evasion, transmission advantage, lineage-defining mutations.
Glasgow Author(s) Enlighten ID:Robertson, Professor David and MacLean, Dr Oscar
Creator Roles:
Robertson, D. L.Writing – original draft, Writing – review and editing
MacLean, O. A.Validation, Formal analysis, Writing – original draft, Writing – review and editing
Authors: Martin, D. P., Weaver, S., Tegally, H., San, J. E., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., Singh, L., Lessells, R. J., Gupta, R. K., Wertheim, J. O., Nekturenko, A., Murrell, B., Harkins, G. W., Lemey, P., MacLean, O. A., Robertson, D. L., de Oliveira, T., and Pond, S. L. K.
College/School: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
Journal Name:Cell
Publisher:Elsevier (Cell Press)
ISSN (Online):1097-4172
Published Online:07 September 2021

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
301049Host determinants of disease outcomes in arboviral infectionsMassimo PalmariniWellcome Trust (WELLCOTR)206369/Z/17/ZIII - Centre for Virus Research
Viral Genomics and BioinformaticsAndrew DavisonMedical Research Council (MRC)MC_UU_12014/12III-MRC-GU Centre for Virus Research