@article{da53dec4cf0741779e4ab4b7128e8364,
title = "The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages",
abstract = "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.",
keywords = "convergent mutations, COVID 19, directional selection, diversifying selection, evolutionary adaptation, immune evasion, lineage-defining mutations, positive selection, recurrent mutations, transmission advantage",
author = "NGS-SA and {The COVID-19 Genomics UK (COG-UK) Consortium} and Martin, {Darren P.} and Steven Weaver and Houriiyah Tegally and San, {James Emmanuel} and Shank, {Stephen D.} and Eduan Wilkinson and Lucaci, {Alexander G.} and Jennifer Giandhari and Sureshnee Naidoo and Yeshnee Pillay and Lavanya Singh and Lessells, {Richard J.} and Gupta, {Ravindra K.} and Wertheim, {Joel O.} and Anton Nekturenko and Ben Murrell and Harkins, {Gordon W.} and Philippe Lemey and MacLean, {Oscar A.} and Robertson, {David L.} and {de Oliveira}, Tulio and {Kosakovsky Pond}, {Sergei L.} and Matthew Bashton and Andrew Nelson and Clare McCann and Greg Young and Darren Smith",
note = "Matthew Bashton, Andrew Nelson, Clare McCann, Greg Young and Darren Smith are members of the COVID-19 Genomics UK (COG-UK) consortium. Funding 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. ",
year = "2021",
month = sep,
day = "30",
doi = "10.1016/j.cell.2021.09.003",
language = "English",
volume = "184",
pages = "5189--5200.e7",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "20",
}
