TY - JOUR
T1 - The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
AU - NGS-SA
AU - The COVID-19 Genomics UK (COG-UK) Consortium
AU - Martin, Darren P.
AU - Weaver, Steven
AU - Tegally, Houriiyah
AU - San, James Emmanuel
AU - Shank, Stephen D.
AU - Wilkinson, Eduan
AU - Lucaci, Alexander G.
AU - Giandhari, Jennifer
AU - Naidoo, Sureshnee
AU - Pillay, Yeshnee
AU - Singh, Lavanya
AU - Lessells, Richard J.
AU - Gupta, Ravindra K.
AU - Wertheim, Joel O.
AU - Nekturenko, Anton
AU - Murrell, Ben
AU - Harkins, Gordon W.
AU - Lemey, Philippe
AU - MacLean, Oscar A.
AU - Robertson, David L.
AU - de Oliveira, Tulio
AU - Kosakovsky Pond, Sergei L.
AU - Bashton, Matthew
AU - Nelson, Andrew
AU - McCann, Clare
AU - Young, Greg
AU - Smith, Darren
N1 - 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.
PY - 2021/9/30
Y1 - 2021/9/30
N2 - 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.
AB - 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.
KW - convergent mutations
KW - COVID 19
KW - directional selection
KW - diversifying selection
KW - evolutionary adaptation
KW - immune evasion
KW - lineage-defining mutations
KW - positive selection
KW - recurrent mutations
KW - transmission advantage
UR - https://www.scopus.com/pages/publications/85116536943
U2 - 10.1016/j.cell.2021.09.003
DO - 10.1016/j.cell.2021.09.003
M3 - Article
C2 - 33688681
AN - SCOPUS:85116536943
SN - 0092-8674
VL - 184
SP - 5189-5200.e7
JO - Cell
JF - Cell
IS - 20
ER -
SDG 3 Good Health and Well-being