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

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...

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Published in:	Cell Vol. 184; no. 20; pp. 5189 - 5200.e7
Main Authors:	Martin, Darren P., Weaver, Steven, Tegally, Houriiyah, San, James Emmanuel, Shank, Stephen D., Wilkinson, Eduan, Lucaci, Alexander G., Giandhari, Jennifer, Naidoo, Sureshnee, Pillay, Yeshnee, Singh, Lavanya, Lessells, Richard J., Gupta, Ravindra K., Wertheim, Joel O., Nekturenko, Anton, Murrell, Ben, Harkins, Gordon W., Lemey, Philippe, MacLean, Oscar A., Robertson, David L., de Oliveira, Tulio, Kosakovsky Pond, Sergei L.
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 30-09-2021 Published by Elsevier Inc
Subjects:	Amino Acid Sequence - genetics Codon - genetics convergent mutations COVID 19 COVID-19 - epidemiology COVID-19 - immunology COVID-19 - transmission COVID-19 - virology directional selection diversifying selection Evolution, Molecular evolutionary adaptation Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi Genes, Viral Genetic Drift Host Adaptation - genetics Humans Hälsovetenskap Immune Evasion Infektionsmedicin Klinisk medicin lineage-defining mutations Medicin och hälsovetenskap Mutation Pandemics Phylogeny positive selection Public Health recurrent mutations SARS-CoV-2 - genetics transmission advantage convergent mutations recurrent mutations evolutionary adaptation lineage-defining mutations immune evasion diversifying selection directional selection positive selection transmission advantage COVID 19
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Summary:	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. [Display omitted] •Detected a major global shift in the SARS-CoV-2 selective landscape in late 2020•Identified ongoing convergent evolution between the alpha, beta, and gamma lineages•Defined the mutational meta-signature upon which these lineages are converging An analysis of synonymous and non-synonymous mutations in SARS-CoV-2 genomes since the inception of the COVID-19 pandemic provides insights into the emergence of a convergent mutational signature in the 501Y lineage (alpha, beta, and gamma variants) that is also likely present in other lineages that impacts host immune recognition.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 A full list of consortium names and affiliations are in Appendix 1 A full list of consortium names and affiliations are in Appendix 2 Lead contact
ISSN:	0092-8674 1097-4172 1097-4172
DOI:	10.1016/j.cell.2021.09.003