Detection of a SARS-CoV-2 variant of concern in South Africa

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus 1 , 2 . Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in...

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Published in:Nature (London) 2021-04, Vol.592 (7854), p.438-443
Main Authors: Tegally, Houriiyah, Wilkinson, Eduan, Giovanetti, Marta, Iranzadeh, Arash, Fonseca, Vagner, Giandhari, Jennifer, Doolabh, Deelan, Pillay, Sureshnee, San, Emmanuel James, Msomi, Nokukhanya, Mlisana, Koleka, von Gottberg, Anne, Walaza, Sibongile, Allam, Mushal, Ismail, Arshad, Mohale, Thabo, Glass, Allison J., Engelbrecht, Susan, Van Zyl, Gert, Preiser, Wolfgang, Petruccione, Francesco, Sigal, Alex, Hardie, Diana, Marais, Gert, Hsiao, Nei-yuan, Korsman, Stephen, Davies, Mary-Ann, Tyers, Lynn, Mudau, Innocent, York, Denis, Maslo, Caroline, Goedhals, Dominique, Abrahams, Shareef, Laguda-Akingba, Oluwakemi, Alisoltani-Dehkordi, Arghavan, Godzik, Adam, Wibmer, Constantinos Kurt, Sewell, Bryan Trevor, Lourenço, José, Alcantara, Luiz Carlos Junior, Kosakovsky Pond, Sergei L., Weaver, Steven, Martin, Darren, Lessells, Richard J., Bhiman, Jinal N., Williamson, Carolyn, de Oliveira, Tulio
Format: Article
Language:English
Subjects:
101/1
631/181/735
631/326/596/4130
692/308/174
Capes (landforms)
COVID-19
COVID-19 - epidemiology
COVID-19 - immunology
COVID-19 - transmission
COVID-19 - virology
DNA Mutational Analysis
Evolution, Molecular
Genetic Fitness
Genomes
Humanities and Social Sciences
Humans
Immune Evasion
Metropolitan areas
Models, Molecular
multidisciplinary
Mutation
Phylogeny
Phylogeography
Proteins
Provinces
SARS-CoV-2 - genetics
SARS-CoV-2 - immunology
SARS-CoV-2 - isolation & purification
SARS-CoV-2 - pathogenicity
Science
Science (multidisciplinary)
Selection, Genetic
Severe acute respiratory syndrome coronavirus 2
South Africa - epidemiology
Spike Glycoprotein, Coronavirus - chemistry
Spike Glycoprotein, Coronavirus - genetics
Spike Glycoprotein, Coronavirus - metabolism
Spike protein
Time Factors
Viral diseases
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Summary:Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus 1 , 2 . Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance 3 – 5 . This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu–Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data—which show rapid expansion and displacement of other lineages in several regions—suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape 6 – 8 . The 501Y.V2 variant of SARS-CoV-2 in South Africa became dominant over other variants within weeks of its emergence, suggesting that this variant is linked to increased transmissibility or immune escape.
ISSN:0028-0836
1476-4687
DOI:10.1038/s41586-021-03402-9