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

Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J. Glass, Susan Engelbrecht, Gert Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Nei-yuan Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, José Lourenço, Luiz Carlos Junior Alcantara, Sergei L. Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J. Lessells, Jinal N. Bhiman, Carolyn Williamson and Tulio Oliveira ()
Additional contact information
Houriiyah Tegally: University of KwaZulu–Natal
Eduan Wilkinson: University of KwaZulu–Natal
Marta Giovanetti: Fundacao Oswaldo Cruz
Arash Iranzadeh: University of Cape Town
Vagner Fonseca: University of KwaZulu–Natal
Jennifer Giandhari: University of KwaZulu–Natal
Deelan Doolabh: University of Cape Town
Sureshnee Pillay: University of KwaZulu–Natal
Emmanuel James San: University of KwaZulu–Natal
Nokukhanya Msomi: University of KwaZulu–Natal
Koleka Mlisana: NHLS
Anne Gottberg: National Institute for Communicable Diseases, NHLS
Sibongile Walaza: National Institute for Communicable Diseases, NHLS
Mushal Allam: National Institute for Communicable Diseases, NHLS
Arshad Ismail: National Institute for Communicable Diseases, NHLS
Thabo Mohale: National Institute for Communicable Diseases, NHLS
Allison J. Glass: University of the Witwatersrand
Susan Engelbrecht: Stellenbosch University and NHLS Tygerberg Hospital
Gert Zyl: Stellenbosch University and NHLS Tygerberg Hospital
Wolfgang Preiser: Stellenbosch University and NHLS Tygerberg Hospital
Francesco Petruccione: Centre for Quantum Technology, University of KwaZulu–Natal
Alex Sigal: Africa Health Research Institute
Diana Hardie: University of Cape Town
Gert Marais: University of Cape Town
Nei-yuan Hsiao: University of Cape Town
Stephen Korsman: University of Cape Town
Mary-Ann Davies: University of Cape Town
Lynn Tyers: University of Cape Town
Innocent Mudau: University of Cape Town
Denis York: Molecular Diagnostics Services
Caroline Maslo: Netcare Hospitals
Dominique Goedhals: University of The Free State
Shareef Abrahams: NHLS
Oluwakemi Laguda-Akingba: NHLS
Arghavan Alisoltani-Dehkordi: University of Cape Town
Adam Godzik: University of California Riverside School of Medicine
Constantinos Kurt Wibmer: National Institute for Communicable Diseases, NHLS
Bryan Trevor Sewell: University of Cape Town
José Lourenço: University of Oxford
Luiz Carlos Junior Alcantara: Fundacao Oswaldo Cruz
Sergei L. Kosakovsky Pond: Temple University
Steven Weaver: Temple University
Darren Martin: University of Cape Town
Richard J. Lessells: University of KwaZulu–Natal
Jinal N. Bhiman: National Institute for Communicable Diseases, NHLS
Carolyn Williamson: University of Cape Town
Tulio Oliveira: University of KwaZulu–Natal

Nature, 2021, vol. 592, issue 7854, 438-443

Abstract: Abstract Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. 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 importance3–5. 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 escape6–8.

Date: 2021
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DOI: 10.1038/s41586-021-03402-9

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