Detection of a SARS-CoV-2 variant of concern in South Africa
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Abstract
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.
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Several SARS-CoV-2 variants of concern, such as Beta and Omicron, evade humoral responses elicited by vaccines based on ancestral S-protein sequences.
“Several VOCs which have mutated, such as Beta1 and Omicron2, evade humoral responses elicited by vaccines based on ancestral S-protein sequences3.”
From Efficacy of an unmodified bivalent mRNA vaccine against SARS-CoV-2 variants in female small animal models (2023) · cites this paper as [1]
The Article (p. 5) reports preliminary evidence that 501Y.V2 (Beta) escapes neutralizing antibodies in convalescent plasma. It says assays using vaccine recipients’ plasma were still underway, so it does not establish escape from vaccine-elicited responses; the cited passages also do not address Omicron. (LLM, conf=0.88)
Experimental — accuracy not yet measuredMutations at K417 are reported to escape neutralization from mAbs, including the recently approved mAb LY-CoV016.
“Importantly, mutations at K417 are reported to escape neutralization from mAbs, including the recently approved mAb LY-CoV016 22,25.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [22]
The E484K substitution is antigenically important and has been reported as an escape mutation for several monoclonal antibodies including C121, C144, REGN10933 and Ly-CoV555.
“The E484K substitution (Fig. 2a) is antigenically important, and has been reported as an escape mutation for several monoclonal antibodies including C121, C144, REGN10933 and Ly-CoV555 22.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [22]
The B.1.1.7 variant emerged in the United Kingdom, B.1.351 in South Africa, and P.1 and P.2 lineages in Brazil.
“The B.1.1.7 variant emerged in the United Kingdom, the B.1.351variant (also termed 501Y.V2) in South Africa and the P.1 and P.2 lineages in Brazil 2,3,5,9-12 .”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [5]
Four SARS-CoV-2 variants of concern (Alpha, Beta, Gamma and Delta) emerged in the past several months.
“The past several months have witnessed the emergence of four SArS-cov-2 variants of concern (Alpha, beta, Gamma and Delta)”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [16]
The Beta variant was estimated to be 50% more transmissible than the lineages that preceded it.
“The Beta variant was estimated to be 50% more transmissible than the lineages that preceded it 16 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [16]
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References 63 · Cited by 2,510
- Authors
- Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., Mlisana, K., von Gottberg, A., Walaza, S., Allam, M., Ismail, A., Mohale, T., Glass, A. J., Engelbrecht, S., Van Zyl, G., Preiser, W., Petruccione, F., Sigal, A., Hardie, D., Marais, G., Hsiao, N.-Y., Korsman, S., Davies, M.-A., Tyers, L., Mudau, I., York, D., Maslo, C., Goedhals, D., Abrahams, S., Laguda-Akingba, O., Alisoltani-Dehkordi, A., Godzik, A., Wibmer, C. K., Sewell, B. T., Lourenço, J., Alcantara, L. C. J., Kosakovsky Pond, S. L., Weaver, S., Martin, D., Lessells, R. J., Bhiman, J. N., Williamson, C., & de Oliveira, T.
- Affiliations
- University of KwaZulu-Natal (ZA)
- Universidade Federal de Minas Gerais (BR)
- University of Cape Town (ZA)
- National Health Laboratory Service (ZA)
- University of the Witwatersrand (ZA)
- Stellenbosch University (ZA)
- National Institute for Theoretical Physics (ZA)
- Max Planck Institute for Infection Biology (DE)
- Molecular Diagnostics Services (ZA)
- University of the Free State (ZA)
- Walter Sisulu University (ZA)
- University of California, Riverside (US)
- University of Oxford (GB)
- Temple University (US)
- Centre for the AIDS Programme of Research in South Africa (ZA)
- ORCID
- Tegally, Houriiyah
- Wilkinson, Eduan
- Giovanetti, Marta
- Iranzadeh, Arash
- Fonseca, Vagner
- Giandhari, Jennifer
- Pillay, Sureshnee
- Msomi, Nokukhanya
- Mlisana, Koleka
- 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
- Korsman, Stephen
- Davies, Mary-Ann
- Tyers, Lynn
- Maslo, Caroline
- Goedhals, Dominique
- Laguda-Akingba, Oluwakemi
- Godzik, Adam
- Wibmer, Constantinos Kurt
- Sewell, Bryan Trevor
- Lourenço, José
- Alcantara, Luiz Carlos Junior
- Weaver, Steven
- Martin, Darren
- Lessells, Richard J.
- Bhiman, Jinal N.
- Williamson, Carolyn
- de Oliveira, Tulio
- Venue
- Nature
- Published
- 2021-03-09
- Volume
- 592
- Issue
- 7854
- Pages
- 438-443
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3135383916
- Cited by
- 2,510
- References
- 63
- Citations by year
- 2026: 52 · 2025: 104 · 2024: 166 · 2023: 307 · 2022: 734 · 2021: 1121 · 2020: 12 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 1 · 2012: 1
- FWCI
- 184.48
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- medRxiv (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Arca - Repositório Institucional da Fiocruz (submittedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- Funders
- Department of Science and Innovation, South Africa
- South African Medical Research Council
- Medical Research Council
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, Beta variant, variants of concern, spike protein mutations, receptor binding domain, K417N, E484K, N501Y, viral evolution, transmissibility, immune evasion, South Africa, Eastern Cape, Nelson Mandela Bay
- MeSH terms
- COVID-19, SARS-CoV-2, DNA Mutational Analysis, Humans, Models, Molecular, Mutation, Phylogeny, Selection, Genetic, South Africa, Time Factors, Evolution, Molecular, Genetic Fitness, Immune Evasion, Phylogeography, Spike Glycoprotein, Coronavirus
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