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 von Gottberg; Sibongile Walaza; Mushal Allam; Arshad Ismail; Thabo Mohale; Allison J. Glass; Susan Engelbrecht; Gert Van 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; Tulio de Oliveira

doi:10.1038/s41586-021-03402-9

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 von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang PreiserFrancesco 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, Tulio de Oliveira^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

1180 Citations (Scopus)

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.

Original language	English
Pages (from-to)	438-443
Number of pages	6
Journal	Nature
Volume	592
Issue number	7854
DOIs	https://doi.org/10.1038/s41586-021-03402-9
Publication status	Published - 15 Apr 2021
Externally published	Yes

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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., ... de Oliveira, T. (2021). Detection of a SARS-CoV-2 variant of concern in South Africa. Nature, 592(7854), 438-443. https://doi.org/10.1038/s41586-021-03402-9

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title = "Detection of a SARS-CoV-2 variant of concern in South Africa",

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.",

author = "Houriiyah Tegally and Eduan Wilkinson and Marta Giovanetti and Arash Iranzadeh and Vagner Fonseca and Jennifer Giandhari and Deelan Doolabh and Sureshnee Pillay and San, {Emmanuel James} and Nokukhanya Msomi and Koleka Mlisana and {von Gottberg}, Anne and Sibongile Walaza and Mushal Allam and Arshad Ismail and Thabo Mohale and Glass, {Allison J.} and Susan Engelbrecht and {Van Zyl}, Gert and Wolfgang Preiser and Francesco Petruccione and Alex Sigal and Diana Hardie and Gert Marais and Hsiao, {Nei yuan} and Stephen Korsman and Davies, {Mary Ann} and Lynn Tyers and Innocent Mudau and Denis York and Caroline Maslo and Dominique Goedhals and Shareef Abrahams and Oluwakemi Laguda-Akingba and Arghavan Alisoltani-Dehkordi and Adam Godzik and Wibmer, {Constantinos Kurt} and Sewell, {Bryan Trevor} and Jos{\'e} Louren{\c c}o and Alcantara, {Luiz Carlos Junior} and {Kosakovsky Pond}, {Sergei L.} and Steven Weaver and Darren Martin and Lessells, {Richard J.} and Bhiman, {Jinal N.} and Carolyn Williamson and {de Oliveira}, Tulio",

note = "Funding Information: Acknowledgements We thank K. Deforche, W. Dumon and S. Cleemput at Emweb for their invaluable help in improving genome assembly and variant calling for SARS-CoV-2, which was central to the achievement of this work; and the global laboratories that generated and made public the SARS-CoV-2 sequences (through GISAID) used as reference dataset in this study (a complete list of individual contributors of sequences is provided in Supplementary Table 5). This research reported in this publication was supported by the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council, with funds received from the South African Department of Science and Innovation. Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature Limited.",

year = "2021",

month = apr,

day = "15",

doi = "10.1038/s41586-021-03402-9",

language = "English",

volume = "592",

pages = "438--443",

journal = "Nature",

issn = "0028-0836",

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Tegally, H, Wilkinson, E, Giovanetti, M, Iranzadeh, A, Fonseca, V, Giandhari, J, Doolabh, D, Pillay, S, San, EJ, Msomi, N, Mlisana, K, von Gottberg, A, Walaza, S, Allam, M, Ismail, A, Mohale, T, Glass, AJ, Engelbrecht, S, Van Zyl, G, Preiser, W, Petruccione, F, Sigal, A, Hardie, D, Marais, G, Hsiao, NY, Korsman, S, Davies, MA, Tyers, L, Mudau, I, York, D, Maslo, C, Goedhals, D, Abrahams, S, Laguda-Akingba, O, Alisoltani-Dehkordi, A, Godzik, A, Wibmer, CK, Sewell, BT, Lourenço, J, Alcantara, LCJ, Kosakovsky Pond, SL, Weaver, S, Martin, D, Lessells, RJ, Bhiman, JN, Williamson, C & de Oliveira, T 2021, 'Detection of a SARS-CoV-2 variant of concern in South Africa', Nature, vol. 592, no. 7854, pp. 438-443. https://doi.org/10.1038/s41586-021-03402-9

TY - JOUR

T1 - Detection of a SARS-CoV-2 variant of concern in South Africa

AU - Tegally, Houriiyah

AU - Wilkinson, Eduan

AU - Giovanetti, Marta

AU - Iranzadeh, Arash

AU - Fonseca, Vagner

AU - Giandhari, Jennifer

AU - Doolabh, Deelan

AU - Pillay, Sureshnee

AU - San, Emmanuel James

AU - Msomi, Nokukhanya

AU - Mlisana, Koleka

AU - von Gottberg, Anne

AU - Walaza, Sibongile

AU - Allam, Mushal

AU - Ismail, Arshad

AU - Mohale, Thabo

AU - Glass, Allison J.

AU - Engelbrecht, Susan

AU - Van Zyl, Gert

AU - Preiser, Wolfgang

AU - Petruccione, Francesco

AU - Sigal, Alex

AU - Hardie, Diana

AU - Marais, Gert

AU - Hsiao, Nei yuan

AU - Korsman, Stephen

AU - Davies, Mary Ann

AU - Tyers, Lynn

AU - Mudau, Innocent

AU - York, Denis

AU - Maslo, Caroline

AU - Goedhals, Dominique

AU - Abrahams, Shareef

AU - Laguda-Akingba, Oluwakemi

AU - Alisoltani-Dehkordi, Arghavan

AU - Godzik, Adam

AU - Wibmer, Constantinos Kurt

AU - Sewell, Bryan Trevor

AU - Lourenço, José

AU - Alcantara, Luiz Carlos Junior

AU - Kosakovsky Pond, Sergei L.

AU - Weaver, Steven

AU - Martin, Darren

AU - Lessells, Richard J.

AU - Bhiman, Jinal N.

AU - Williamson, Carolyn

AU - de Oliveira, Tulio

N1 - Funding Information: Acknowledgements We thank K. Deforche, W. Dumon and S. Cleemput at Emweb for their invaluable help in improving genome assembly and variant calling for SARS-CoV-2, which was central to the achievement of this work; and the global laboratories that generated and made public the SARS-CoV-2 sequences (through GISAID) used as reference dataset in this study (a complete list of individual contributors of sequences is provided in Supplementary Table 5). This research reported in this publication was supported by the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council, with funds received from the South African Department of Science and Innovation. Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature Limited.

PY - 2021/4/15

Y1 - 2021/4/15

N2 - 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.

AB - 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.

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DO - 10.1038/s41586-021-03402-9

M3 - Article

C2 - 33690265

AN - SCOPUS:85102321294

SN - 0028-0836

VL - 592

SP - 438

EP - 443

JO - Nature

JF - Nature

IS - 7854

ER -

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

Abstract

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