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

doi:10.1038/s41586-021-03402-9

. 2021 Apr;592(7854):438-443.

doi: 10.1038/s41586-021-03402-9. Epub 2021 Mar 9.

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

Houriiyah Tegally^#¹, Eduan Wilkinson^#¹, Marta Giovanetti^#^{2

3}, Arash Iranzadeh^#⁴, Vagner Fonseca^{1

3}, Jennifer Giandhari¹, Deelan Doolabh⁵, Sureshnee Pillay¹, Emmanuel James San¹, Nokukhanya Msomi⁶, Koleka Mlisana^{7

8}, Anne von Gottberg^{9

10}, Sibongile Walaza^{9

11}, Mushal Allam⁹, Arshad Ismail⁹, Thabo Mohale⁹, Allison J Glass^{10

12}, Susan Engelbrecht¹³, Gert Van Zyl¹³, Wolfgang Preiser¹³, Francesco Petruccione^{14

15}, Alex Sigal^{16

17

18}, Diana Hardie¹⁹, Gert Marais¹⁹, Nei-Yuan Hsiao¹⁹, Stephen Korsman¹⁹, Mary-Ann Davies^{20

21}, Lynn Tyers⁵, Innocent Mudau⁵, Denis York²², Caroline Maslo²³, Dominique Goedhals²⁴, Shareef Abrahams²⁵, Oluwakemi Laguda-Akingba^{25

26}, Arghavan Alisoltani-Dehkordi^{27

28}, Adam Godzik²⁸, Constantinos Kurt Wibmer⁹, Bryan Trevor Sewell²⁹, José Lourenço³⁰, Luiz Carlos Junior Alcantara^{2

3}, Sergei L Kosakovsky Pond³¹, Steven Weaver³¹, Darren Martin^{4

5}, Richard J Lessells^{1

8}, Jinal N Bhiman^{9

10}, Carolyn Williamson^{5

8

19}, Tulio de Oliveira^{32

33

34}

Affiliations

¹ KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
² Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
³ Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
⁴ Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
⁵ Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
⁶ Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa.
⁷ NHLS, Johannesburg, South Africa.
⁸ Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
⁹ National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa.
¹⁰ School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹¹ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹² Department of Molecular Pathology, Lancet Laboratories, Johannesburg, South Africa.
¹³ Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa.
¹⁴ Centre for Quantum Technology, University of KwaZulu-Natal, Durban, South Africa.
¹⁵ National Institute for Theoretical Physics (NITheP), University of KwaZulu-Natal, Durban, South Africa.
¹⁶ Africa Health Research Institute, Durban, South Africa.
¹⁷ School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
¹⁸ Max Planck Institute for Infection Biology, Berlin, Germany.
¹⁹ Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.
²⁰ Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa.
²¹ Western Cape Government: Health, Cape Town, South Africa.
²² Molecular Diagnostics Services, Durban, South Africa.
²³ Department of Quality Leadership, Netcare Hospitals, Johannesburg, South Africa.
²⁴ Division of Virology, NHLS Universitas Academic Laboratories, University of The Free State, Bloemfontein, South Africa.
²⁵ NHLS, Port Elizabeth, South Africa.
²⁶ Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa.
²⁷ Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
²⁸ Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA.
²⁹ Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
³⁰ Department of Zoology, University of Oxford, Oxford, UK.
³¹ Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
³² KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa. tuliodna@gmail.com.
³³ Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa. tuliodna@gmail.com.
³⁴ Department of Global Health, University of Washington, Seattle, WA, USA. tuliodna@gmail.com.

^# Contributed equally.

PMID: 33690265
DOI: 10.1038/s41586-021-03402-9

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

Houriiyah Tegally et al. Nature. 2021 Apr.

. 2021 Apr;592(7854):438-443.

doi: 10.1038/s41586-021-03402-9. Epub 2021 Mar 9.

Authors

Affiliations

¹ KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
² Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
³ Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
⁴ Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
⁵ Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
⁶ Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa.
⁷ NHLS, Johannesburg, South Africa.
⁸ Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
⁹ National Institute for Communicable Diseases, NHLS, Johannesburg, South Africa.
¹⁰ School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹¹ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
¹² Department of Molecular Pathology, Lancet Laboratories, Johannesburg, South Africa.
¹³ Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa.
¹⁴ Centre for Quantum Technology, University of KwaZulu-Natal, Durban, South Africa.
¹⁵ National Institute for Theoretical Physics (NITheP), University of KwaZulu-Natal, Durban, South Africa.
¹⁶ Africa Health Research Institute, Durban, South Africa.
¹⁷ School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
¹⁸ Max Planck Institute for Infection Biology, Berlin, Germany.
¹⁹ Division of Medical Virology, NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.
²⁰ Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa.
²¹ Western Cape Government: Health, Cape Town, South Africa.
²² Molecular Diagnostics Services, Durban, South Africa.
²³ Department of Quality Leadership, Netcare Hospitals, Johannesburg, South Africa.
²⁴ Division of Virology, NHLS Universitas Academic Laboratories, University of The Free State, Bloemfontein, South Africa.
²⁵ NHLS, Port Elizabeth, South Africa.
²⁶ Department of Laboratory Medicine and Pathology, Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa.
²⁷ Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
²⁸ Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA.
²⁹ Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
³⁰ Department of Zoology, University of Oxford, Oxford, UK.
³¹ Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
³² KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa. tuliodna@gmail.com.
³³ Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa. tuliodna@gmail.com.
³⁴ Department of Global Health, University of Washington, Seattle, WA, USA. tuliodna@gmail.com.

^# Contributed equally.

PMID: 33690265
DOI: 10.1038/s41586-021-03402-9

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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The Infection and Pathogenicity of SARS-CoV-2 Variant B.1.351 in hACE2 Mice.
Chen Q, Huang XY, Tian Y, Fan C, Sun M, Zhou C, Li R, Zhang RR, Wu G, Qin CF. Chen Q, et al. Virol Sin. 2021 Oct;36(5):1232-1235. doi: 10.1007/s12250-021-00452-1. Epub 2021 Sep 27. Virol Sin. 2021. PMID: 34569016 Free PMC article. No abstract available.

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References

1. Fontanet, A. et al. SARS-CoV-2 variants and ending the COVID-19 pandemic. Lancet 397, 952–954 (2021).
1. Mascola, J. R., Graham, B. S. & Fauci, A. S. SARS-CoV-2 viral variants—tackling a moving target. J. Am. Med. Assoc. https://doi.org/10.1001/jama.2021.2088 (2021).
1. Starr, T. N. et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 182, 1295–1310 (2020). - DOI
1. Greaney, A. J. et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 29, 463–476.e6 (2021).
1. Greaney, A. J. et al. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host Microbe 29, 44–57 (2021). - DOI

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[1] Fontanet, A. et al. SARS-CoV-2 variants and ending the COVID-19 pandemic. Lancet 397, 952–954 (2021).

[2] Fontanet, A. et al. SARS-CoV-2 variants and ending the COVID-19 pandemic. Lancet 397, 952–954 (2021).

[3] Mascola, J. R., Graham, B. S. & Fauci, A. S. SARS-CoV-2 viral variants—tackling a moving target. J. Am. Med. Assoc. https://doi.org/10.1001/jama.2021.2088 (2021).

[4] Mascola, J. R., Graham, B. S. & Fauci, A. S. SARS-CoV-2 viral variants—tackling a moving target. J. Am. Med. Assoc. https://doi.org/10.1001/jama.2021.2088 (2021).

[5] Starr, T. N. et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 182, 1295–1310 (2020). - DOI

[6] Starr, T. N. et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 182, 1295–1310 (2020). - DOI

[7] Greaney, A. J. et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 29, 463–476.e6 (2021).

[8] Greaney, A. J. et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 29, 463–476.e6 (2021).

[9] Greaney, A. J. et al. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host Microbe 29, 44–57 (2021). - DOI

[10] Greaney, A. J. et al. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host Microbe 29, 44–57 (2021). - DOI

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

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

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