Nature

, volume 603 , issue 7902 , pages 679-686

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana ¹

Sikhulile Moyo ^{2, 3, 4}

Daniel G. Amoako ⁵

Houriiyah Tegally ⁶

Cathrine Scheepers ^{5, 7}

Christian L. Althaus ⁸

Ugochukwu J. Anyaneji ⁶

Phillip A Bester ^{9, 10}

Tran Tinh Hien ¹¹

Mohammed Chand ¹²

Wonderful T. Choga ³

Rachel Colquhoun ¹³

Michaela Davids ¹⁴

Koen Deforche ¹⁵

Deelan Doolabh ¹⁶

Louis du Plessis ^{17, 18}

Susan Engelbrecht ¹⁹

Josie Everatt ⁵

Jennifer Giandhari ⁶

Marta Giovanetti ^{20, 21}

Diana Hardie ^{16, 22}

Verity Hill ¹³

Nei-Yuan Hsiao ^{16, 22, 23}

Arash Iranzadeh ²⁴

Arshad Ismail ⁵

Charity Joseph ¹²

Rageema Joseph ¹⁶

Legodile Koopile ²

Sergei L. Kosakovsky Pond ²⁵

Moritz U.G. Kraemer ¹⁷

Kuate Lere Lesego ²⁶

Oluwakemi Laguda Akingba ^{27, 28}

Onalethatha Lesetedi Mafoko ²⁹

Richard J Lessells ⁶

Shahin Lockman ^{2, 30}

Alexander G Lucaci ²⁵

Arisha Maharaj ⁶

Boitshoko Mahlangu ⁵

Tongai Maponga ¹⁹

Kamela Mahlakwane ^{19, 31}

Zinhle Makatini ³²

Gert Marais ^{16, 22}

Dorcas Maruapula ²

Kereng Masupu ⁴

Mogomotsi Matshaba ^{4, 33, 34}

Simnikiwe Mayaphi ³⁵

Nokuzola Mbhele ¹⁶

Mpaphi B Mbulawa ³⁶

Adriano Mendes ¹⁴

Koleka Mlisana ^{37, 38}

Anele Mnguni ⁵

Thabo Mohale ⁵

Monika Moir ³⁹

Kgomotso Moruisi ²⁶

Mosepele Mosepele ^{4, 40}

Gerald Motsatsi ⁵

Modisa S Motswaledi ^{4, 41}

Thongbotho Mphoyakgosi ³⁶

Nokukhanya Msomi ⁴²

Peter N. Mwangi ^{10, 43}

Yeshnee Naidoo ⁶

Noxolo Ntuli ⁵

Martin Nyaga ^{10, 43}

Lucier Olubayo ^{23, 24}

Sureshnee Pillay ⁶

Botshelo Radibe ²

Yajna Ramphal ⁶

Upasana Ramphal ⁶

James E San ⁶

Lesley Scott ⁴⁴

Roger Shapiro ^{2, 30}

Lavanya Singh ⁶

Pamela Smith Lawrence ²⁶

Wendy Stevens ⁴⁴

Amy Strydom ¹⁴

Kathleen Subramoney ³²

Naume Tebeila ⁵

Derek Tshiabuila ⁶

Joseph Tsui ¹⁷

Stephanie van Wyk ³⁹

Steven P. Weaver ²⁵

Constantinos K. Wibmer ⁵

Eduan Wilkinson ³⁹

NICOLE WOLTER ^{5, 45}

Alexander E Zarebski ¹⁷

Boitumelo Zuze ²

Dominique Goedhals ^{10, 46}

Wolfgang Preiser ^{19, 31}

Florette Treurnicht ³²

Marietje Venter ¹⁴

Carolyn Williamson ^{16, 22, 23, 47}

Mark Danta ¹⁷

Jinal N. Bhiman ^{5, 7}

Allison Glass ^{1, 48}

Darren P. Martin ^{23, 47}

Andrew Rambaut ¹³

Simani Gaseitsiwe ^{2, 3}

Anne von Gottberg ^{5, 45}

Tulio De Oliveira ^{6, 39, 49}

Hide authors affiliations Show authors affiliations: 49 affiliations

Lancet Laboratories, Johannesburg, South Africa |

Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana |

Harvard T.H. Chan School of Public Health, Boston, USA |

⁴

Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana |

⁵

National Institute For Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa |

⁶

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa |

⁷

South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa

University of the Witwatersrand

South African Medical Research Council

⁸

Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland |

⁹

Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa |

¹⁰

Division of Virology, University of the Free State, Bloemfontein, South Africa |

¹¹

Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, USA |

¹²

Diagnofirm Medical Laboratories, Gaborone, Botswana |

¹³

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK |

¹⁴

Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa |

¹⁵

Emweb, Herent, Belgium |

¹⁶

Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa |

¹⁷

Department of Zoology, University of Oxford, Oxford, UK |

¹⁸

Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland |

¹⁹

Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa |

²⁰

Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil |

²¹

Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil |

²²

Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa |

²³

Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa |

²⁴

Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa |

²⁵

Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, USA |

²⁶

Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana |

²⁷

NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa |

²⁸

Faculty of health Sciences, Walter Sisulu University, Mthatha, South Africa |

²⁹

Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana |

³⁰

Department of Immunology and infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA |

³¹

NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa

National Health Laboratory Services

Tygerberg Hospital

³²

Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa |

³³

Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana |

³⁴

Baylor College of medicine, Houston, USA |

³⁵

Department of Medical Virology, University of Pretoria, Pretoria, South Africa |

³⁶

National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana |

³⁷

National Health Laboratory Service (NHLS), Johannesburg, South Africa |

³⁸

Centre for the AIDS Programme of Research In South Africa (CAPRISA), Durban, South Africa |

³⁹

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa |

⁴⁰

Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana |

⁴¹

Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana |

⁴²

Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa

University of KwaZulu-Natal

National Health Laboratory Services

⁴³

Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa |

⁴⁴

Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa |

⁴⁵

School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa |

⁴⁶

Pathcare Vermaak, Pretoria, South Africa |

⁴⁷

Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa |

⁴⁸

Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa |

⁴⁹

Department of Global Health, University of Washington, Seattle, USA |

Publication type: Journal Article

Publication date: 2022-01-07

Springer Nature

Nature

scimago Q1

wos Q1

SJR: 18.288

CiteScore: 78.1

Impact factor: 48.5

ISSN: 00280836, 14764687

DOI: 10.1038/s41586-022-04411-y

Copy DOI

PubMed ID: 35042229

Multidisciplinary

Abstract

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity. The genomic profile and early transmission dynamics of the Omicron strain of SARS-CoV-2.

Found

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Claude Jean

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Dedkov Vladimir

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Sechenov First Moscow State Medical University

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Villapol Sonia

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Viana R. et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa // Nature. 2022. Vol. 603. No. 7902. pp. 679-686.

GOST all authors (up to 50) Copy

Viana R. et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa // Nature. 2022. Vol. 603. No. 7902. pp. 679-686.

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BibTex (up to 50 authors) Copy

@article{2022_Viana,

author = {Raquel Viana and Sikhulile Moyo and Daniel G. Amoako and Houriiyah Tegally and Cathrine Scheepers and Christian L. Althaus and Ugochukwu J. Anyaneji and Phillip A Bester and Tran Tinh Hien and Mohammed Chand and Wonderful T. Choga and Rachel Colquhoun and Michaela Davids and Koen Deforche and Deelan Doolabh and Louis du Plessis and Susan Engelbrecht and Josie Everatt and Jennifer Giandhari and Marta Giovanetti and Diana Hardie and Verity Hill and Nei-Yuan Hsiao and Arash Iranzadeh and Arshad Ismail and Charity Joseph and Rageema Joseph and Legodile Koopile and Sergei L. Kosakovsky Pond and Moritz U.G. Kraemer and Kuate Lere Lesego and Oluwakemi Laguda Akingba and Onalethatha Lesetedi Mafoko and Richard J Lessells and Shahin Lockman and Alexander G Lucaci and Arisha Maharaj and Boitshoko Mahlangu and Tongai Maponga and Kamela Mahlakwane and Zinhle Makatini and Gert Marais and Dorcas Maruapula and Kereng Masupu and Mogomotsi Matshaba and Simnikiwe Mayaphi and Nokuzola Mbhele and Mpaphi B Mbulawa and Adriano Mendes and Koleka Mlisana and others},

title = {Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa},

journal = {Nature},

year = {2022},

volume = {603},

publisher = {Springer Nature},

month = {jan},

url = {https://doi.org/10.1038/s41586-022-04411-y},

number = {7902},

pages = {679--686},

doi = {10.1038/s41586-022-04411-y}

}

MLA

Cite this

MLA Copy

Viana, Raquel, et al. “Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.” Nature, vol. 603, no. 7902, Jan. 2022, pp. 679-686. https://doi.org/10.1038/s41586-022-04411-y.

Publisher

Springer Nature

Journal

Nature

scimago Q1

wos Q1

SJR

18.288

CiteScore

78.1

Impact factor

48.5

ISSN

00280836 (Print)

14764687 (Electronic)