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

Author

Listed:
  • Raquel Viana

    (Lancet Laboratories)

  • Sikhulile Moyo

    (Botswana Harvard HIV Reference Laboratory
    Harvard T.H. Chan School of Public Health
    Botswana Presidential COVID-19 Taskforce)

  • Daniel G. Amoako

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Houriiyah Tegally

    (University of KwaZulu-Natal)

  • Cathrine Scheepers

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
    University of the Witwatersrand)

  • Christian L. Althaus

    (University of Bern)

  • Ugochukwu J. Anyaneji

    (University of KwaZulu-Natal)

  • Phillip A. Bester

    (National Health Laboratory Service
    University of the Free State)

  • Maciej F. Boni

    (Pennsylvania State University)

  • Mohammed Chand

    (Diagnofirm Medical Laboratories)

  • Wonderful T. Choga

    (Harvard T.H. Chan School of Public Health)

  • Rachel Colquhoun

    (University of Edinburgh)

  • Michaela Davids

    (University of Pretoria)

  • Koen Deforche

    (Emweb)

  • Deelan Doolabh

    (University of Cape Town)

  • Louis Plessis

    (University of Oxford
    ETH Zurich)

  • Susan Engelbrecht

    (Stellenbosch University, Tygerberg)

  • Josie Everatt

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Jennifer Giandhari

    (University of KwaZulu-Natal)

  • Marta Giovanetti

    (Fundacao Oswaldo Cruz
    Universidade Federal de Minas Gerais)

  • Diana Hardie

    (University of Cape Town
    NHLS Groote Schuur Laboratory)

  • Verity Hill

    (University of Edinburgh)

  • Nei-Yuan Hsiao

    (University of Cape Town
    NHLS Groote Schuur Laboratory
    Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa))

  • Arash Iranzadeh

    (University of Cape Town)

  • Arshad Ismail

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Charity Joseph

    (Diagnofirm Medical Laboratories)

  • Rageema Joseph

    (University of Cape Town)

  • Legodile Koopile

    (Botswana Harvard HIV Reference Laboratory)

  • Sergei L. Kosakovsky Pond

    (Temple University)

  • Moritz U. G. Kraemer

    (University of Oxford)

  • Lesego Kuate-Lere

    (Ministry of Health and Wellness)

  • Oluwakemi Laguda-Akingba

    (NHLS Port Elizabeth Laboratory
    Walter Sisulu University)

  • Onalethatha Lesetedi-Mafoko

    (Ministry of Health and Wellness)

  • Richard J. Lessells

    (University of KwaZulu-Natal)

  • Shahin Lockman

    (Botswana Harvard HIV Reference Laboratory
    Harvard T.H. Chan School of Public Health, Boston)

  • Alexander G. Lucaci

    (Temple University)

  • Arisha Maharaj

    (University of KwaZulu-Natal)

  • Boitshoko Mahlangu

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Tongai Maponga

    (Stellenbosch University, Tygerberg)

  • Kamela Mahlakwane

    (Stellenbosch University, Tygerberg
    Tygerberg Hospital)

  • Zinhle Makatini

    (Charlotte Maxeke Johannesburg Academic Hospital)

  • Gert Marais

    (University of Cape Town
    NHLS Groote Schuur Laboratory)

  • Dorcas Maruapula

    (Botswana Harvard HIV Reference Laboratory)

  • Kereng Masupu

    (Botswana Presidential COVID-19 Taskforce)

  • Mogomotsi Matshaba

    (Botswana Presidential COVID-19 Taskforce
    Botswana-Baylor Children’s Clinical Centre of Excellence
    Baylor College of Medicine)

  • Simnikiwe Mayaphi

    (University of Pretoria)

  • Nokuzola Mbhele

    (University of Cape Town)

  • Mpaphi B. Mbulawa

    (Ministry of Health and Wellness)

  • Adriano Mendes

    (University of Pretoria)

  • Koleka Mlisana

    (National Health Laboratory Service (NHLS)
    Centre for the AIDS Programme of Research in South Africa (CAPRISA))

  • Anele Mnguni

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Thabo Mohale

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Monika Moir

    (Stellenbosch University)

  • Kgomotso Moruisi

    (Ministry of Health and Wellness)

  • Mosepele Mosepele

    (Botswana Presidential COVID-19 Taskforce
    University of Botswana)

  • Gerald Motsatsi

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Modisa S. Motswaledi

    (Botswana Presidential COVID-19 Taskforce
    University of Botswana)

  • Thongbotho Mphoyakgosi

    (Ministry of Health and Wellness)

  • Nokukhanya Msomi

    (University of KwaZulu-Natal)

  • Peter N. Mwangi

    (University of the Free State
    University of the Free State)

  • Yeshnee Naidoo

    (University of KwaZulu-Natal)

  • Noxolo Ntuli

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Martin Nyaga

    (University of the Free State
    University of the Free State)

  • Lucier Olubayo

    (Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa)
    University of Cape Town)

  • Sureshnee Pillay

    (University of KwaZulu-Natal)

  • Botshelo Radibe

    (Botswana Harvard HIV Reference Laboratory)

  • Yajna Ramphal

    (University of KwaZulu-Natal)

  • Upasana Ramphal

    (University of KwaZulu-Natal)

  • James E. San

    (University of KwaZulu-Natal)

  • Lesley Scott

    (University of the Witwatersrand)

  • Roger Shapiro

    (Botswana Harvard HIV Reference Laboratory
    Harvard T.H. Chan School of Public Health, Boston)

  • Lavanya Singh

    (University of KwaZulu-Natal)

  • Pamela Smith-Lawrence

    (Ministry of Health and Wellness)

  • Wendy Stevens

    (University of the Witwatersrand)

  • Amy Strydom

    (University of Pretoria)

  • Kathleen Subramoney

    (Charlotte Maxeke Johannesburg Academic Hospital)

  • Naume Tebeila

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Derek Tshiabuila

    (University of KwaZulu-Natal)

  • Joseph Tsui

    (University of Oxford)

  • Stephanie Wyk

    (Stellenbosch University)

  • Steven Weaver

    (Temple University)

  • Constantinos K. Wibmer

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS))

  • Eduan Wilkinson

    (Stellenbosch University)

  • Nicole Wolter

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
    University of the Witwatersrand)

  • Alexander E. Zarebski

    (University of Oxford)

  • Boitumelo Zuze

    (Botswana Harvard HIV Reference Laboratory)

  • Dominique Goedhals

    (University of the Free State
    PathCare Vermaak)

  • Wolfgang Preiser

    (Stellenbosch University, Tygerberg
    Tygerberg Hospital)

  • Florette Treurnicht

    (Charlotte Maxeke Johannesburg Academic Hospital)

  • Marietje Venter

    (University of Pretoria)

  • Carolyn Williamson

    (University of Cape Town
    NHLS Groote Schuur Laboratory
    Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa)
    University of Cape Town)

  • Oliver G. Pybus

    (University of Oxford)

  • Jinal Bhiman

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
    University of the Witwatersrand)

  • Allison Glass

    (Lancet Laboratories
    University of the Witwatersrand)

  • Darren P. Martin

    (Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa)
    University of Cape Town)

  • Andrew Rambaut

    (University of Edinburgh)

  • Simani Gaseitsiwe

    (Botswana Harvard HIV Reference Laboratory
    Harvard T.H. Chan School of Public Health)

  • Anne Gottberg

    (National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
    University of the Witwatersrand)

  • Tulio Oliveira

    (University of KwaZulu-Natal
    Stellenbosch University
    University of Washington)

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.

Suggested Citation

  • Raquel Viana & Sikhulile Moyo & Daniel G. Amoako & Houriiyah Tegally & Cathrine Scheepers & Christian L. Althaus & Ugochukwu J. Anyaneji & Phillip A. Bester & Maciej F. Boni & Mohammed Chand & Wonderf, 2022. "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa," Nature, Nature, vol. 603(7902), pages 679-686, March.
    • Handle: RePEc:nat:nature:v:603:y:2022:i:7902:d:10.1038_s41586-022-04411-y
    DOI: 10.1038/s41586-022-04411-y
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