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

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, Wonderful T. Choga, Rachel Colquhoun, Michaela Davids, Koen Deforche, Deelan Doolabh, Louis Plessis, Susan Engelbrecht, Josie Everatt, Jennifer Giandhari, Marta Giovanetti, Diana Hardie, Verity Hill, Nei-Yuan Hsiao, Arash Iranzadeh, Arshad Ismail, Charity Joseph, Rageema Joseph, Legodile Koopile, Sergei L. Kosakovsky Pond, Moritz U. G. Kraemer, Lesego Kuate-Lere, Oluwakemi Laguda-Akingba, Onalethatha Lesetedi-Mafoko, Richard J. Lessells, Shahin Lockman, Alexander G. Lucaci, Arisha Maharaj, Boitshoko Mahlangu, Tongai Maponga, Kamela Mahlakwane, Zinhle Makatini, Gert Marais, Dorcas Maruapula, Kereng Masupu, Mogomotsi Matshaba, Simnikiwe Mayaphi, Nokuzola Mbhele, Mpaphi B. Mbulawa, Adriano Mendes, Koleka Mlisana, Anele Mnguni, Thabo Mohale, Monika Moir, Kgomotso Moruisi, Mosepele Mosepele, Gerald Motsatsi, Modisa S. Motswaledi, Thongbotho Mphoyakgosi, Nokukhanya Msomi, Peter N. Mwangi, Yeshnee Naidoo, Noxolo Ntuli, Martin Nyaga, Lucier Olubayo, Sureshnee Pillay, Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, James E. San, Lesley Scott, Roger Shapiro, Lavanya Singh, Pamela Smith-Lawrence, Wendy Stevens, Amy Strydom, Kathleen Subramoney, Naume Tebeila, Derek Tshiabuila, Joseph Tsui, Stephanie Wyk, Steven Weaver, Constantinos K. Wibmer, Eduan Wilkinson, Nicole Wolter, Alexander E. Zarebski, Boitumelo Zuze, Dominique Goedhals, Wolfgang Preiser, Florette Treurnicht, Marietje Venter, Carolyn Williamson, Oliver G. Pybus, Jinal Bhiman, Allison Glass, Darren P. Martin, Andrew Rambaut, Simani Gaseitsiwe, Anne Gottberg and Tulio Oliveira ()
Additional contact information
Raquel Viana: Lancet Laboratories
Sikhulile Moyo: Botswana Harvard HIV Reference Laboratory
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)
Christian L. Althaus: University of Bern
Ugochukwu J. Anyaneji: University of KwaZulu-Natal
Phillip A. Bester: National Health Laboratory Service
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
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
Diana Hardie: University of Cape Town
Verity Hill: University of Edinburgh
Nei-Yuan Hsiao: University of Cape Town
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
Onalethatha Lesetedi-Mafoko: Ministry of Health and Wellness
Richard J. Lessells: University of KwaZulu-Natal
Shahin Lockman: Botswana Harvard HIV Reference Laboratory
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
Zinhle Makatini: Charlotte Maxeke Johannesburg Academic Hospital
Gert Marais: University of Cape Town
Dorcas Maruapula: Botswana Harvard HIV Reference Laboratory
Kereng Masupu: Botswana Presidential COVID-19 Taskforce
Mogomotsi Matshaba: Botswana Presidential COVID-19 Taskforce
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)
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
Gerald Motsatsi: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Modisa S. Motswaledi: Botswana Presidential COVID-19 Taskforce
Thongbotho Mphoyakgosi: Ministry of Health and Wellness
Nokukhanya Msomi: University of KwaZulu-Natal
Peter N. Mwangi: 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
Lucier Olubayo: Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa)
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
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)
Alexander E. Zarebski: University of Oxford
Boitumelo Zuze: Botswana Harvard HIV Reference Laboratory
Dominique Goedhals: University of the Free State
Wolfgang Preiser: Stellenbosch University, Tygerberg
Florette Treurnicht: Charlotte Maxeke Johannesburg Academic Hospital
Marietje Venter: University of Pretoria
Carolyn Williamson: 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)
Allison Glass: Lancet Laboratories
Darren P. Martin: Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa)
Andrew Rambaut: University of Edinburgh
Simani Gaseitsiwe: Botswana Harvard HIV Reference Laboratory
Anne Gottberg: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Tulio Oliveira: University of KwaZulu-Natal

Nature, 2022, vol. 603, issue 7902, 679-686

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41586-022-04411-y

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