Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Raquel Viana(Lancet Laboratories), Sikhulile Moyo(Harvard University), Daniel G. Amoako(National Health Laboratory Service), Houriiyah Tegally(University of KwaZulu-Natal), Cathrine Scheepers(National Health Laboratory Service), Christian L. Althaus(University of Bern), Ugochukwu J. Anyaneji(University of KwaZulu-Natal), Phillip Armand Bester(National Health Laboratory Service), Maciej F. Boni(Pennsylvania State University), Mohammed Chand, Wonderful T. Choga(Harvard University), Rachel Colquhoun(University of Edinburgh), Michaela Davids(University of Pretoria), Koen Deforche(Emweb (Belgium)), Deelan Doolabh(University of Cape Town), Louis du Plessis(ETH Zurich), Susan Engelbrecht(Stellenbosch University), Josie Everatt(National Health Laboratory Service), Jennifer Giandhari(University of KwaZulu-Natal), Marta Giovanetti(Universidade Federal de Minas Gerais), Diana Hardie(University of Cape Town), Verity Hill(University of Edinburgh), Marvin Hsiao(University of Cape Town), Arash Iranzadeh(University of Cape Town), Arshad Ismail(National Health Laboratory Service), Charity Joseph, R Joseph(University of Cape Town), Legodile Koopile(Botswana Harvard AIDS Institute Partnership), Sergei L. Kosakovsky Pond(Temple University), Moritz U. G. Kraemer(University of Oxford), Lesego Kuate-Lere(Ministry of Health), Oluwakemi Laguda-Akingba(Walter Sisulu University), Onalethatha Lesetedi-Mafoko(Ministry of Health), Richard Lessells(University of KwaZulu-Natal), Shahin Lockman(Harvard University), Alexander G. Lucaci(Temple University), Arisha Maharaj(University of KwaZulu-Natal), Boitshoko Mahlangu(National Health Laboratory Service), Tongai Maponga(Stellenbosch University), Kamela Mahlakwane(Stellenbosch University), Zinhle Makatini(Johannesburg Hospital), Gert Marais(University of Cape Town), Dorcas Maruapula(Botswana Harvard AIDS Institute Partnership), Kereng Masupu(Botswana Open University), Mogomotsi Matshaba(Baylor College of Medicine), Simnikiwe H. Mayaphi(University of Pretoria), Nokuzola Mbhele(University of Cape Town), Mpaphi B. Mbulawa(Ministry of Health), Adriano Mendes(University of Pretoria), Koleka Mlisana(National Health Laboratory Service), Anele Mnguni(National Health Laboratory Service), Thabo Mohale(National Health Laboratory Service), Monika Moir(Stellenbosch University), Kgomotso Moruisi(Ministry of Health), Mosepele Mosepele(University of Botswana), Gerald Motsatsi(National Health Laboratory Service), Modisa S. Motswaledi(University of Botswana), Thongbotho Mphoyakgosi(Ministry of Health), Nokukhanya Msomi(National Health Laboratory Service), Peter N. Mwangi(University of the Free State), Yeshnee Naidoo(University of KwaZulu-Natal), Noxolo Ntuli(National Health Laboratory Service), Martin M. Nyaga(University of the Free State), Lucier Olubayo(University of Cape Town), Sureshnee Pillay(University of KwaZulu-Natal), Botshelo Radibe(Botswana Harvard AIDS Institute Partnership), Yajna Ramphal(University of KwaZulu-Natal), Upasana Ramphal(University of KwaZulu-Natal), James Emmanuel San(University of KwaZulu-Natal), Lesley Scott(University of the Witwatersrand), Roger Shapiro(Harvard University), Lavanya Singh(University of KwaZulu-Natal), Pamela Smith-Lawrence(Ministry of Health), Wendy Stevens(University of the Witwatersrand), Amy Strydom(University of Pretoria), Kathleen Subramoney(Johannesburg Hospital), Naume Tebeila(National Health Laboratory Service), Derek Tshiabuila(University of KwaZulu-Natal), Joseph Tsui(University of Oxford), Stephanie van Wyk(Stellenbosch University), Steven Weaver(Temple University), Constantinos Kurt Wibmer(National Health Laboratory Service), Eduan Wilkinson(Stellenbosch University), Nicole Wolter(National Health Laboratory Service), Alexander E. Zarebski(University of Oxford), Boitumelo Zuze(Botswana Harvard AIDS Institute Partnership), Dominique Goedhals(University of the Free State), Wolfgang Preiser(Stellenbosch University), Florette K. Treurnicht(Johannesburg Hospital), Marietjie Venter(University of Pretoria), Carolyn Williamson(University of Cape Town), Oliver G. Pybus(University of Oxford), Jinal N. Bhiman(National Health Laboratory Service), Allison Glass(University of the Witwatersrand), Darren P. Martin(University of Cape Town), Andrew Rambaut(University of Edinburgh), Simani Gaseitsiwe(Harvard University), Anne von Gottberg(National Health Laboratory Service), Túlio de Oliveira(Washington State Department of Health)
Cited by 1,894Open Access
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, respectively 1–3 . 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 function 4 . Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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