Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Author:
Viana Raquel, Moyo SikhulileORCID, Amoako Daniel G.ORCID, Tegally Houriiyah, Scheepers Cathrine, Althaus Christian L.ORCID, Anyaneji Ugochukwu J., Bester Phillip A., Boni Maciej F.ORCID, Chand Mohammed, Choga Wonderful T., Colquhoun Rachel, Davids Michaela, Deforche KoenORCID, Doolabh Deelan, du Plessis LouisORCID, Engelbrecht SusanORCID, Everatt JosieORCID, Giandhari Jennifer, Giovanetti MartaORCID, Hardie Diana, Hill Verity, Hsiao Nei-YuanORCID, Iranzadeh ArashORCID, Ismail ArshadORCID, Joseph Charity, Joseph Rageema, Koopile Legodile, Kosakovsky Pond Sergei L.ORCID, Kraemer Moritz U. G.ORCID, Kuate-Lere Lesego, Laguda-Akingba Oluwakemi, Lesetedi-Mafoko Onalethatha, Lessells Richard J.ORCID, Lockman Shahin, Lucaci Alexander G., Maharaj Arisha, Mahlangu BoitshokoORCID, Maponga Tongai, Mahlakwane Kamela, Makatini Zinhle, Marais Gert, Maruapula Dorcas, Masupu Kereng, Matshaba Mogomotsi, Mayaphi Simnikiwe, Mbhele Nokuzola, Mbulawa Mpaphi B., Mendes Adriano, Mlisana Koleka, Mnguni Anele, Mohale Thabo, Moir Monika, Moruisi Kgomotso, Mosepele Mosepele, Motsatsi Gerald, Motswaledi Modisa S., Mphoyakgosi Thongbotho, Msomi Nokukhanya, Mwangi Peter N., Naidoo Yeshnee, Ntuli Noxolo, Nyaga Martin, Olubayo Lucier, Pillay Sureshnee, Radibe Botshelo, Ramphal Yajna, Ramphal UpasanaORCID, San James E., Scott Lesley, Shapiro Roger, Singh Lavanya, Smith-Lawrence Pamela, Stevens Wendy, Strydom Amy, Subramoney Kathleen, Tebeila Naume, Tshiabuila Derek, Tsui Joseph, van Wyk Stephanie, Weaver StevenORCID, Wibmer Constantinos K., Wilkinson Eduan, Wolter Nicole, Zarebski Alexander E., Zuze Boitumelo, Goedhals Dominique, Preiser WolfgangORCID, Treurnicht Florette, Venter Marietje, Williamson CarolynORCID, Pybus Oliver G.ORCID, Bhiman JinalORCID, Glass Allison, Martin Darren P., Rambaut AndrewORCID, Gaseitsiwe Simani, von Gottberg Anne, de Oliveira TulioORCID
Abstract
AbstractThe 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.
Publisher
Springer Science and Business Media LLC
Subject
Multidisciplinary
Cited by
1328 articles.
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