RESEARCH BRIEFINGS 07 January 2022 Raquel Viana 0 , Sikhulile Moyo 1 , Daniel G. Amoako 2 , Houriiyah Tegally 3 , Cathrine Scheepers 4 , Christian L. Althaus 5 , Ugochukwu J. Anyaneji 6 , Phillip A. Bester 7 , Maciej F. Boni 8 , Mohammed Chand 9 , Wonderful T. Choga 10 , Rachel Colquhoun 11 , Michaela Davids 12 , Koen Deforche 13 , Deelan Doolabh 14 , Louis du Plessis 15 , Susan Engelbrecht 16 , Josie Everatt 17 , Jennifer Giandhari 18 , Marta Giovanetti 19 , Diana Hardie 20 , Verity Hill 21 , Nei-Yuan Hsiao 22 , Arash Iranzadeh 23 , Arshad Ismail 24 , Charity Joseph 25 , Rageema Joseph 26 , Legodile Koopile 27 , Sergei L. Kosakovsky Pond 28 , Moritz U. G. Kraemer 29 , Lesego Kuate-Lere 30 , Oluwakemi Laguda-Akingba 31 , Onalethatha Lesetedi-Mafoko 32 , Richard J. Lessells 33 , Shahin Lockman 34 , Alexander G. Lucaci 35 , Arisha Maharaj 36 , Boitshoko Mahlangu 37 , Tongai Maponga 38 , Kamela Mahlakwane 39 , Zinhle Makatini 40 , Gert Marais 41 , Dorcas Maruapula 42 , Kereng Masupu 43 , Mogomotsi Matshaba 44 , Simnikiwe Mayaphi 45 , Nokuzola Mbhele 46 , Mpaphi B. Mbulawa 47 , Adriano Mendes 48 , Koleka Mlisana 49 , Anele Mnguni 50 , Thabo Mohale 51 , Monika Moir 52 , Kgomotso Moruisi 53 , Mosepele Mosepele 54 , Gerald Motsatsi 55 , Modisa S. Motswaledi 56 , Thongbotho Mphoyakgosi 57 , Nokukhanya Msomi 58 , Peter N. Mwangi 59 , Yeshnee Naidoo 60 , Noxolo Ntuli 61 , Martin Nyaga 62 , Lucier Olubayo 63 , Sureshnee Pillay 64 , Botshelo Radibe 65 , Yajna Ramphal 66 , Upasana Ramphal 67 , James E. San 68 , Lesley Scott 69 , Roger Shapiro 70 , Lavanya Singh 71 , Pamela Smith-Lawrence 72 , Wendy Stevens 73 , Amy Strydom 74 , Kathleen Subramoney 75 , Naume Tebeila 76 , Derek Tshiabuila 77 , Joseph Tsui 78 , Stephanie van Wyk 79 , Steven Weaver 80 , Constantinos K. Wibmer 81 , Eduan Wilkinson 82 , Nicole Wolter 83 , Alexander E. Zarebski 84 , Boitumelo Zuze 85 , Dominique Goedhals 86 , Wolfgang Preiser 87 , Florette Treurnicht 88 , Marietje Venter 89 , Carolyn Williamson 90 , Oliver G. Pybus 91 , Jinal Bhiman 92 , Allison Glass 93 , Darren P. Martin 94 , Andrew Rambaut 95 , Simani Gaseitsiwe 96 , Anne von Gottberg 97 & Tulio de Oliveira 98
This manuscript has been peer reviewed and accepted for publication in Nature and is provided in this format here as a response to the exceptional public-health crisis. This accepted manuscript will continue through the processes of copy editing and formatting to publication of a finalized version of record on nature.com. Please note there may be errors present in this version, which may affect the content, and all legal disclaimers apply. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta 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) 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, 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. doi: https://doi.org/10.1038/d41586-021-03832-5 Supplementary Information De Oliveira reporting summary De Oliveira supplementary table 1
https://www.nature.com/articles/d41586-021-03832-5
