This repository will be updated with all materials soon. Please direct any specific queries to houriiyah.tegally@gmail.com and sanemmanueljames@gmail.com.
Raquel Viana1*, Sikhulile Moyo2,3,4*, Daniel G Amoako5*, Houriiyah Tegally6*, Cathrine Scheepers5,7*, Christian L Althaus8, Ugochukwu J Anyaneji6, Phillip A Bester9,10, Maciej F Boni11, Mohammed Chand12, Wonderful T Choga3, Rachel Colquhoun13, Michaela Davids14, Koen Deforche15, Deelan Doolabh16, Louis du Plessis24,49, Susan Engelbrecht17, Josie Everatt5, Jennifer Giandhari6, Marta Giovanetti18,19, Diana Hardie16,20, Verity Hill13, Nei-Yuan Hsiao16,20,21, Arash Iranzadeh22, Arshad Ismail5, Charity Joseph12, Rageema Joseph16, Legodile Koopile2, Sergei L Kosakovsky Pond23, Moritz UG Kraemer24, Lesego Kuate-Lere25, Oluwakemi Laguda-Akingba26,27, Onalethatha Lesetedi-Mafoko28, Richard J Lessells6, Shahin Lockman2,29, Alexander G Lucaci23, Arisha Maharaj6, Boitshoko Mahlangu5, Tongai Maponga17, Kamela Mahlakwane17,30, Zinhle Makatini31, Gert Marais16,20, Dorcas Maruapula2, Kereng Masupu4, Mogomotsi Matshaba4,32,33, Simnikiwe Mayaphi34, Nokuzola Mbhele16, Mpaphi B Mbulawa35, Adriano Mendes14, Koleka Mlisana36,37, Anele Mnguni5, Thabo Mohale5, Monika Moir38, Kgomotso Moruisi25, Mosepele Mosepele4,39, Gerald Motsatsi5, Modisa S Motswaledi4,40, Thongbotho Mphoyakgosi35, Nokukhanya Msomi41, Peter N Mwangi10,42, Yeshnee Naidoo6, Noxolo Ntuli5, Martin Nyaga10,42, Lucier Olubayo21,22, Sureshnee Pillay6, Botshelo Radibe2, Yajna Ramphal6, Upasana Ramphal6, James E San6, Lesley Scott43, Roger Shapiro2,29, Lavanya Singh6, Pamela Smith-Lawrence25, Wendy Stevens43, Amy Strydom14, Kathleen Subramoney31, Naume Tebeila5, Derek Tshiabuila6, Joseph Tsui24, Stephanie van Wyk38, Steven Weaver23, Constantinos K Wibmer5, Eduan Wilkinson38, Nicole Wolter5,44, Alexander E Zarebski24, Boitumelo Zuze2, Dominique Goedhals10,45, Wolfgang Preiser17,30, Florette Treurnicht31, Marietje Venter14, Carolyn Williamson16,20,21,46, Oliver G Pybus24, Jinal Bhiman5,7, Allison Glass1,47, Darren P Martin21,46, Andrew Rambaut13, Simani Gaseitsiwe2,3**, Anne von Gottberg5,44**, Tulio de Oliveira6,38,48**✉
1Lancet Laboratories, Johannesburg, South Africa
2Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
3Harvard T.H. Chan School of Public Health, Boston, Massachusetts
4Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
5National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
6KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
7South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
8Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
9Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa
10Division of Virology, University of the Free State, Bloemfontein, South Africa
11Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
12Diagnofirm Medical Laboratories, Gaborone, Botswana
13Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
14Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
15Emweb bv, Herent, Belgium
16Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
17Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
18Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
19Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
20Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
21Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa)
22Division of Computational Biology, Faculty of Health Sciences, University of Cape Town
23Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
24Department of Zoology, University of Oxford, Oxford, UK
25Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
26NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
27Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa
28Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana
29Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
30NHLS Tygerberg Laboratory, Tygerberg, Cape Town, South Africa
31Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
32Botswana-Baylor Children's Clinical Centre of Excellence
33Baylor College of Medicine, Houston, Texas, USA
34Department of Medical Virology, University of Pretoria, Pretoria, South Africa
35National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
36National Health Laboratory Service (NHLS), Johannesburg, South Africa
37Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
38Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
39Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana
40Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
41Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu–Natal, Durban, South Africa
42Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
43Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
44School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
45PathCare Vermaak, Pretoria, South Africa
46Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
47Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
48Department of Global Health, University of Washington, Seattle, WA, USA
49Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
*These authors contributed equally: Raquel Viana, Sikhulile Moyo, Daniel G Amoako, Houriiyah Tegally, Cathrine Scheepers
**These authors jointly supervised the work: Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira
Summary
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.