National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa.
Division of Virology, University of the Free State, Bloemfontein, South Africa.
Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
Diagnofirm Medical Laboratories, Gaborone, Botswana.
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Emweb, Herent, Belgium.
Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Department of Zoology, University of Oxford, Oxford, UK.
Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland.
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.
Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.
Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.
Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa.
Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa.
Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana.
Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa.
Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.
Baylor College of Medicine, Houston, TX, USA.
Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana.
Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana.
Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa.
Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.
School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
PathCare Vermaak, Pretoria, South Africa.
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. tulio@sun.ac.za.
Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa. tulio@sun.ac.za.
Department of Global Health, University of Washington, Seattle, WA, USA. tulio@sun.ac.za.
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.
