Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

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.

Keywords

Affiliated Institutions

• Stellenbosch University ZA
• Wellcome Centre for Infectious Diseases Research in Africa ZA
• Harvard University US
• Johannesburg Hospital ZA
• Temple University US
• Botswana Open University BW
• South African Medical Research Council ZA
• Emweb (Belgium) BE
• University of the Witwatersrand ZA
• Ministry of Health BW
• Pennsylvania State University US
• University of Cape Town ZA
• Center for Disease Dynamics, Economics & Policy US
• University of Pretoria ZA
• Botswana Harvard AIDS Institute Partnership BW
• University of Bern CH
• Fundação Oswaldo Cruz BR
• University of the Free State ZA
• University of Oxford GB
• Lancet Laboratories ZA
• National Health Laboratory Service ZA
• University of KwaZulu-Natal ZA
• Institute of Social and Preventive Medicine CH
• University of Edinburgh GB

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