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

Abstract The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. 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 .

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• 1 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 .
• 2 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.
• 3 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.

Understanding this could lead to better treatments, improved diagnostics, or a deeper grasp of how the human body works — benefiting patient care globally.

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