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

TLDR

The SARS‑CoV‑2 epidemic in southern Africa has progressed through three waves driven by distinct variants, and the newly emerged Omicron variant carries over 30 spike mutations predicted to alter antibody neutralization and spike function. This study aims to describe Omicron’s genomic profile and early transmission dynamics, emphasizing its rapid spread in areas with high population immunity. The authors analyze genomic surveillance data and transmission patterns to characterize Omicron’s spread. Omicron was first detected in November 2021, designated a variant of concern within three days, and reported in 87 countries within three weeks.

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.