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, 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.
Highlights
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D The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves
The first was Eassociated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants, respectively[1–3]
Summary
ROampiicdreopnivdaermiaincteixnpsaonustiohneronfAthfreiScAa RS-VCIoEV-2W Received:18December2021 E Accepted: 7 January 2022 R Accelerated Article Preview Published P online 7 January 2022. The Delta variant evolved into multiple sub-lineages[7], some of which demonstrated ber and December 2020, the world witnessed the emergence of the signs of having a growth advantage in certain locations[8], prompting first variants of concern (VOCs) These variants exhibited increased speculation that the VOC to drive a resurgence of infections would transmissibility and/or immune evasion properties that threatened be likely derived from Delta. A list of affiliations appears at the end of the paper This wave coincided with the emergence of a novel SARS-CoV-2 variant week of December 2021, Omicron was causing a rapid and sustained that, within days of its near-simultaneous discovery in four individuals increase in cases in South Africa and Botswana (Fig. 1C, Extended Data in Botswana, a traveler from South Africa in Hong Kong, and 54 individu- Fig. 2 for Botswana). Since and the beginning of 2022, over 100 000 genomes of Omicron have been produced as Omicron has started to dominate SARS-CoV-2 infections in the world
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