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Nature Research, Nature, 7902(603), p. 679-686, 2022

DOI: 10.1038/s41586-022-04411-y

Nature Research, Nature, 2022

DOI: 10.1038/d41586-021-03832-5

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

Journal article published in 2022 by Raquel Viana, Stephanie van Wyk, Anne von Gottberg, Sikhulile Moyo ORCID, Daniel Gyamfi Amoako ORCID, Houriiyah Tegally, Christian L. Althaus ORCID, Cathrine Scheepers, Ugochukwu J. Anyaneji, Dr. Christian L. Althaus Pd, Phillip A. Bester, Maciej F. Boni ORCID, Mohammed Chand, Wonderful T. Choga, Rachel Colquhoun and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

AbstractThe 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.