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

By R. Viana, S. Moyo, D. Amoako, H. Tegally, C. Scheepers, Christian L. Althaus, U. J. Anyaneji, P. Bester, Maciej F. Boni, M. Chand and 89 more. Nature, 2021

1,621 citations recorded by the source corpus.

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. The genomic profile and early transmission dynamics of the Omicron strain of SARS-CoV-2.

Subfields: Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/620080b3e88fcaf05619f54a765e6d73dcab1bce

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In Molecular Biology

1. Marc A. Suchard
2. B. Sankaran

Citations in the corpus

• Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization (2021, neutral): “Here we investigated Omicron escape from neutralization by antibodies from South African individuals vaccinated with Pfizer BNT162b2.”
• Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography (2022, background): “A case in point is the current ongoing global COVID-19 pandemic caused by SARS-CoV-2 15 .”
• Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa (2022, neutral): “529/21K) variant was detected in Gauteng Province, the smallest yet most populous province in South Africa, andwas associatedwith rapidly increasing case numbers (3).”
• Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations (2023, positive): “The Omicron lineage, first detected in November 2021 [9], was able to outcompete Delta and grew much more rapidly relative to previous VOCs during their emergence (Figure 4A).”