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 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.

Paediatric hospitalisations due to COVID-19 during the first SARS-CoV-2 omicron (B.1.1.529) variant wave in South Africa: a multicentre observational study

“…The omicron viral genomic sequence includes 26-32 spike protein changes and 45-52 amino acid changes in total compared with the original strain, causing worldwide concern regarding possible immune evasion. 5 Clinical characteristics and disease profiles of paedi atric (ie, aged 0-19 years) COVID-19 cases in South Africa in the first three waves of the epidemic-namely, between June and September, 2020 (first wave); November, 2020, and February, 2021 (second wave; beta [B. 1.351] variant predominance); and June and October, 2021 (third wave; www.thelancet.com/child-adolescent Published online February, 2022 https://doi.org/10.1016/S2352-4642(22)00027-X delta variant predominance)-have been broadly similar to descriptions in international literature, ranging from asymptomatic to mild-to-moderate disease in most children.…”

SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated individuals

“…The copyright holder for this this version posted February 14, 2022. ; https://doi.org/10.1101/2022.02. 10.22270789 doi: medRxiv preprint Omicron is defined by multiple mutations across its genome, including more than 30 mutations in the spike protein, many of which are associated with immune evasion 1 . These mutations confer neutralization escape across multiple vaccine platforms and in donors previously infected with other variants [2][3][4][5] .…”

Virus neutralization of SARS-CoV-2 Omicron variant BA.2 in those vaccinated with three doses of BNT162b2 or CoronaVac vaccines.

“…A new variant of SARS-CoV-2 within Pango lineage B.1.1.529 was recognized in Southern Africa in November 2021 and was classified as "variant of concern" Omicron soon thereafter 1,2 . Three subvariants of Omicron were noted at the time of its first recognition, designated BA.1, BA.2 and BA.3, but the subvariant that initially spread world-wide was BA.1 3 .…”