Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa-Reference-Cited by-同舟云学术

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

Published:2022-01-07 Issue:7902 Volume:603 Page:679-686
ISSN:0028-0836
Container-title:Nature
language:en
Short-container-title:Nature

Author:

Viana Raquel,Moyo Sikhulile^ORCID,Amoako Daniel G.^ORCID,Tegally Houriiyah,Scheepers Cathrine,Althaus Christian L.^ORCID,Anyaneji Ugochukwu J.,Bester Phillip A.,Boni Maciej F.^ORCID,Chand Mohammed,Choga Wonderful T.,Colquhoun Rachel,Davids Michaela,Deforche Koen^ORCID,Doolabh Deelan,du Plessis Louis^ORCID,Engelbrecht Susan^ORCID,Everatt Josie^ORCID,Giandhari Jennifer,Giovanetti Marta^ORCID,Hardie Diana,Hill Verity,Hsiao Nei-Yuan^ORCID,Iranzadeh Arash^ORCID,Ismail Arshad^ORCID,Joseph Charity,Joseph Rageema,Koopile Legodile,Kosakovsky Pond Sergei L.^ORCID,Kraemer Moritz U. G.^ORCID,Kuate-Lere Lesego,Laguda-Akingba Oluwakemi,Lesetedi-Mafoko Onalethatha,Lessells Richard J.^ORCID,Lockman Shahin,Lucaci Alexander G.,Maharaj Arisha,Mahlangu Boitshoko^ORCID,Maponga Tongai,Mahlakwane Kamela,Makatini Zinhle,Marais Gert,Maruapula Dorcas,Masupu Kereng,Matshaba Mogomotsi,Mayaphi Simnikiwe,Mbhele Nokuzola,Mbulawa Mpaphi B.,Mendes Adriano,Mlisana Koleka,Mnguni Anele,Mohale Thabo,Moir Monika,Moruisi Kgomotso,Mosepele Mosepele,Motsatsi Gerald,Motswaledi Modisa S.,Mphoyakgosi Thongbotho,Msomi Nokukhanya,Mwangi Peter N.,Naidoo Yeshnee,Ntuli Noxolo,Nyaga Martin,Olubayo Lucier,Pillay Sureshnee,Radibe Botshelo,Ramphal Yajna,Ramphal Upasana^ORCID,San James E.,Scott Lesley,Shapiro Roger,Singh Lavanya,Smith-Lawrence Pamela,Stevens Wendy,Strydom Amy,Subramoney Kathleen,Tebeila Naume,Tshiabuila Derek,Tsui Joseph,van Wyk Stephanie,Weaver Steven^ORCID,Wibmer Constantinos K.,Wilkinson Eduan,Wolter Nicole,Zarebski Alexander E.,Zuze Boitumelo,Goedhals Dominique,Preiser Wolfgang^ORCID,Treurnicht Florette,Venter Marietje,Williamson Carolyn^ORCID,Pybus Oliver G.^ORCID,Bhiman Jinal^ORCID,Glass Allison,Martin Darren P.,Rambaut Andrew^ORCID,Gaseitsiwe Simani,von Gottberg Anne,de Oliveira Tulio^ORCID

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.

Publisher

Springer Science and Business Media LLC

Subject

Multidisciplinary

Link

https://www.nature.com/articles/s41586-022-04411-y.pdf

Reference83 articles.

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2. Tegally, H. et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 592, 438–443 (2021).

3. Tegally, H. et al. Rapid replacement of the Beta variant by the Delta variant in South Africa. Preprint at medRxiv https://doi.org/10.1101/2021.09.23.21264018 (2021).

4. Martin, D. P. et al. Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function. Preprint at bioRxiv https://doi.org/10.1101/2022.01.14.476382 (2022).

5. Faria, N. R. et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 372, 815–821 (2021).

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