Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
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Date
Authors
Viana, Raquel
Moyo, Sikhulile
Amoako, Daniel G.
Tegally, Houriiyah
Scheepers, Cathrine
Althaus, Christian L.
Anyaneji, Ugochukwu J.
Bester, Phillip A.
Boni, Maciej F.
Chand, Mohammed
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research
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.
Description
DATA AVAILABILITY : All SARS-CoV-2 whole-genome sequences produced by NGS-SA are deposited in the GISAID sequence database and are publicly available subject to the terms and conditions of the GISAID database. The GISAID accession numbers of sequences used in the phylogenetic analysis, including Omicron and global references, are provided in the Supplementary Table 1. Raw reads for our sequences have also been deposited at the NCBI Sequence Read Archive (SRA) (BioProject: PRJNA784038). Other raw data for this study are provided as a supplementary dataset at our GitHub repository (https://github.com/krisp-kwazulu-natal/ SARSCoV2_Omicron_Southern_Africa). The reference SARS-CoV-2 genome (MN908947.3) was downloaded from the NCBI database (https://www.ncbi.nlm.nih.gov/). Other publicly available data used in this study are as follows: NCBI SARS-CoV-2 Data Hub (https://www. ncbi.nlm.nih.gov/sars-cov-2/), Protein Data Bank coordinate set 7A94 (https://www.rcsb.org/), Nexstrain global build (https://nextstrain. org/ncov/gisaid/global), Covid-19 Re repository (https://github.com/ covid-19-Re), daily Covid-19 case numbers from the Data Science for Social Impact Research Group at the University of Pretoria (https:// github.com/dsfsi/covid19za), daily case numbers from OWID (https:// github.com/owid/covid-19-data) and the Virus Pathogen Database and Analysis Resource (ViPR) (https://www.viprbrc.org/).
CODE AVAILABILITY : All input files (such as raw data for figures, alignments or XML files), along with all resulting output files and scripts used in the present study are publicly shared at GitHub (https://github.com/krisp-kwazulu-natal/ SARSCoV2_Omicron_Southern_Africa).
CODE AVAILABILITY : All input files (such as raw data for figures, alignments or XML files), along with all resulting output files and scripts used in the present study are publicly shared at GitHub (https://github.com/krisp-kwazulu-natal/ SARSCoV2_Omicron_Southern_Africa).
Keywords
Infections, Gauteng Province, South Africa, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Omicron, B.1.1.529, SDG-03: Good health and well-being
Sustainable Development Goals
SDG-03:Good heatlh and well-being
Citation
Viana, R., Moyo, S., Amoako, D.G. et al. 2022, 'Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa', Nature, vol. 603, pp. 679-686. https://DOI.org/10.1038/s41586-022-04411-y.