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

dc.contributor.authorViana, Raquel
dc.contributor.authorMoyo, Sikhulile
dc.contributor.authorAmoako, Daniel G.
dc.contributor.authorTegally, Houriiyah
dc.contributor.authorScheepers, Cathrine
dc.contributor.authorAlthaus, Christian L.
dc.contributor.authorAnyaneji, Ugochukwu J.
dc.contributor.authorBester, Phillip A.
dc.contributor.authorBoni, Maciej F.
dc.contributor.authorChand, Mohammed
dc.contributor.authorChoga, Wonderful T.
dc.contributor.authorColquhoun, Rachel
dc.contributor.authorDavids, Michaela
dc.contributor.authorDeforche, Koen
dc.contributor.authorDoolabh, Deelan
dc.contributor.authorDu Plessis, Louis
dc.contributor.authorEngelbrecht, Susan
dc.contributor.authorEveratt, Josie
dc.contributor.authorGiandhari, Jennifer
dc.contributor.authorGiovanetti, Marta
dc.contributor.authorHardie, Diana
dc.contributor.authorHill, Verity
dc.contributor.authorHsiao, Nei-Yuan
dc.contributor.authorIranzadeh, Arash
dc.contributor.authorIsmail, Arshad
dc.contributor.authorJoseph, Charity
dc.contributor.authorJoseph, Rageema
dc.contributor.authorKoopile, Legodile
dc.contributor.authorPond, Sergei L. Kosakovsky
dc.contributor.authorKraemer, Moritz U.G.
dc.contributor.authorKuate-Lere, Lesego
dc.contributor.authorLaguda-Akingba, Oluwakemi
dc.contributor.authorLesetedi-Mafoko, Onalethatha
dc.contributor.authorLessells, Richard
dc.contributor.authorLockman, Shahin
dc.contributor.authorLucaci, Alexander G.
dc.contributor.authorMaharaj, Arisha
dc.contributor.authorMahlangu, Boitshoko
dc.contributor.authorMaponga, Tongai
dc.contributor.authorMahlakwane, Kamela
dc.contributor.authorMakatini, Zinhle
dc.contributor.authorMarais, Gert
dc.contributor.authorMaruapula, Dorcas
dc.contributor.authorMasupu, Kereng
dc.contributor.authorMatshaba, Mogomotsi
dc.contributor.authorMayaphi, Simnikiwe
dc.contributor.authorMbhele, Nokuzola
dc.contributor.authorMbulawa, Mpaphi B.
dc.contributor.authorMendes, Adriano
dc.contributor.authorMlisana, Koleka
dc.contributor.authorMnguni, Anele
dc.contributor.authorMohale, Thabo
dc.contributor.authorMoir, Monika
dc.contributor.authorMoruisi, Kgomotso
dc.contributor.authorMosepele, Mosepele
dc.contributor.authorMotsatsi, Gerald
dc.contributor.authorMotswaledi, Modisa S.
dc.contributor.authorMphoyakgosi, Thongbotho
dc.contributor.authorMsomi, Nokukhanya
dc.contributor.authorMwangi, Peter N.
dc.contributor.authorNaidoo, Yeshnee
dc.contributor.authorNtuli, Noxolo
dc.contributor.authorNyaga, Martin
dc.contributor.authorOlubayo, Lucier
dc.contributor.authorPillay, Sureshnee
dc.contributor.authorRadibe, Botshelo
dc.contributor.authorRamphal, Yajna
dc.contributor.authorRamphal, Upasana
dc.contributor.authorSan, James E.
dc.contributor.authorScott, Lesley
dc.contributor.authorShapiro, Roger
dc.contributor.authorSmith-Lawrence, Pamela
dc.contributor.authorStevens, Wendy
dc.contributor.authorStrydom, Amy
dc.contributor.authorSubramoney, Kathleen
dc.contributor.authorTebeila, Naume
dc.contributor.authorTshiabuila, Derek
dc.contributor.authorTsui, Joseph
dc.contributor.authorVan Wyk, Stephanie
dc.contributor.authorWeaver, Steven
dc.contributor.authorWibmer, Constantinos K.
dc.contributor.authorWilkinson, Eduan
dc.contributor.authorWolter, Nicole
dc.contributor.authorZarebski, Alexander E.
dc.contributor.authorZuze, Boitumelo
dc.contributor.authorGoedhals, Dominique
dc.contributor.authorPreise, Wolfgang
dc.contributor.authorTreurnicht, Florette
dc.contributor.authorVenter, Marietjie
dc.contributor.authorWilliamson, Carolyn
dc.contributor.authorPybus, Oliver G.
dc.contributor.authorBhiman, Jinal
dc.contributor.authorGlass, Allison
dc.contributor.authorMartin, Darren P.
dc.contributor.authorRambaut, Andrew
dc.contributor.authorGaseitsiwe, Simani
dc.contributor.authorVon Gottberg, Anne
dc.contributor.authorDe Oliveira, Tulio
dc.date.accessioned2023-11-23T13:11:00Z
dc.date.available2023-11-23T13:11:00Z
dc.date.issued2022-03-24
dc.descriptionDATA 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/).en_US
dc.descriptionCODE 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).en_US
dc.description.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.en_US
dc.description.departmentMedical Virologyen_US
dc.description.librarianam2023en_US
dc.description.sdgSDG-03:Good heatlh and well-beingen_US
dc.description.sponsorshipThe research reported in this publication was supported by the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council, with funds received from the South African Department of Science and Innovation. Sequencing activities at KRISP and CERI were supported in part by the WHO, the National Institutes of Health (NIH) (U01 AI151698) for the United World Antivirus Research Network (UWARN), and the Rockefeller Foundation (grants 2021 HTH 017 and 2020 HTH 062). C.L.A. received funding from the European Union’s Horizon 2020 research and innovation programme, project EpiPose (no. 101003688). D.P.M. was funded by the Wellcome Trust (222574/Z/21/Z). R.C. and A.R. acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z, ARTIC network) and A.R. from the European Research Council (no. 725422, ReservoirDOCS). V.H. was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant no. BB/M010996/1). A.E.Z., J.T., M.U.G.K. and O.G.P. acknowledge support from the Oxford Martin School. M.U.G.K. acknowledges support from the Rockefeller Foundation, Google.org, and the European Horizon 2020 programme MOOD (no. 874850). M.V. and the members of the Zoonotic Arbo and Respiratory Virus Program, UP was funded through the ANDEMIA G7 Global Health Concept: contributions to improvement of International Health, COVID-19 funds through the Robert Koch Institute. The genomic sequencing at UCT/NHLS is funded from the South African Medical Research Council and Department of Science and Innovation; and by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). C.W. and J.B. are funded by the EDCTP (RADIATES Consortium; RIA2020EF-3030). Sequencing activities at the NICD were supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (no. 5U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a subaward from the Bill and Melinda Gates Foundation grant no. INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (no. 221003/Z/20/Z); the South African Medical Research Council (SHIPNCD 76756); the UK Department of Health and Social Care, managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. The genomic sequencing in Botswana was supported by the Foundation for Innovative New Diagnostics and Fogarty International Center (5D43TW009610), NIH (5K24AI131924-04; 5K24AI131928-05) and support from the Botswana government through the Ministry of Health & Wellness and Presidential COVID-19 Task Force. S. Moyo. was supported in part by the Bill & Melinda Gates Foundation (036530). Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission.en_US
dc.description.urihttp://www.nature.com/natureen_US
dc.identifier.citationViana, 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.en_US
dc.identifier.issn0028-0836 (print)
dc.identifier.other1476-4687 (online)
dc.identifier.other10.1038/s41586-022-04411-y
dc.identifier.urihttp://hdl.handle.net/2263/93418
dc.language.isoenen_US
dc.publisherNature Researchen_US
dc.rights© The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License.en_US
dc.subjectInfectionsen_US
dc.subjectGauteng Province, South Africaen_US
dc.subjectSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2)en_US
dc.subjectOmicron, B.1.1.529en_US
dc.subjectSDG-03: Good health and well-beingen_US
dc.titleRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africaen_US
dc.typeArticleen_US

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