ArticleNature2022
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
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In one paragraph
Article in Nature, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,162 papers, 3 of them syntheses that pooled it.
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1,162citing papers in PubMed, 3 pooled it
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What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
1,162 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Consolidating Estimates of the Incubation Period for Omicron Subvariants From the Literature and Their Comparison to the Estimate From Taiwan: A Systematic Review and Meta-Analysis, September 2024.Influenza and other respiratory viruses · 2025Pooled it
- Incidence, severity, risk factors and outcomes of SARS-CoV-2 reinfections during the Omicron period: a systematic review and meta-analysis.Journal of global health · 2025Pooled it
- Pooled it
- Broad cross-T cell immunity between emerging SARS-CoV-2 serotypes waved by spike-signature mutations.Emerging microbes & infections · 2026Article
- COVID vaccination and economic game decisions: The role of analytical thinking.Human vaccines & immunotherapeutics · 2026Article
- Impact of Digital Contact Tracing and Other Nonpharmaceutical Interventions on Pandemic Control: Microlevel, Behavior-Driven Agent-Based Model Analysis.Journal of medical Internet research · 2026Article
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- Toward a quality-managed operational architecture for wastewater surveillance of zoonotic and emerging pathogens.Applied and environmental microbiology · 2026Review
- Functional and structural basis of Omicron BA.3.2.1 spike.Cell reports · 2026Article
- Identification and computational analysis of B-cell epitopes on the hemagglutinin protein of the H3N2 influenza virus.Archives of microbiology · 2026Article
- Healthcare-facility-based SARS-CoV-2 genomic surveillance in Brazil: experience from the global action in healthcare network.Microbiology spectrum · 2026Article
- Dose-dependent effects of recombinant spike protein-based vaccination on SARS-CoV-2 evolutionary dynamics and the emergence of variants in hamster models.The Journal of general virology · 2026Article
- NTD Remodeling in the SARS-CoV-2 BA.3.2 Variant May Influence Spike Stability and Immune Escape.Pathogens (Basel, Switzerland) · 2026Article
- Six Years of COVID-19: Lessons from Epidemiology, Vaccination Campaigns, Clinical Risk Stratification, and Thromboembolic Surveillance.Vaccines · 2026Review
- Inferring variant-specific effective reproduction numbers from combined case and sequencing data.eLife · 2026Article
- Evaluating Memory B Cell Cross-Reactivity Between Ancestral and Future SARS-CoV-2 Variants-Evidence for Original Antigenic Sin.Vaccines · 2026Article
- DNA oligonucleotides block viral entry of SARS-CoV-2 Omicron variants.PLoS pathogens · 2026Article
- COVID-19 vaccination induces cross-neutralisation of sarbecoviruses related to SARS-CoV-2.NPJ vaccines · 2026Article
1,102 more citing papers are in PubMed but not listed here.
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Authors and funding
99 authors.
Raquel Viana *Lancet Laboratories, Johannesburg, South Africa.
Sikhulile Moyo *Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.ORCID http://orcid.org/0000-0003-3821-4592
Daniel G Amoako *National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.ORCID http://orcid.org/0000-0003-3551-3458
Houriiyah Tegally *KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Cathrine Scheepers *National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Christian L AlthausInstitute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.ORCID http://orcid.org/0000-0002-5230-6760
Ugochukwu J AnyanejiKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Phillip A BesterDivision of Virology, National Health Laboratory Service, Bloemfontein, South Africa.
Maciej F BoniCenter for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.ORCID http://orcid.org/0000-0002-0830-9630
Mohammed ChandDiagnofirm Medical Laboratories, Gaborone, Botswana.
Wonderful T ChogaHarvard T.H. Chan School of Public Health, Boston, MA, USA.
Rachel ColquhounInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Michaela DavidsZoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Koen DeforcheEmweb, Herent, Belgium.ORCID http://orcid.org/0000-0003-3898-9494
Deelan DoolabhDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Louis du PlessisDepartment of Zoology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-0352-6289
Susan EngelbrechtDivision of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.ORCID http://orcid.org/0000-0002-1318-5994
Josie EverattNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.ORCID http://orcid.org/0000-0002-0373-2093
Jennifer GiandhariKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Marta GiovanettiLaboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.ORCID http://orcid.org/0000-0002-5849-7326
Diana HardieDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Verity HillInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Nei-Yuan HsiaoDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID http://orcid.org/0000-0003-4926-6216
Arash IranzadehDivision of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID http://orcid.org/0000-0003-4413-2569
Arshad IsmailNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.ORCID http://orcid.org/0000-0003-4672-5915
Charity JosephDiagnofirm Medical Laboratories, Gaborone, Botswana.
Rageema JosephDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Legodile KoopileBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Sergei L Kosakovsky PondInstitute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0003-4817-4029
Moritz U G KraemerDepartment of Zoology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-8838-7147
Lesego Kuate-LereHealth Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
Oluwakemi Laguda-AkingbaNHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa.
Onalethatha Lesetedi-MafokoPublic Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana.
Richard J LessellsKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.ORCID http://orcid.org/0000-0003-0926-710X
Shahin LockmanBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Alexander G LucaciInstitute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.
Arisha MaharajKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Boitshoko MahlanguNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.ORCID http://orcid.org/0000-0002-2129-527X
Tongai MapongaDivision of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
Kamela MahlakwaneDivision of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
Zinhle MakatiniDepartment of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
Gert MaraisDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Dorcas MaruapulaBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Kereng MasupuBotswana Presidential COVID-19 Taskforce, Gaborone, Botswana.
Mogomotsi MatshabaBotswana Presidential COVID-19 Taskforce, Gaborone, Botswana.
Simnikiwe MayaphiDepartment of Medical Virology, University of Pretoria, Pretoria, South Africa.
Nokuzola MbheleDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Mpaphi B MbulawaNational Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
Adriano MendesZoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Koleka MlisanaNational Health Laboratory Service (NHLS), Johannesburg, South Africa.
Anele MnguniNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Thabo MohaleNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Monika MoirCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Kgomotso MoruisiHealth Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
Mosepele MosepeleBotswana Presidential COVID-19 Taskforce, Gaborone, Botswana.
Gerald MotsatsiNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Modisa S MotswalediBotswana Presidential COVID-19 Taskforce, Gaborone, Botswana.
Thongbotho MphoyakgosiNational Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
Nokukhanya MsomiDiscipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa.
Peter N MwangiDivision of Virology, University of the Free State, Bloemfontein, South Africa.
Yeshnee NaidooKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Noxolo NtuliNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Martin NyagaDivision of Virology, University of the Free State, Bloemfontein, South Africa.
Lucier OlubayoWellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.
Sureshnee PillayKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Botshelo RadibeBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Yajna RamphalKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Upasana RamphalKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.ORCID http://orcid.org/0000-0002-2441-3868
James E SanKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Lesley ScottDepartment of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.
Roger ShapiroBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Lavanya SinghKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Pamela Smith-LawrenceHealth Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
Wendy StevensDepartment of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.
Amy StrydomZoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Kathleen SubramoneyDepartment of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
Naume TebeilaNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Derek TshiabuilaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Joseph TsuiDepartment of Zoology, University of Oxford, Oxford, UK.
Stephanie van WykCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Steven WeaverInstitute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-6931-7191
Constantinos K WibmerNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Eduan WilkinsonCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Nicole WolterNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Alexander E ZarebskiDepartment of Zoology, University of Oxford, Oxford, UK.
Boitumelo ZuzeBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Dominique GoedhalsDivision of Virology, University of the Free State, Bloemfontein, South Africa.
Wolfgang PreiserDivision of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.ORCID http://orcid.org/0000-0002-0254-7910
Florette TreurnichtDepartment of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
Marietje VenterZoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Carolyn WilliamsonDivision of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID http://orcid.org/0000-0003-0125-1226
Oliver G PybusDepartment of Zoology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-8797-2667
Jinal BhimanNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.ORCID http://orcid.org/0000-0001-6354-4003
Allison GlassLancet Laboratories, Johannesburg, South Africa.
Darren P MartinWellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.
Andrew RambautInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0003-4337-3707
Simani GaseitsiweBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Anne von GottbergNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Tulio de OliveiraKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. tulio@sun.ac.za.ORCID http://orcid.org/0000-0002-3027-5254
Funding
Research on the Epidemiology,Prevention,Vaccine Effectiveness and Treatment of Influenza and Other Respiratory Viruses in South Africa.09U01IP001048 · IP · NATIONAL HEALTH LABORATORY SERVICE · PI COHEN, CHERYL · 2016 to 2020
$19.9MUniversity of Washington Arboviral Research Network (UWARN)U01AI151698 · NIAID · UNIVERSITY OF WASHINGTON · PI Michael Gale, PETER MACGARR RABINOWITZ · 2020 to 2026
$13.3MTraining in HIV Genomics, Treatment, and Cure Research in BotswanaD43TW009610 · FIC · THE BOTSWANA HARVARD HEALTH PARTNERSHIP · PI SHAHIN LOCKMAN, Joseph Moeketsi Makhema · 2013 to 2026
$4.4MMentoring in Patient-Oriented HIV Research in the Era of Universal ARTK24AI131928 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI SHAHIN LOCKMAN · 2017 to 2026
$1.9MExpansion of research and mentoring to improve birth outcomes and treatment outcomes among HIV-affected children in BotswanaK24AI131924 · NIAID · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI Roger L Shapiro · 2018 to 2026
$1.6MACL HHS U01IP001048European Research CouncilFIC NIH HHS D43 TW009610NCIRD CDC HHS U01 IP001048NIAID NIH HHS K24 AI131924NIAID NIH HHS K24 AI131928NIAID NIH HHS U01 AI151698Wellcome TrustWellcome Trust 203135/Z/16/ZWellcome Trust 206298/Z/17/ZWellcome Trust 221003/Z/20/ZWellcome Trust 222574/Z/21/ZWellcome Trust 222754
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, respectively
Indexed as
Immune EvasionAntibodies, NeutralizingBotswanaCOVID-19HumansModels, MolecularMutationPhylogenyRecombination, GeneticSARS-CoV-2South AfricaSpike Glycoprotein, CoronavirusAntibodies, NeutralizingSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.