ArticleNature medicine2022
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa.
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Article in Nature medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 446 papers.
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446citing papers in PubMed
67.2field-weighted citation impact, top 1% of its field
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Who cites it
446 citing papers in PubMed, 690 citations in OpenAlex.
- A Bivalent Omicron-BA.4/BA.5-Adapted BNT162b2 Booster in ≥12-Year-Olds.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2024Trial
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- Long-Term Wastewater Genomic Surveillance Reveals SARS-CoV-2 Variant Dynamics in Italy from 2021 to 2025.Food and environmental virology · 2026Article
- R1-32-like public antibodies acquire tolerance to SARS-CoV-2 antigenic drift through somatic hypermutation.PLoS biology · 2026Article
- SARS-CoV-2 Delta variant-specific ORF3a mutations destabilize lysosomal homeostasis to trigger lysosomal damage-mediated cell death.Communications biology · 2026Article
- Functional and structural basis of Omicron BA.3.2.1 spike.Cell reports · 2026Article
- DNA oligonucleotides block viral entry of SARS-CoV-2 Omicron variants.PLoS pathogens · 2026Article
- Structure-Guided Design of Therapeutic Antibodies Targeting SARS-CoV-2 Omicron Variants.Research square · 2026Article
- Genomic Surveillance of SARS-CoV-2 in Senegal (2020-2024): Variant Turnover, Omicron Introductions, and Interregional Spread.Influenza and other respiratory viruses · 2026Article
- A multiplexed, systems-based approach for prediction of antibody neutralization breadth for soluble human receptors.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- Profile of COVID-19 cases during four waves of the pandemic from May 2020 to March 2022 in the Haut-Ogooué region in Gabon.BMC public health · 2026Article
- CGM23 corresponds to a pan-coronavirus lipopeptide inhibitor potently inhibiting virion fusion.iScience · 2026Article
- GraphBAN-based identification of active ingredients and key gene targets in compound Chinese herbal medicines for polycystic ovary syndrome.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Structural mimics of SARS-CoV-2.Infection · 2026Review
- Self-amplifying COVID-19 mRNA vaccination induces longitudinally enhanced antibody function in a Phase 3 trial.NPJ vaccines · 2026Article
- Genome characterization of the SARS-CoV-2 omicron in Cameroon.BMC infectious diseases · 2026Article
- Genomic analysis reveals dynamics of SARS-CoV-2 during the initial phases of the COVID-19 outbreak in the Dominican Republic.Microbiology spectrum · 2026Article
- Beyond the Mutation Abyss: Revisiting SARS-CoV-2 Receptor-Binding Domain Evolution from ACE2 Binding Optimization to Immune Epitope Remodeling.Pathogens (Basel, Switzerland) · 2026Article
- Implementation of a SARS-CoV-2 genomic surveillance network as a strategy to face other health challenges in Peru.Revista peruana de medicina experimental y salud publica · 2026Article
386 more citing papers are in PubMed but not listed here.
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Authors and funding
57 authors at 20 institutions in 6 countries.
Houriiyah TegallyCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Monika MoirCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
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
Marta GiovanettiLaboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.ORCID http://orcid.org/0000-0002-5849-7326
Cathrine ScheepersNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.ORCID http://orcid.org/0000-0002-1683-0282
Eduan WilkinsonCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Kathleen SubramoneyDepartment of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
Zinhle MakatiniDepartment of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
Sikhulile MoyoBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Daniel G AmoakoNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.ORCID http://orcid.org/0000-0003-3551-3458
Cheryl BaxterCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.ORCID http://orcid.org/0000-0002-6033-7655
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.
Dikeledi KekanaNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Raquel VianaLancet Laboratories, Johannesburg, South Africa.
Jennifer GiandhariKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
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
Tongai MapongaDivision of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.ORCID http://orcid.org/0000-0002-6876-3712
Dorcas MaruapulaBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Wonderful ChogaBotswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
Mogomotsi MatshabaBotswana Presidential COVID-19 Taskforce, Gaborone, Botswana.
Mpaphi B MbulawaNational 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.
NGS-SA consortium
Yeshnee NaidooCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Sureshnee PillayKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Tomasz Janusz SankoCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.ORCID http://orcid.org/0000-0002-4154-7067
James E SanKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.ORCID http://orcid.org/0000-0002-5736-664X
Lesley ScottDepartment of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
Lavanya SinghKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Nonkululeko A MaginiKwaZulu-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, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
Graeme DorNational Priority Program of the National Health Laboratory Service, Johannesburg, South Africa.ORCID http://orcid.org/0000-0001-9036-9933
Derek TshiabuilaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Nicole WolterNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
Wolfgang PreiserDivision of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.ORCID http://orcid.org/0000-0002-0254-7910
Florette K TreurnichtDepartment of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
Marietjie VenterZoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.ORCID http://orcid.org/0000-0003-2696-824X
Georginah ChiloaneZoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Caitlyn McIntyreZoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
Aine O'TooleInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0001-8083-474X
Christopher RuisDepartment of Medicine, University of Cambridge, Cambridge, UK.
Thomas P PeacockDepartment of Infectious Disease, Imperial College London, London, UK.ORCID http://orcid.org/0000-0001-7077-2928
Cornelius RoemerBiozentrum, University of Basel, Basel, Switzerland.ORCID http://orcid.org/0000-0002-6138-6539
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
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 N 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 GlassSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.ORCID http://orcid.org/0000-0002-4275-3225
Darren P MartinWellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.
Ben JacksonInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Andrew RambautInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0003-4337-3707
Oluwakemi Laguda-AkingbaNHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa.
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.ORCID http://orcid.org/0000-0002-0243-7455
Tulio de OliveiraCentre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa. tulio@sun.ac.za.ORCID http://orcid.org/0000-0002-3027-5254
National Health Laboratory Service · ZAStellenbosch University · ZAUniversity of KwaZulu-Natal · ZAUniversity of Cape Town · ZAUniversity of Pretoria · ZAUniversity of the Witwatersrand · ZABotswana Harvard AIDS Institute Partnership · BWTemple University · USUniversity of Edinburgh · GBUniversity of the Free State · ZAHarvard University · USMinistry of Health · BWBotswana Open University · BWImperial College London · GBJohannesburg Hospital · ZALancet Laboratories · ZAUniversidade Federal de Minas Gerais · BRUniversity of Basel · CHUniversity of Bern · CHUniversity of Cambridge · GB
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
$13.3MRole of Data Streams In Informing Infection Dynamics in Africa- INFORM AfricaU54TW012041 · FIC · INSTITUTE OF HUMAN VIROLOGY · PI Alash'le G. Abimiku, Tulio de Paiva Nazareth Andrade De Oliveira · 2021 to 2026
$6.9MTraining 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
$1.6MDepartment of HealthFIC NIH HHS D43 TW009610FIC NIH HHS U54 TW012041NCIRD CDC HHS U01 IP001048NIAID NIH HHS K24 AI131924NIAID NIH HHS K24 AI131928NIAID NIH HHS U01 AI151698Wellcome TrustWellcome Trust 221003/Z/20/Z
Abstract
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.
Indexed as
COVID-19SARS-CoV-2Amino AcidsAnimalsHumansSouth AfricaSpike Glycoprotein, CoronavirusAmino AcidsSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2
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