Observational studyThe Lancet. Global health2025
Emergence and spread of the SARS-CoV-2 omicron (BA.1) variant across Africa: an observational study.
Abstract readMulticenter StudyObservational Study
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Observational study in The Lancet. Global health, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6citing papers in PubMed
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6 citing papers in PubMed.
- Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations.PLoS computational biology · 2026Article
- Strengthening microbial genomics capacity in Africa for epidemic preparedness: key lessons from the AFROSCREEN programme.Journal of global health · 2026Article
- Genomic surveillance and phylo-evolutionary analysis of SARS-CoV-2 variants in Osun state, Nigeria during the second wave of COVID-19 pandemic.BMC medical genomics · 2025Article
- Seasonal trends and molecular evolution of SARS-CoV-2 in acute respiratory illness patients during the fifth year of COVID-19, Thailand.Scientific reports · 2025Article
- A longitudinal study examining determinants of essential health services during the COVID-19 pandemic in regional referral hospitals across Uganda.Scientific reports · 2025Observational
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Authors and funding
94 authors.
Carlo FischerInstitute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
Tongai Gibson MapongaDivision of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa; National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa.
Anges YadouletonLaboratoire dés Fievres Hemorragiques Virales de Cotonou, Akpakpa, Benin.
Nuro AbílioInstituto Nacional de Saúde, Maputo, Mozambique.
Emmanuel AboceMBN Clinical Laboratories, Kampala, Uganda.
Praise AdewumiLaboratoire dés Fievres Hemorragiques Virales de Cotonou, Akpakpa, Benin.
Pedro AfonsoInstituto Nacional de Investigação em Saúde (INIS), Luanda, Angola.
Jewelna AkorliNoguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
Soa Fy AndriamandimbyInstitut Pasteur de Madagascar, Antananarivo, Madagascar.
Latifa AngaMedical Virology and BSL-3 Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
Yvonne AshongNoguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
Mohamed Amine BeloufaInstitut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria.
Aicha BensalemInstitut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria.
Richard BirtlesGulu University Multifunctional Laboratories, Gulu, Uganda; School of Science, Engineering and Environment, University of Salford, Salford, UK.
Anicet Luc Magloire BoumbaMarien Ngouabi University, Pointe-Noire, Republic of the Congo; Molecular Diagnostic Laboratory HDL, Pointe-Noire, Republic of the Congo.
Freddie BwangaMBN Clinical Laboratories, Kampala, Uganda; Makerere University College of Health Sciences, Kampala, Uganda.
Mike ChapondaTropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia.
Paradzai ChibukiraFaculty of Medicine and Health Sciences, National Virology Laboratory, University of Zimbabwe, Avondale, Zimbabwe.
R Matthew ChicoLondon School of Hygiene & Tropical Medicine, London, UK.
Justin ChilesheTropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia.
Wonderful ChogaBotswana Harvard AIDS Institute Partnership Gaborone, Botswana; Department of Medical Laboratory Sciences, School of Allied Health Professions, University of Botswana, Gaborone, Botswana.
Gershom ChongweTropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia.
Assana CisséLaboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso.
Fatoumata CisséInstitut Pasteur de Guinée, Conakry, Guinea.
Umberto D'AlessandroMedical Research Council Unit at London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
Xavier de LamballerieAix Marseille Université-Inserm-IRD, Unité des Virus Émergents, Marseille, France.
Joana F M de MoraisInstituto Nacional de Investigação em Saúde (INIS), Luanda, Angola.
Fawzi DerrarInstitut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria.
Ndongo DiaInstitut Pasteur de Dakar (IPD), Dakar, Senegal.
Youssouf DiarraUniversité des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali.
Lassina DoumbiaUniversité des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali.
Christian DrostenInstitute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; German Centre for Infection Research (DZIF), associated Partner Charité - Universitätsmedizin Berlin, Berlin, Germany.
Philippe DussartInstitut Pasteur de Madagascar, Antananarivo, Madagascar.
Richard EchoduGulu University Multifunctional Laboratories, Gulu, Uganda.
Abdelmajid EloualidMedical Virology and BSL-3 Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
Ousmane FayeInstitut Pasteur de Dakar (IPD), Dakar, Senegal.
Torsten FeldtHirsch Institute of Tropical Medicine, Asella, Ethiopia; Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
Anna FrühaufInstitute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
Simani GaseitsiweBotswana Harvard AIDS Institute Partnership Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA.
Afiwa HalatokoInstitut National d'Hygiène, Lomé, Togo.
Etuhole IipumbuSchool of Medicine, University of Namibia, Windhoek, Namibia.
Pauliana-Vanessa IlougaCentre Pasteur du Cameroun, Yaounde, Cameroon.
Nalia IsmaelInstituto Nacional de Saúde, Maputo, Mozambique.
Ronan JambouCentre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger.
Sheikh JarjuMedical Research Council Unit at London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
Antje KampradInstitute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
Ben KatowaMacha Research Trust, Choma, Zambia; School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.
John KayiwaUganda Virus Research Institute, Entebbe, Uganda.
Leonard King'waraMinistry of Health, National Public Health Reference Laboratory, Nairobi, Kenya.
Ousmane KoitaUniversité des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali.
Vincent LacosteInstitut Pasteur de Madagascar, Antananarivo, Madagascar.
Adamou LagareCentre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger.
Olfert LandtTIB-Molbiol Syntheselabor, Berlin, Germany.
Sonia Etenna Lekana-DoukiCentre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.
Jean-Bernard Lekana-DoukiCentre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.
Hugues LoembaMolecular Diagnostic Laboratory HDL, Pointe-Noire, Republic of the Congo; Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
Tom LueddeHirsch Institute of Tropical Medicine, Asella, Ethiopia; Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
Julius LutwamaUganda Virus Research Institute, Entebbe, Uganda.
Santou MamadouCentre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger.
Issaka MamanInstitut National d'Hygiène, Lomé, Togo.
Brendon ManyisaFaculty of Medicine and Health Sciences, National Virology Laboratory, University of Zimbabwe, Avondale, Zimbabwe.
Pedro A MartinezInstituto Nacional de Investigação em Saúde (INIS), Luanda, Angola.
Japhet MatobaMacha Research Trust, Choma, Zambia; School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.
Lusia MhuuluSchool of Medicine, University of Namibia, Windhoek, Namibia.
Andrés Moreira-SotoInstitute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
Sikhulile MoyoBotswana Harvard AIDS Institute Partnership Gaborone, Botswana; Department of Medical Laboratory Sciences, School of Allied Health Professions, University of Botswana, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA; School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
Judy MwangiGulu University Multifunctional Laboratories, Gulu, Uganda; School of Science, Engineering and Environment, University of Salford, Salford, UK.
Nadine N'dilimabakaCentre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.
Charity Angella NassunaUganda Virus Research Institute, Entebbe, Uganda.
Mamadou Ousmane NdiathMedical Research Council Unit at London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
Emmanuel NepoloSchool of Medicine, University of Namibia, Windhoek, Namibia.
Richard NjouomCentre Pasteur du Cameroun, Yaounde, Cameroon.
Jalal NourlilMedical Virology and BSL-3 Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
Steven Ger NyanjomSchool of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
Eddy Okoth OdariSchool of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
Alfred OkengMBN Clinical Laboratories, Kampala, Uganda.
Jean Bienvenue OuobaLaboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso.
Michael OwusuKumasi Centre for Collaborative Research in Tropical Medicine (KCCR), KNUST, Kumasi, Ghana.
Irene Owusu DonkorNoguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
Karabo Kristen PhaduDivision of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.
Richard Odame PhillipsKumasi Centre for Collaborative Research in Tropical Medicine (KCCR), KNUST, Kumasi, Ghana.
Wolfgang PreiserDivision of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa; National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa.
Pierre RoquesInstitut Pasteur de Guinée, Conakry, Guinea; Commissariat à l'Energie Atomique, Institut de Biologie François Jacob, Fontenay-aux-Roses, France.
Vurayai RuhanyaFaculty of Medicine and Health Sciences, National Virology Laboratory, University of Zimbabwe, Avondale, Zimbabwe.
Fortune SalahInstitut National d'Hygiène, Lomé, Togo.
Sourakatou SalifouMinistère de la Santé, Akpakpa, Benin.
Amadou Alpha SallInstitut Pasteur de Dakar (IPD), Dakar, Senegal.
Augustina Angelina SylverkenKumasi Centre for Collaborative Research in Tropical Medicine (KCCR), KNUST, Kumasi, Ghana; Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana.
Paul Alain Tagnouokam-NgoupoCentre Pasteur du Cameroun, Yaounde, Cameroon.
Zekiba TarnagdaLaboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso.
Francis Olivier TchikayaMolecular Diagnostic Laboratory HDL, Pointe-Noire, Republic of the Congo.
Noël TordoInstitut Pasteur de Guinée, Conakry, Guinea.
Tafese Beyene TufaHirsch Institute of Tropical Medicine, Asella, Ethiopia; Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
Jan Felix DrexlerInstitute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany; German Centre for Infection Research (DZIF), associated Partner Charité - Universitätsmedizin Berlin, Berlin, Germany. Electronic address: felix.drexler@charite.de.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn mid-November, 2021, the SARS-CoV-2 omicron variant (B.1.1.529; BA.1 sublineage) was detected in southern Africa, prompting international travel restrictions. We aimed to investigate the spread of omicron BA.1 in Africa.
methodsIn this observational study, samples from patients infected with SARS-CoV-2 from 27 laboratories in 24 African countries, collected between June 1, 2021 and April 14, 2022, were tested for omicron BA.1 and delta (B.1.617.2) variants using real-time RT-PCR. Samples that tested positive for BA.1 by RT-PCR and were collected before estimated BA.1 emergence according to epidemiological properties were excluded from downstream analyses. The diagnostic precision of the assays was evaluated by high-throughput sequencing of samples from four countries. The observed spread of BA.1 was compared with mobility-based mathematical simulations and entries for SARS-CoV-2 in the Global Initiative on Sharing All Influenza Data (GISAID) genomic database. We estimated the effective reproduction number (R
findingsThrough testing of 13 294 samples from patients infected with SARS-CoV-2, we established that, by November-December, 2021, omicron BA.1 had replaced the delta variant of SARS-CoV-2 in all African subregions, following a south-north gradient, with a median R
interpretationOmicron BA.1 was widespread in Africa when travel bans were implemented, limiting their effectiveness. Combined with genomic surveillance and mobility-based mathematical modelling, PCR-based strategies can inform R
fundingBill & Melinda Gates Foundation. TRANSLATIONS: For the French, Portugese and Spanish translations of the abstract see Supplementary Materials section.
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