Emergence and spread of the SARS-CoV-2 omicron (BA.1) variant across Africa: an observational study
- Type de publi. : Article dans une revue
- Date de publi. : 01/02/2025
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Auteurs :
Carlo FischerTongai Gibson MapongaAnges YadouletonNuro AbílioEmmanuel AbocePraise AdewumiPedro AfonsoJewelna AkorliSoa Fy AndriamandimbyLatifa AngaYvonne AshongMohamed Amine BeloufaAicha BensalemRichard BirtlesAnicet Luc Magloire BoumbaFreddie BwangaMike ChapondaParadzai ChibukiraR Matthew ChicoJustin ChilesheWonderful ChogaGershom ChongweAssana CisséFatoumata CisséUmberto D’alessandroXavier de LamballerieJoana de MoraisFawzi DerrarNdongo DiaYoussouf DiarraLassina DoumbiaChristian DrostenPhilippe DussartRichard EchoduAbdelmajid EloualidOusmane FayeTorsten FeldtAnna FrühaufSimani GaseitsiweAfiwa HalatokoEtuhole IipumbuPauliana-Vanessa IlougaNalia IsmaelRonan JambouSheikh JarjuAntje KampradBen KatowaJohn KayiwaLeonard King’waraOusmane KoitaVincent LacosteAdamou LagareOlfert LandtSonia Etenna Lekana-DoukiJean-Bernard Lekana-DoukiHugues LoembaTom LueddeJulius LutwamaSantou MamadouIssaka MamanBrendon ManyisaPedro MartinezJaphet MatobaLusia MhuuluAndrés Moreira-SotoSikhulile MoyoJudy MwangiNadine N’dilimabakaCharity Angella NassunaMamadou Ousmane NdiathEmmanuel NepoloRichard NjouomJalal NourlilSteven Ger NyanjomEddy Okoth OdariAlfred OkengJean Bienvenue OuobaMichael OwusuIrene Owusu DonkorKarabo Kristen PhaduRichard Odame PhillipsWolfgang PreiserPierre RoquesVurayai RuhanyaFortune SalahSourakatou SalifouAmadou Alpha SallAugustina Angelina SylverkenPaul Alain Tagnouokam-NgoupoZekiba TarnagdaFrancis Olivier TchikayaNoël TordoTafese Beyene TufaJan Felix Drexler
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Organismes :
Freie Universität Berlin = Free University of Berlin
Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
Stellenbosch University
National Health Laboratory Service [Johannesburg, South Africa]
Laboratoire des Fièvres hémorragiques virales [Cotonou, Bénin]
Instituto Nacional de Saude [Maputo, Mozambique]
MBN Clinical Laboratories [Kampala, Uganda]
Laboratoire des Fièvres hémorragiques virales [Cotonou, Bénin]
Instituto Nacional de Investigação em Saúde - National Institute for Health [Luanda, Angola]
Université du Ghana = University of Ghana
Institut Pasteur de Madagascar
Institut Pasteur du Maroc
Université du Ghana = University of Ghana
Institut Pasteur d'Algérie
Institut Pasteur d'Algérie
Gulu University
University of Salford
Université Marien-Ngouabi [Université de Brazzaville] = Marien Ngouabi University [University of Brazzaville]
Molecular Diagnostic Laboratory HDL [Pointe Noire, République Démocratique du Congo]
MBN Clinical Laboratories [Kampala, Uganda]
Makerere University [Kampala, Ouganda]
Tropical Diseases Research Centre [Zambia]
University of Zimbabwe
London School of Hygiene & Tropical Medicine [Fajara, The Gambia]
Tropical Diseases Research Centre [Zambia]
Botswana Harvard AIDS Institute Partnership
University of Botswana
Tropical Diseases Research Centre [Zambia]
Laboratoire National de Référence-Grippes [Ouagadougou, Burkina Faso]
Institut Pasteur de Guinée
London School of Hygiene & Tropical Medicine [Fajara, The Gambia]
Unité des Virus Emergents
Instituto Nacional de Investigação em Saúde - National Institute for Health [Luanda, Angola]
Institut Pasteur d'Algérie
Institut Pasteur de Dakar
Université des Sciences, des Techniques et des Technologies de Bamako
Université des Sciences, des Techniques et des Technologies de Bamako
Freie Universität Berlin = Free University of Berlin
Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
German Centre for Infection Research
Institut Pasteur de Madagascar
Gulu University
Institut Pasteur du Maroc
Institut Pasteur de Dakar
University Hospital Düsseldorf
Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]
Freie Universität Berlin = Free University of Berlin
Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
Botswana Harvard AIDS Institute Partnership
Harvard T.H. Chan School of Public Health
Institut National D'Hygiène [Lomé, Togo]
University of Namibia
Centre Pasteur du Cameroun
Instituto Nacional de Saude [Maputo, Mozambique]
Centre de Recherche Médicale et Sanitaire [Niamey, Niger]
London School of Hygiene & Tropical Medicine [Fajara, The Gambia]
Freie Universität Berlin = Free University of Berlin
Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
Macha Research Trust [Macha, Zambia]
Uganda Virus Research Institute
Ministry of Health [Kenya]
Université des Sciences, des Techniques et des Technologies de Bamako
Institut Pasteur de Madagascar
Centre de Recherche Médicale et Sanitaire [Niamey, Niger]
TIB MOLBIOL GmbH [Berlin]
Centre Interdisciplinaire de Recherches Médicales de Franceville
Centre Interdisciplinaire de Recherches Médicales de Franceville
Molecular Diagnostic Laboratory HDL [Pointe Noire, République Démocratique du Congo]
University of Ottawa [Ottawa]
University Hospital Düsseldorf
Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]
Uganda Virus Research Institute
Centre de Recherche Médicale et Sanitaire [Niamey, Niger]
Institut National D'Hygiène [Lomé, Togo]
University of Zimbabwe
Instituto Nacional de Investigação em Saúde - National Institute for Health [Luanda, Angola]
Macha Research Trust [Macha, Zambia]
University of Zambia [Lusaka]
University of Namibia
Freie Universität Berlin = Free University of Berlin
Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
Botswana Harvard AIDS Institute Partnership
University of Botswana
Harvard T.H. Chan School of Public Health
University of Pretoria [South Africa]
Stellenbosch University
Gulu University
University of Salford
Centre Interdisciplinaire de Recherches Médicales de Franceville
Uganda Virus Research Institute
London School of Hygiene & Tropical Medicine [Fajara, The Gambia]
University of Namibia
Centre Pasteur du Cameroun
Institut Pasteur du Maroc
Jomo Kenyatta University of Agriculture and Technology
Jomo Kenyatta University of Agriculture and Technology
MBN Clinical Laboratories [Kampala, Uganda]
Laboratoire National de Référence-Grippes [Ouagadougou, Burkina Faso]
Kumasi Centre for Collaborative Research in Tropical Medicine
Université du Ghana = University of Ghana
Stellenbosch University
Kumasi Centre for Collaborative Research in Tropical Medicine
Stellenbosch University
National Health Laboratory Service [Johannesburg, South Africa]
Institut Pasteur de Guinée
Institut de Biologie François JACOB
University of Zimbabwe
Institut National D'Hygiène [Lomé, Togo]
Ministère de la Santé - Ministry of Health [Cotonou, Bénin]
Institut Pasteur de Dakar
Kumasi Centre for Collaborative Research in Tropical Medicine
Kwame Nkrumah University of Science and Technology
Centre Pasteur du Cameroun
Laboratoire National de Référence-Grippes [Ouagadougou, Burkina Faso]
Molecular Diagnostic Laboratory HDL [Pointe Noire, République Démocratique du Congo]
Institut Pasteur de Guinée
University Hospital Düsseldorf
Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]
Freie Universität Berlin = Free University of Berlin
Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
German Centre for Infection Research
- Publié dans The Lancet global health le 26/10/2020
Résumé : Background: In 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. Methods: In 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 (Rt) at the country level considering the BA.1 fraction and the reported numbers of infections. Phylogeographical analyses were done in a Bayesian framework. Findings: Through 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 Rt of 2·60 (95% CI 2·46-2·71). This south-north spread, established on the basis of PCR data, was substantiated by phylogeographical reconstructions, ancestral state reconstructions, and GISAID data. PCR-based reconstructions of country-level BA.1 predominance and the availability of BA.1 genomic sequences in GISAID correlated significantly in time (p=0·0002, r=0·78). The first detections of BA.1 in high-income settings beyond Africa were predicted accurately in time by mobility-based mathematical simulations (p<0·0001). Comparing PCR-based reconstructions with mobility-based mathematical simulations suggested that SARS-CoV-2 infections in Africa were under-reported by approximately ten times. Inbound travellers infected with BA.1, departing from five continents, were identified in six African countries by early December, 2021. Interpretation: Omicron 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 Rt and the geographical spread of emerging pathogens in a cost-effective and timely manner, and can guide evidence-based, non-pharmaceutical interventions such as travel restrictions or physical distancing.
Fichiers liés :
PIIS2214109X24004194.pdf
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