Carlo Fischer, Tongai Gibson Maponga, Anges Yadouleton, Nuro Abílio, Emmanuel Aboce, Praise Adewumi, Pedro Afonso, Jewelna Akorli, Soa Fy Andriamandimby, Latifa Anga, Yvonne Ashong, Mohamed Amine Beloufa, Aicha Bensalem, Richard Birtles, Anicet Luc Magloire Boumba, Freddie Bwanga, Mike Chaponda, Paradzai Chibukira, R Matthew Chico, Justin Chileshe, Wonderful Choga, Gershom Chongwe, Assana Cissé, Fatoumata Cissé, Umberto D'Alessandro, Xavier de Lamballerie, Joana F M de Morais, Fawzi Derrar, Ndongo Dia, Youssouf Diarra, Lassina Doumbia, Christian Drosten, Philippe Dussart, Richard Echodu, Abdelmajid Eloualid, Ousmane Faye, Torsten Feldt, Anna Frühauf, Simani Gaseitsiwe, Afiwa Halatoko, Etuhole Iipumbu, Pauliana-Vanessa Ilouga, Nalia Ismael, Ronan Jambou, Sheikh Jarju, Antje Kamprad, Ben Katowa, John Kayiwa, Leonard King'wara, Ousmane Koita, Vincent Lacoste, Adamou Lagare, Olfert Landt, Sonia Etenna Lekana-Douki, Jean-Bernard Lekana-Douki, Hugues Loemba, Tom Luedde, Julius Lutwama, Santou Mamadou, Issaka Maman, Brendon Manyisa, Pedro A Martinez, Japhet Matoba, Lusia Mhuulu, Andrés Moreira-Soto, Sikhulile Moyo, Judy Mwangi, Nadine N'dilimabaka, Charity Angella Nassuna, Mamadou Ousmane Ndiath, Emmanuel Nepolo, Richard Njouom, Jalal Nourlil, Steven Ger Nyanjom, Eddy Okoth Odari, Alfred Okeng, Jean Bienvenue Ouoba, Michael Owusu, Irene Owusu Donkor, Karabo Kristen Phadu, Richard Odame Phillips, Wolfgang Preiser, Pierre Roques, Vurayai Ruhanya, Fortune Salah, Sourakatou Salifou, Amadou Alpha Sall, Augustina Angelina Sylverken, Paul Alain Tagnouokam-Ngoupo, Zekiba Tarnagda, Francis Olivier Tchikaya, Noël Tordo, Tafese Beyene Tufa, Jan Felix Drexler
{"title":"Emergence and spread of the SARS-CoV-2 omicron (BA.1) variant across Africa: an observational study.","authors":"Carlo Fischer, Tongai Gibson Maponga, Anges Yadouleton, Nuro Abílio, Emmanuel Aboce, Praise Adewumi, Pedro Afonso, Jewelna Akorli, Soa Fy Andriamandimby, Latifa Anga, Yvonne Ashong, Mohamed Amine Beloufa, Aicha Bensalem, Richard Birtles, Anicet Luc Magloire Boumba, Freddie Bwanga, Mike Chaponda, Paradzai Chibukira, R Matthew Chico, Justin Chileshe, Wonderful Choga, Gershom Chongwe, Assana Cissé, Fatoumata Cissé, Umberto D'Alessandro, Xavier de Lamballerie, Joana F M de Morais, Fawzi Derrar, Ndongo Dia, Youssouf Diarra, Lassina Doumbia, Christian Drosten, Philippe Dussart, Richard Echodu, Abdelmajid Eloualid, Ousmane Faye, Torsten Feldt, Anna Frühauf, Simani Gaseitsiwe, Afiwa Halatoko, Etuhole Iipumbu, Pauliana-Vanessa Ilouga, Nalia Ismael, Ronan Jambou, Sheikh Jarju, Antje Kamprad, Ben Katowa, John Kayiwa, Leonard King'wara, Ousmane Koita, Vincent Lacoste, Adamou Lagare, Olfert Landt, Sonia Etenna Lekana-Douki, Jean-Bernard Lekana-Douki, Hugues Loemba, Tom Luedde, Julius Lutwama, Santou Mamadou, Issaka Maman, Brendon Manyisa, Pedro A Martinez, Japhet Matoba, Lusia Mhuulu, Andrés Moreira-Soto, Sikhulile Moyo, Judy Mwangi, Nadine N'dilimabaka, Charity Angella Nassuna, Mamadou Ousmane Ndiath, Emmanuel Nepolo, Richard Njouom, Jalal Nourlil, Steven Ger Nyanjom, Eddy Okoth Odari, Alfred Okeng, Jean Bienvenue Ouoba, Michael Owusu, Irene Owusu Donkor, Karabo Kristen Phadu, Richard Odame Phillips, Wolfgang Preiser, Pierre Roques, Vurayai Ruhanya, Fortune Salah, Sourakatou Salifou, Amadou Alpha Sall, Augustina Angelina Sylverken, Paul Alain Tagnouokam-Ngoupo, Zekiba Tarnagda, Francis Olivier Tchikaya, Noël Tordo, Tafese Beyene Tufa, Jan Felix Drexler","doi":"10.1016/S2214-109X(24)00419-4","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Methods: </strong>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 (R<sub>t</sub>) at the country level considering the BA.1 fraction and the reported numbers of infections. Phylogeographical analyses were done in a Bayesian framework.</p><p><strong>Findings: </strong>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 R<sub>t</sub> 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.</p><p><strong>Interpretation: </strong>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 R<sub>t</sub> 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.</p><p><strong>Funding: </strong>Bill & Melinda Gates Foundation.</p><p><strong>Translations: </strong>For the French, Portugese and Spanish translations of the abstract see Supplementary Materials section.</p>","PeriodicalId":48783,"journal":{"name":"Lancet Global Health","volume":"13 2","pages":"e256-e267"},"PeriodicalIF":19.9000,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Lancet Global Health","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1016/S2214-109X(24)00419-4","RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH","Score":null,"Total":0}
引用次数: 0
Abstract
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.
Funding: Bill & Melinda Gates Foundation.
Translations: For the French, Portugese and Spanish translations of the abstract see Supplementary Materials section.
期刊介绍：
The Lancet Global Health is an online publication that releases monthly open access (subscription-free) issues.Each issue includes original research, commentary, and correspondence.In addition to this, the publication also provides regular blog posts.
The main focus of The Lancet Global Health is on disadvantaged populations, which can include both entire economic regions and marginalized groups within prosperous nations.The publication prefers to cover topics related to reproductive, maternal, neonatal, child, and adolescent health; infectious diseases (including neglected tropical diseases); non-communicable diseases; mental health; the global health workforce; health systems; surgery; and health policy.
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