Carlo Fischer
Emergence and spread of the SARS-CoV-2 omicron (BA.1) variant across Africa: an observational study.
Fischer, Carlo; Maponga, Tongai Gibson; Yadouleton, Anges; Abílio, Nuro; Aboce, Emmanuel; Adewumi, Praise; Afonso, Pedro; Akorli, Jewelna; Andriamandimby, Soa Fy; Anga, Latifa; Ashong, Yvonne; Beloufa, Mohamed Amine; Bensalem, Aicha; Birtles, Richard; Boumba, Anicet Luc Magloire; Bwanga, Freddie; Chaponda, Mike; Chibukira, Paradzai; Chico, R Matthew; Chileshe, Justin; Choga, Wonderful; Chongwe, Gershom; Cissé, Assana; Cissé, Fatoumata; D'Alessandro, Umberto; de Lamballerie, Xavier; de Morais, Joana F M; Derrar, Fawzi; Dia, Ndongo; Diarra, Youssouf; Doumbia, Lassina; Drosten, Christian; Dussart, Philippe; Echodu, Richard; Eloualid, Abdelmajid; Faye, Ousmane; Feldt, Torsten; Frühauf, Anna; Gaseitsiwe, Simani; Halatoko, Afiwa; Iipumbu, Etuhole; Ilouga, Pauliana-Vanessa; Ismael, Nalia; Jambou, Ronan; Jarju, Sheikh; Kamprad, Antje; Katowa, Ben; Kayiwa, John; King'wara, Leonard; Koita, Ousmane; Lacoste, Vincent; Lagare, Adamou; Landt, Olfert; Lekana-Douki, Sonia Etenna; Lekana-Douki, Jean-Be...
Authors
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
Prof Richard Birtles R.J.Birtles@salford.ac.uk
Professor
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
Abstract
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. 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 ) at the country level considering the BA.1 fraction and the reported numbers of infections. Phylogeographical analyses were done in a Bayesian framework. 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 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. 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 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. Bill & Melinda Gates Foundation. For the French, Portugese and Spanish translations of the abstract see Supplementary Materials section. [Abstract copyright: Copyright © 2025 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.]
Journal Article Type | Article |
---|---|
Acceptance Date | Sep 23, 2024 |
Publication Date | Feb 14, 2025 |
Deposit Date | Mar 14, 2025 |
Publicly Available Date | Mar 14, 2025 |
Journal | The Lancet. Global health |
Electronic ISSN | 2214-109X |
Publisher | Elsevier |
Peer Reviewed | Peer Reviewed |
Volume | 13 |
Issue | 2 |
Pages | e256-e267 |
DOI | https://doi.org/10.1016/S2214-109X%2824%2900419-4 |
Keywords | Humans, SARS-CoV-2 - genetics, Africa - epidemiology, COVID-19 - epidemiology - virology |
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