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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...

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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

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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