Emergence and spread of the SARS-CoV-2 omicron (BA.1) variant across Africa: an observational study
Carlo Fischer, Tongai Maponga, Anges Yadouléton, Nuro Abílio, Emmanuel Aboce, Praise Adewumi, Pedro Afonso, Jewelna Akorli, Soa Fy Andriamandimby, Latifa Anga, Yvonne Ashong, Mohamed Amine Beloufa, Aïcha Bensalem, Richard J. Birtles, Anicet Luc Magloire Boumba, Freddie Bwanga, Mike Chaponda, Paradzai Chibukira, R Matthew Chico, Justin Chileshe, Wonderful T. Choga, Gershom Chongwe, Assana Cissé, Fatoumata Cissé, Umberto D’Alessandro, Xavier de Lamballerie, Joana 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, Nália Ismael, Ronan Jambou, Sheikh Jarju, Antje Kamprad, Ben Katowa, John Kayiwa, Leonard Kingwara, Ousmane Koita, Vincent Lacoste, Adamou Lagaré, Olfert Landt, Sonia Etenna Lekana-Douki, Jean Bernard Lékana-Douki, Hugues Loemba, Tom Luedde, Julius J. Lutwama, Santou Mamadou, Issaka Maman, Brendon Manyisa, Pedro Martı́nez, 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, Zékiba Tarnagda, Francis Olivier Tchikaya, Noël Tordo, Tafese Beyene Tufa, Jan Felix Drexler
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: ) at the country level considering the BA.1 fraction and the reported numbers of infections. Phylogeographical analyses were done in a Bayesian framework. FINDINGS: 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: 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.