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Lancet Glob Health
. 2025 Feb;13(2):e256-e267.
doi: 10.1016/S2214-109X(24)00419-4. Emergence and spread of the SARS-CoV-2 omicron (BA.1) variant across Africa: an observational study
Carlo Fischer 1 , Tongai Gibson Maponga 2 , Anges Yadouleton 3 , Nuro Abílio 4 , Emmanuel Aboce 5 , Praise Adewumi 3 , Pedro Afonso 6 , Jewelna Akorli 7 , Soa Fy Andriamandimby 8 , Latifa Anga 9 , Yvonne Ashong 7 , Mohamed Amine Beloufa 10 , Aicha Bensalem 10 , Richard Birtles 11 , Anicet Luc Magloire Boumba 12 , Freddie Bwanga 13 , Mike Chaponda 14 , Paradzai Chibukira 15 , R Matthew Chico 16 , Justin Chileshe 14 , Wonderful Choga 17 , Gershom Chongwe 14 , Assana Cissé 18 , Fatoumata Cissé 19 , Umberto D'Alessandro 20 , Xavier de Lamballerie 21 , Joana F M de Morais 6 , Fawzi Derrar 10 , Ndongo Dia 22 , Youssouf Diarra 23 , Lassina Doumbia 23 , Christian Drosten 24 , Philippe Dussart 8 , Richard Echodu 25 , Abdelmajid Eloualid 9 , Ousmane Faye 22 , Torsten Feldt 26 , Anna Frühauf 1 , Simani Gaseitsiwe 27 , Afiwa Halatoko 28 , Etuhole Iipumbu 29 , Pauliana-Vanessa Ilouga 30 , Nalia Ismael 4 , Ronan Jambou 31 , Sheikh Jarju 20 , Antje Kamprad 1 , Ben Katowa 32 , John Kayiwa 33 , Leonard King'wara 34 , Ousmane Koita 23 , Vincent Lacoste 8 , Adamou Lagare 31 , Olfert Landt 35 , Sonia Etenna Lekana-Douki 36 , Jean-Bernard Lekana-Douki 36 , Hugues Loemba 37 , Tom Luedde 26 , Julius Lutwama 33 , Santou Mamadou 31 , Issaka Maman 28 , Brendon Manyisa 15 , Pedro A Martinez 6 , Japhet Matoba 32 , Lusia Mhuulu 29 , Andrés Moreira-Soto 1 , Sikhulile Moyo 38 , Judy Mwangi 11 , Nadine N'dilimabaka 36 , Charity Angella Nassuna 33 , Mamadou Ousmane Ndiath 20 , Emmanuel Nepolo 29 , Richard Njouom 30 , Jalal Nourlil 9 , Steven Ger Nyanjom 39 , Eddy Okoth Odari 39 , Alfred Okeng 5 , Jean Bienvenue Ouoba 18 , Michael Owusu 40 , Irene Owusu Donkor 7 , Karabo Kristen Phadu 41 , Richard Odame Phillips 40 , Wolfgang Preiser 2 , Pierre Roques 42 , Vurayai Ruhanya 15 , Fortune Salah 28 , Sourakatou Salifou 43 , Amadou Alpha Sall 22 , Augustina Angelina Sylverken 44 , Paul Alain Tagnouokam-Ngoupo 30 , Zekiba Tarnagda 18 , Francis Olivier Tchikaya 45 , Noël Tordo 19 , Tafese Beyene Tufa 26 , Jan Felix Drexler 46
Affiliations
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.
. 2025 Feb;13(2):e256-e267.
doi: 10.1016/S2214-109X(24)00419-4. Emergence and spread of the SARS-CoV-2 omicron (BA.1) variant across Africa: an observational study
Carlo Fischer 1 , Tongai Gibson Maponga 2 , Anges Yadouleton 3 , Nuro Abílio 4 , Emmanuel Aboce 5 , Praise Adewumi 3 , Pedro Afonso 6 , Jewelna Akorli 7 , Soa Fy Andriamandimby 8 , Latifa Anga 9 , Yvonne Ashong 7 , Mohamed Amine Beloufa 10 , Aicha Bensalem 10 , Richard Birtles 11 , Anicet Luc Magloire Boumba 12 , Freddie Bwanga 13 , Mike Chaponda 14 , Paradzai Chibukira 15 , R Matthew Chico 16 , Justin Chileshe 14 , Wonderful Choga 17 , Gershom Chongwe 14 , Assana Cissé 18 , Fatoumata Cissé 19 , Umberto D'Alessandro 20 , Xavier de Lamballerie 21 , Joana F M de Morais 6 , Fawzi Derrar 10 , Ndongo Dia 22 , Youssouf Diarra 23 , Lassina Doumbia 23 , Christian Drosten 24 , Philippe Dussart 8 , Richard Echodu 25 , Abdelmajid Eloualid 9 , Ousmane Faye 22 , Torsten Feldt 26 , Anna Frühauf 1 , Simani Gaseitsiwe 27 , Afiwa Halatoko 28 , Etuhole Iipumbu 29 , Pauliana-Vanessa Ilouga 30 , Nalia Ismael 4 , Ronan Jambou 31 , Sheikh Jarju 20 , Antje Kamprad 1 , Ben Katowa 32 , John Kayiwa 33 , Leonard King'wara 34 , Ousmane Koita 23 , Vincent Lacoste 8 , Adamou Lagare 31 , Olfert Landt 35 , Sonia Etenna Lekana-Douki 36 , Jean-Bernard Lekana-Douki 36 , Hugues Loemba 37 , Tom Luedde 26 , Julius Lutwama 33 , Santou Mamadou 31 , Issaka Maman 28 , Brendon Manyisa 15 , Pedro A Martinez 6 , Japhet Matoba 32 , Lusia Mhuulu 29 , Andrés Moreira-Soto 1 , Sikhulile Moyo 38 , Judy Mwangi 11 , Nadine N'dilimabaka 36 , Charity Angella Nassuna 33 , Mamadou Ousmane Ndiath 20 , Emmanuel Nepolo 29 , Richard Njouom 30 , Jalal Nourlil 9 , Steven Ger Nyanjom 39 , Eddy Okoth Odari 39 , Alfred Okeng 5 , Jean Bienvenue Ouoba 18 , Michael Owusu 40 , Irene Owusu Donkor 7 , Karabo Kristen Phadu 41 , Richard Odame Phillips 40 , Wolfgang Preiser 2 , Pierre Roques 42 , Vurayai Ruhanya 15 , Fortune Salah 28 , Sourakatou Salifou 43 , Amadou Alpha Sall 22 , Augustina Angelina Sylverken 44 , Paul Alain Tagnouokam-Ngoupo 30 , Zekiba Tarnagda 18 , Francis Olivier Tchikaya 45 , Noël Tordo 19 , Tafese Beyene Tufa 26 , Jan Felix Drexler 46
Affiliations
- PMID: 39890226
- DOI: 10.1016/S2214-109X(24)00419-4
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.