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