Ineffectiveness of international travel restrictions to contain spread of the SARS-CoV-2 Omicron BA.1 variant: a continent-wide laboratory-based observational study from Africa
Authors: Fischer Carlo , Maponga Tongai Gibson , Yadouleton Anges , Abilio Nuro , Aboce Emmanuel , Adewumi Praise , Afonso Pedro , Akorli Jewelna , Andriamandimby Soa Fy , Anga Latifa , Ashong Yvonne , Beloufa Mohamed Amine , Bensalem Aicha , Birtles Richard , Magloire Boumba Anicet Luc , Bwanga Freddie , Chaponda Mike , Chibukira Paradzai , Chico R Matthew , Chileshe Justin , Choga Wonderful , Chongwe Gershom , Cisse Assana , Cisse 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 , Luedde Tom , Eloualid Abdelmajid , Faye Ousmane , Feldt Torsten , Fruehauf Anna , Gaseitsiwe Simani , Halatoko Afiwa , Ilouga Pauliana-Vanessa , Ismael Nalia , Jambou Ronan , Jarju Sheikh , Kamprad Antje , Katowa Ben , Kayiwa John , Kingwara Leonard , Koita Ousmane , Lacoste Vincent , Lagare Adamou , Landt Olfert , Lekana-Douki Sonia Etenna , Lekana-Douki Jean-Bernard , Iipumbu Etuhole , Loemba Hugues , Lutwama Julius , Mamadou Santou , Maman Issaka , Manyisa Brendon , Martinez Pedro A. , Matoba Japhet , Mhuulu Lusia , Moreira-Soto Andres , Moyo Sikhulile , Mwangi Judy , Ndilimabaka Nadine , Nassuna Charity Angella , Ndiath Mamadou Ousmane , Nepolo Emmanuel , Njouom Richard , Nourlil Jalal , Nyanjom Steven Ger , Odari Eddy Okoth , Okeng Alfred , Ouoba Jean Bienvenue , Owusu Michael , Donkor Irene Owusu , Phadu Karabo Kristen , Phillips Richard Odame , Preiser Wolfgang , Roques Pierre , Ruhanya Vurayai , Salah Fortune , Salifou Sourakatou , Sall Amadou Alpha , Sylverken Augustina Angelina , Tagnouokam-Ngoupo Paul Alain , Tarnagda Zekiba , Tchikaya Francis Olivier , Tordo Noel , Tufa Tafese Beyene , Drexler Jan Felix 
Published: March 2024

Background: In mid-November 2021, the SARS-CoV-2 Omicron BA.1 variant was detected in Southern Africa, prompting international travel restrictions of unclear effectiveness that exacted a substantial economic toll. Methods: Amidst the BA.1 wave, we tested 13,294 COVID-19 patients in 24 African countries between mid-2021 to early 2022 for BA.1 and Delta variants using real-time reverse transcription-PCR tests. The diagnostic precision of the assays was evaluated by high-throughput sequencing in four countries. The observed BA.1 spread was compared to mobility-based mathematical simulations. Findings: By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a median Rt of 2.4 up to 30 days before BA.1 became predominant. PCR-based South-North spread was in agreement with phylogeographic reconstructions relying on 939 SARS-CoV-2 genomes from GISAID. PCR-based reconstructions of country-level BA.1 predominance correlated significantly in time with the emergence of BA.1 genomic sequences on GISAID (p=0.0035, cor=0.70). First BA.1 detections in affluent settings beyond Africa were predicted adequately in time by mobility-based mathematical simulations (p<0.0001). BA.1-infected inbound travelers departing from five continents were identified in five Western countries and one Northern African country by late November/early December 2021, highlighting fast global BA.1 spread aided by international travel. Interpretation: Unilateral travel bans were poorly effective because by the time they came into effect, BA.1 was already widespread in Africa and beyond. PCR-based variant typing combined with mobility-based mathematical modelling can inform rapidly and cost-efficiently on Rt, spread to inform non-pharmaceutical interventions.