1. Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa
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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, Richard Birtles, Anicet Luc Magloire Boumba, Freddie Bwanga, Mike Chaponda, Paradzai Chibukira, R. Matthew Chico, Justin Chileshe, Gershom Chongwe, Assana Cissé, Umberto D’Alessandro, Xavier Nicolas de Lamballerie, Joana F. M. de Morais, Fawzi Derrar, Ndongo Dia, Youssouf Diarra, Lassina Doumbia, Christian Drosten, Philippe Dussart, Richard Echodu, Yannik Eggers, Abdelmajid Eloualid, Ousmane Faye, Torsten Feldt, Anna Frühauf, Afiwa Halatoko, 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, Etuhole Iipumbu, Hugues Loemba, Julius Lutwama, Santou Mamadou, Issaka Maman, Brendon Manyisa, Pedro A. Martinez, Japhet Matoba, Lusia Mhuulu, Andres Moreira-Soto, 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, Vurayai Ruhanya, Fortune Salah, Sourakatou Salifou, Amadou Alpha Sall, Augustina Angelina Sylverken, Paul Alain Tagnouokam-Ngoupo, Zekiba Tarnagda, Francis Olivier Tchikaya, Tafese Beyene Tufa, and Jan Felix Drexler
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Multidisciplinary ,SARS-CoV-2 ,Humans ,COVID-19 ,Real-Time Polymerase Chain Reaction ,Africa, Southern - Abstract
The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.
- Published
- 2022
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