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RETRACTED: Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa

2022; American Association for the Advancement of Science; Volume: 378; Issue: 6623 Linguagem: Inglês

10.1126/science.add8737

1095-9203

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, Gershom Chongwe, Assana Cissé, Umberto D’Alessandro, Xavier de Lamballerie, Joana 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, 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, Etuhole Iipumbu, Hugues Loemba, Julius J. Lutwama, Santou Mamadou, Issaka Maman, Brendon Manyisa, Pedro A. Martinez, Japhet Matoba, Lusia Mhuulu, Andrés 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, Zékiba Tarnagda, Francis Olivier Tchikaya, Tafese Beyene Tufa, Jan Felix Drexler,

Viral Infections and Outbreaks Research

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.