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

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Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa
Science ( IF 44.7 ) Pub Date : 2022-12-01 , DOI: 10.1126/science.add8737
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,

12} , Anicet Luc Magloire Boumba _{13,

14} , Freddie Bwanga _{5,

15} , Mike Chaponda ₁₆ , Paradzai Chibukira ₁₇ , R Matthew Chico ₁₈ , Justin Chileshe ₁₆ , Gershom Chongwe ₁₆ , Assana Cissé ₁₉ , Umberto D'Alessandro ₂₀ , Xavier Nicolas de Lamballerie ₂₁ , Joana F M de Morais ₆ , Fawzi Derrar ₁₀ , Ndongo Dia ₂₂ , Youssouf Diarra ₂₃ , Lassina Doumbia ₂₃ , Christian Drosten _{1,

24} , Philippe Dussart ₈ , Richard Echodu ₁₁ , Yannik Eggers _{25,

26} , Abdelmajid Eloualid ₉ , Ousmane Faye ₂₂ , Torsten Feldt _{25,

26} , Anna Frühauf ₁ , Afiwa Halatoko ₂₇ , Pauliana-Vanessa Ilouga ₂₈ , Nalia Ismael ₄ , Ronan Jambou ₂₉ , Sheikh Jarju ₂₀ , Antje Kamprad ₁ , Ben Katowa _{30,

31} , John Kayiwa ₃₂ , Leonard King'wara ₃₃ , Ousmane Koita ₂₃ , Vincent Lacoste ₈ , Adamou Lagare ₂₉ , Olfert Landt ₃₄ , Sonia Etenna Lekana-Douki ₃₅ , Jean-Bernard Lekana-Douki ₃₅ , Etuhole Iipumbu ₃₆ , Hugues Loemba _{14,

37} , Julius Lutwama ₃₂ , Santou Mamadou ₂₉ , Issaka Maman ₂₇ , Brendon Manyisa ₁₇ , Pedro A Martinez ₆ , Japhet Matoba _{30,

31} , Lusia Mhuulu ₃₆ , Andres Moreira-Soto ₁ , Judy Mwangi _{11,

12} , Nadine N Dilimabaka ₃₅ , Charity Angella Nassuna ₃₂ , Mamadou Ousmane Ndiath ₂₀ , Emmanuel Nepolo ₃₆ , Richard Njouom ₂₈ , Jalal Nourlil ₉ , Steven Ger Nyanjom ₃₈ , Eddy Okoth Odari ₃₈ , Alfred Okeng ₅ , Jean Bienvenue Ouoba ₁₉ , Michael Owusu ₃₉ , Irene Owusu Donkor ₇ , Karabo Kristen Phadu ₂ , Richard Odame Phillips ₃₉ , Wolfgang Preiser _{2,

40} , Vurayai Ruhanya ₁₇ , Fortune Salah ₂₇ , Sourakatou Salifou ₄₁ , Amadou Alpha Sall ₂₂ , Augustina Angelina Sylverken _{39,

42} , Paul Alain Tagnouokam-Ngoupo ₂₈ , Zekiba Tarnagda ₁₉ , Francis Olivier Tchikaya ₁₄ , Tafese Beyene Tufa _{25,

26} , Jan Felix Drexler _{1,

24}

Affiliation

Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.
Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.
Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin.
Instituto Nacional de Saúde, Maputo, Mozambique.
MBN Clinical Laboratories, Kampala, Uganda.
Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola.
Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
Institut Pasteur de Madagascar, Antananarivo, Madagascar.
Institut Pasteur du Maroc, Casablanca, Morocco.
Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria.
Gulu University Multifunctional Research Laboratories, Gulu, Uganda.
School of Science, Engineering and Environment, University of Salford, Salford, UK.
Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.
Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.
Makerere University College of Health Sciences, Kampala, Uganda.
Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia.
National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe.
London School of Hygiene and Tropical Medicine, London, UK.
Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso.
Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia.
Unité des Virus Émergents, Aix Marseille Université, Marseille, France.
Institut Pasteur de Dakar (IPD), Dakar, Senegal.
Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali.
German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany.
Hirsch Institute of Tropical Medicine, Asella, Ethiopia.
Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
Institut National d'Hygiène, Lomé, Togo.
Centre Pasteur du Cameroun, Yaounde, Cameroon.
Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger.
Macha Research Trust, Choma, Zambia.
School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.
Uganda Virus Research Institute, Entebbe, Uganda.
National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya.
TiB-Molbiol GmbH, Berlin, Germany.
Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.
School of Medicine, University of Namibia, Windhoek, Namibia.
Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.
National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa.
Ministère de la Santé, Akpakpa, Benin.
Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana.

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.

中文翻译：

SARS-CoV-2 Omicron 变体在非洲逐渐出现，随后呈指数级传播

SARS-CoV-2 Omicron 变体 (BA.1) 于 2021 年 11 月中旬在南部非洲首次被发现，其地理和进化起源仍然未知。我们通过实时 RT-PCR 对 2021 年中至 2022 年初从 22 个非洲国家抽样的 13,097 名 COVID-19 患者进行了 BA.1 检测。到 2021 年 11 月至 12 月，BA.1 已沿南北梯度取代了所有非洲次区域的 Delta 变体，Rt 峰值为 4.1。聚合酶链反应和近乎完整的基因组测序数据显示，到 2021 年 8 月，遗传多样性的 Omicron 祖先已经在非洲各地存在。改变病毒嗜性、复制和免疫逃逸的突变逐渐在刺突基因中积累。因此，在 Omicron 主导传播之前几个月，Omicron 的祖先就出现在几个非洲国家。

更新日期：2022-12-01

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