Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa-Reference-Cited by-同舟云学术

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

Published:2022-12-02 Issue:6623 Volume:378 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Fischer Carlo¹^ORCID,Maponga Tongai Gibson²^ORCID,Yadouleton Anges³^ORCID,Abílio Nuro⁴,Aboce Emmanuel⁵^ORCID,Adewumi Praise³,Afonso Pedro⁶,Akorli Jewelna⁷^ORCID,Andriamandimby Soa Fy⁸^ORCID,Anga Latifa⁹,Ashong Yvonne⁷,Beloufa Mohamed Amine¹⁰,Bensalem Aicha¹⁰,Birtles Richard¹¹¹²,Boumba Anicet Luc Magloire¹³¹⁴,Bwanga Freddie⁵¹⁵,Chaponda Mike¹⁶^ORCID,Chibukira Paradzai¹⁷,Chico R. Matthew¹⁸^ORCID,Chileshe Justin¹⁶^ORCID,Chongwe Gershom¹⁶^ORCID,Cissé Assana¹⁹,D’Alessandro Umberto²⁰^ORCID,de Lamballerie Xavier Nicolas²¹^ORCID,de Morais Joana F. M.⁶^ORCID,Derrar Fawzi¹⁰^ORCID,Dia Ndongo²²,Diarra Youssouf²³^ORCID,Doumbia Lassina²³,Drosten Christian¹²⁴^ORCID,Dussart Philippe⁸^ORCID,Echodu Richard¹¹^ORCID,Eggers Yannik²⁵²⁶,Eloualid Abdelmajid⁹,Faye Ousmane²²^ORCID,Feldt Torsten²⁵²⁶,Frühauf Anna¹,Halatoko Afiwa²⁷,Ilouga Pauliana-Vanessa²⁸^ORCID,Ismael Nalia⁴,Jambou Ronan²⁹,Jarju Sheikh²⁰^ORCID,Kamprad Antje¹^ORCID,Katowa Ben³⁰³¹,Kayiwa John³²,King’wara Leonard³³^ORCID,Koita Ousmane²³,Lacoste Vincent⁸^ORCID,Lagare Adamou²⁹,Landt Olfert³⁴^ORCID,Lekana-Douki Sonia Etenna³⁵^ORCID,Lekana-Douki Jean-Bernard³⁵^ORCID,Iipumbu Etuhole³⁶,Loemba Hugues¹⁴³⁷^ORCID,Lutwama Julius³²^ORCID,Mamadou Santou²⁹,Maman Issaka²⁷^ORCID,Manyisa Brendon¹⁷,Martinez Pedro A.⁶,Matoba Japhet³⁰³¹^ORCID,Mhuulu Lusia³⁶,Moreira-Soto Andres¹,Mwangi Judy¹¹¹²^ORCID,N´dilimabaka Nadine³⁵,Nassuna Charity Angella³²,Ndiath Mamadou Ousmane²⁰^ORCID,Nepolo Emmanuel³⁶,Njouom Richard²⁸,Nourlil Jalal⁹^ORCID,Nyanjom Steven Ger³⁸,Odari Eddy Okoth³⁸^ORCID,Okeng Alfred⁵,Ouoba Jean Bienvenue¹⁹,Owusu Michael³⁹^ORCID,Owusu Donkor Irene⁷^ORCID,Phadu Karabo Kristen²,Phillips Richard Odame³⁹^ORCID,Preiser Wolfgang²⁴⁰^ORCID,Ruhanya Vurayai¹⁷,Salah Fortune²⁷,Salifou Sourakatou⁴¹,Sall Amadou Alpha²²,Sylverken Augustina Angelina³⁹⁴²^ORCID,Tagnouokam-Ngoupo Paul Alain²⁸^ORCID,Tarnagda Zekiba¹⁹^ORCID,Tchikaya Francis Olivier¹⁴,Tufa Tafese Beyene²⁵²⁶^ORCID,Drexler Jan Felix¹²⁴^ORCID

Affiliation:

1. Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.

2. Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.

3. Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin.

4. Instituto Nacional de Saúde, Maputo, Mozambique.

5. MBN Clinical Laboratories, Kampala, Uganda.

6. Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola.

7. Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.

8. Institut Pasteur de Madagascar, Antananarivo, Madagascar.

9. Institut Pasteur du Maroc, Casablanca, Morocco.

10. Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria.

11. Gulu University Multifunctional Research Laboratories, Gulu, Uganda.

12. School of Science, Engineering and Environment, University of Salford, Salford, UK.

13. Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.

14. Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.

15. Makerere University College of Health Sciences, Kampala, Uganda.

16. Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia.

17. National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe.

18. London School of Hygiene and Tropical Medicine, London, UK.

19. Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso.

20. Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia.

21. Unité des Virus Émergents, Aix Marseille Université, Marseille, France.

22. Institut Pasteur de Dakar (IPD), Dakar, Senegal.

23. Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali.

24. German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany.

25. Hirsch Institute of Tropical Medicine, Asella, Ethiopia.

26. Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.

27. Institut National d’Hygiène, Lomé, Togo.

28. Centre Pasteur du Cameroun, Yaounde, Cameroon.

29. Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger.

30. Macha Research Trust, Choma, Zambia.

31. School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.

32. Uganda Virus Research Institute, Entebbe, Uganda.

33. National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya.

34. TiB-Molbiol GmbH, Berlin, Germany.

35. Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.

36. School of Medicine, University of Namibia, Windhoek, Namibia.

37. Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.

38. School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.

39. Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.

40. National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa.

41. Ministère de la Santé, Akpakpa, Benin.

42. Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana.

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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference46 articles.

1. World Health Organization WHO Coronavirus (COVID-19) Dashboard; https://covid19.who.int.

2. An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa

3. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

4. WHO (World Health Organization 2021) vol. 2022.

5. C. J. Gill L. Mwananyanda W. MacLeod G. Kwenda R. Pieciak L. Etter D. J. Bridges C. Chikoti S. Chirwa C. Chimoga L. Forman B. Katowa R. Lapidot J. Lungu J. Matoba G. Mwinga B. Mubemba Z. Mupila W. Muleya M. Mwenda B. Ngoma R. Nkazwe D. Nzara N. Pawlak L. Pemba N. Saasa E. Simulundu B. Yankonde D. M. Thea Sustained high prevalence of COVID-19 deaths from a systematic post-mortem study in Lusaka Zambia: one year later. medRxiv 2022.03.08.22272087 [Preprint] (2022). https://doi.org/10.1101/2022.03.08.22272087.10.1101/2022.03.08.22272087 2022.03.08.22272087

Cited by 6 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020–2022;Emerging Microbes & Infections;2023-08-22

2. Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses;Viruses;2023-02-20

3. Inspiration of SARS-CoV-2 envelope protein mutations on pathogenicity of Omicron XBB;2023-01-10

4. Health informatics and data science for pandemic preparedness;Genomic Surveillance and Pandemic Preparedness;2023

5. Surprising Omicron origins study comes under scrutiny;Nature;2022-12-06