A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa-Reference-Cited by-同舟云学术

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

Published:2021-10-22 Issue:6566 Volume:374 Page:423-431
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Wilkinson Eduan¹²^ORCID,Giovanetti Marta³⁴^ORCID,Tegally Houriiyah¹^ORCID,San James E.¹^ORCID,Lessells Richard¹^ORCID,Cuadros Diego⁵,Martin Darren P.⁶⁷,Rasmussen David A.⁸⁹^ORCID,Zekri Abdel-Rahman N.¹⁰^ORCID,Sangare Abdoul K.¹¹,Ouedraogo Abdoul-Salam¹²,Sesay Abdul K.¹³,Priscilla Abechi¹⁴,Kemi Adedotun-Sulaiman¹⁴,Olubusuyi Adewunmi M.¹⁵^ORCID,Oluwapelumi Adeyemi O. O.¹⁶^ORCID,Hammami Adnène¹⁷,Amuri Adrienne A.¹⁸¹⁹^ORCID,Sayed Ahmad²⁰,Ouma Ahmed E. O.²¹^ORCID,Elargoubi Aida²²²³,Ajayi Nnennaya A.²⁴^ORCID,Victoria Ajogbasile F.¹⁴,Kazeem Akano¹⁴,George Akpede²⁵,Trotter Alexander J.²⁶,Yahaya Ali A.²⁷^ORCID,Keita Alpha K.²⁸²⁹,Diallo Amadou³⁰^ORCID,Kone Amadou³¹,Souissi Amal³²^ORCID,Chtourou Amel¹⁷,Gutierrez Ana V.²⁶^ORCID,Page Andrew J.²⁶^ORCID,Vinze Anika³³,Iranzadeh Arash⁶⁷,Lambisia Arnold³⁴^ORCID,Ismail Arshad³⁵^ORCID,Rosemary Audu³⁶^ORCID,Sylverken Augustina³⁷^ORCID,Femi Ayoade¹⁴^ORCID,Ibrahimi Azeddine³⁸,Marycelin Baba³⁹,Oderinde Bamidele S.³⁹,Bolajoko Bankole¹⁴,Dhaala Beatrice⁴⁰,Herring Belinda L.²⁷,Njanpop-Lafourcade Berthe-Marie²⁷,Kleinhans Bronwyn⁴¹^ORCID,McInnis Bronwyn¹⁰,Tegomoh Bryan⁴²,Brook Cara⁴³⁴⁴^ORCID,Pratt Catherine B.⁴⁵^ORCID,Scheepers Cathrine³⁵⁴⁶^ORCID,Akoua-Koffi Chantal G.⁴⁷,Agoti Charles N.³⁴⁴⁸,Peyrefitte Christophe³⁰,Daubenberger Claudia⁴⁹^ORCID,Morang’a Collins M.⁵⁰^ORCID,Nokes D. James³⁴⁵¹^ORCID,Amoako Daniel G.³⁵^ORCID,Bugembe Daniel L.⁴⁰^ORCID,Park Danny³³^ORCID,Baker David²⁶,Doolabh Deelan⁷,Ssemwanga Deogratius⁴⁰⁵²^ORCID,Tshiabuila Derek¹^ORCID,Bassirou Diarra³⁰^ORCID,Amuzu Dominic S. Y.⁵⁰^ORCID,Goedhals Dominique⁵³,Omuoyo Donwilliams O.³⁴,Maruapula Dorcas⁵⁴,Foster-Nyarko Ebenezer²⁶,Lusamaki Eddy K.¹⁸¹⁹^ORCID,Simulundu Edgar⁵⁵^ORCID,Ong’era Edidah M.³⁴,Ngabana Edith N.¹⁸¹⁹,Shumba Edwin⁵⁶,El Fahime Elmostafa⁵⁷^ORCID,Lokilo Emmanuel¹⁸^ORCID,Mukantwari Enatha⁵⁸^ORCID,Philomena Eromon¹⁴,Belarbi Essia⁵⁹^ORCID,Simon-Loriere Etienne⁶⁰^ORCID,Anoh Etilé A.⁴⁷^ORCID,Leendertz Fabian⁵⁹^ORCID,Ajili Faida⁶¹,Enoch Fakayode O.⁶²,Wasfi Fares⁶³^ORCID,Abdelmoula Fatma³²⁶⁴,Mosha Fausta S.²⁷,Takawira Faustinos T.⁶⁵,Derrar Fawzi⁶⁶^ORCID,Bouzid Feriel³²^ORCID,Onikepe Folarin¹⁴^ORCID,Adeola Fowotade⁶⁷,Muyembe Francisca M.¹⁸¹⁹,Tanser Frank⁶⁸⁶⁹⁷⁰^ORCID,Dratibi Fred A.²⁷,Mbunsu Gabriel K.¹⁹,Thilliez Gaetan²⁶^ORCID,Kay Gemma L.²⁶^ORCID,Githinji George³⁴⁷¹,van Zyl Gert⁴¹⁷²^ORCID,Awandare Gordon A.⁵⁰,Schubert Grit⁵⁹,Maphalala Gugu P.⁷³,Ranaivoson Hafaliana C.⁴⁴^ORCID,Lemriss Hajar⁷⁴^ORCID,Anise Happi¹⁴,Abe Haruka⁷⁵,Karray Hela H.¹⁷^ORCID,Nansumba Hellen⁷⁶,Elgahzaly Hesham A.⁷⁷,Gumbo Hlanai⁶⁵,Smeti Ibtihel³²,Ayed Ikhlas B.³²,Odia Ikponmwosa²⁵,Ben Boubaker Ilhem Boutiba⁷⁸⁷⁹,Gaaloul Imed²²,Gazy Inbal⁸⁰,Mudau Innocent⁷,Ssewanyana Isaac⁷⁶,Konstantinus Iyaloo⁸¹,Lekana-Douk Jean B.⁸²,Makangara Jean-Claude C.¹⁸¹⁹^ORCID,Tamfum Jean-Jacques M.¹⁸¹⁹,Heraud Jean-Michel³⁰⁴⁴^ORCID,Shaffer Jeffrey G.⁸³^ORCID,Giandhari Jennifer¹^ORCID,Li Jingjing⁸⁴^ORCID,Yasuda Jiro⁷⁵^ORCID,Mends Joana Q.⁸⁵^ORCID,Kiconco Jocelyn⁵²,Morobe John M.³⁴^ORCID,Gyapong John O.⁸⁵^ORCID,Okolie Johnson C.¹⁴,Kayiwa John T.⁴⁰,Edwards Johnathan A.⁶⁸⁸⁶^ORCID,Gyamfi Jones⁸⁵^ORCID,Farah Jouali⁸⁷,Nakaseegu Joweria⁵²,Ngoi Joyce M.⁵⁰,Namulondo Joyce⁵²,Andeko Julia C.⁸²,Lutwama Julius J.⁴⁰^ORCID,O’Grady Justin²⁶,Siddle Katherine³³^ORCID,Adeyemi Kayode T.¹⁴,Tumedi Kefentse A.⁸⁸^ORCID,Said Khadija M.³⁴^ORCID,Hae-Young Kim⁸⁹^ORCID,Duedu Kwabena O.⁸⁵^ORCID,Belyamani Lahcen³⁸,Fki-Berrajah Lamia¹⁷,Singh Lavanya¹^ORCID,Martins Leonardo de O.²⁶^ORCID,Tyers Lynn⁷^ORCID,Ramuth Magalutcheemee⁹⁰^ORCID,Mastouri Maha²²²³^ORCID,Aouni Mahjoub²²,el Hefnawi Mahmoud⁹¹^ORCID,Matsheka Maitshwarelo I.⁸⁸^ORCID,Kebabonye Malebogo⁹²,Diop Mamadou³⁰,Turki Manel³²,Paye Marietou³³,Nyaga Martin M.⁹³,Mareka Mathabo⁹⁴,Damaris Matoke-Muhia⁹⁵^ORCID,Mburu Maureen W.³⁴,Mpina Maximillian⁴⁹⁹⁶⁹⁷^ORCID,Nwando Mba⁹⁸,Owusu Michael⁹⁹,Wiley Michael R.⁴⁵^ORCID,Youtchou Mirabeau T.¹⁰⁰,Ayekaba Mitoha O.⁹⁶,Abouelhoda Mohamed¹⁰¹¹⁰²,Seadawy Mohamed G.¹⁰³,Khalifa Mohamed K.²⁰^ORCID,Sekhele Mooko⁹⁴,Ouadghiri Mouna³⁸^ORCID,Diagne Moussa M.³⁰,Mwenda Mulenga¹⁰⁴^ORCID,Allam Mushal³⁵^ORCID,Phan My V. T.⁴⁰^ORCID,Abid Nabil⁷⁹¹⁰⁵^ORCID,Touil Nadia¹⁰⁶,Rujeni Nadine¹⁰⁷¹⁰⁸,Kharrat Najla³²^ORCID,Ismael Nalia¹⁰⁹,Dia Ndongo³⁰,Mabunda Nedio¹⁰⁹,Hsiao Nei-yuan⁷¹¹⁰^ORCID,Silochi Nelson B.⁹⁶^ORCID,Nsenga Ngoy²⁷,Gumede Nicksy²⁷,Mulder Nicola¹¹¹^ORCID,Ndodo Nnaemeka⁹⁸,Razanajatovo Norosoa H⁴⁴,Iguosadolo Nosamiefan¹⁴,Judith Oguzie¹⁴^ORCID,Kingsley Ojide C.¹¹²,Sylvanus Okogbenin²⁵,Peter Okokhere²⁵,Femi Oladiji¹¹³,Idowu Olawoye¹⁴,Testimony Olumade¹⁴,Chukwuma Omoruyi E.⁶⁷,Ogah Onwe E.¹¹⁴,Onwuamah Chika K.³⁶¹¹⁵^ORCID,Cyril Oshomah²⁵^ORCID,Faye Ousmane³⁰^ORCID,Tomori Oyewale¹⁴^ORCID,Ondoa Pascale⁵⁶,Combe Patrice¹¹⁶,Semanda Patrick⁷⁶^ORCID,Oluniyi Paul E.¹⁴^ORCID,Arnaldo Paulo¹⁰⁹^ORCID,Quashie Peter K.⁵⁰^ORCID,Dussart Philippe⁴⁴^ORCID,Bester Phillip A.⁵³,Mbala Placide K.¹⁸¹⁹,Ayivor-Djanie Reuben⁸⁵^ORCID,Njouom Richard¹¹⁷,Phillips Richard O.¹¹⁸^ORCID,Gorman Richmond¹¹⁸,Kingsley Robert A.²⁶,Carr Rosina A. A.⁸⁵,El Kabbaj Saâd¹¹⁹,Gargouri Saba¹⁷,Masmoudi Saber³²,Sankhe Safietou³⁰^ORCID,Lawal Salako B.³⁶,Kassim Samar⁷⁷^ORCID,Trabelsi Sameh¹²⁰,Metha Samar³³,Kammoun Sami¹²¹,Lemriss Sanaâ¹¹⁹^ORCID,Agwa Sara H. A.⁷⁷^ORCID,Calvignac-Spencer Sébastien⁵⁹^ORCID,Schaffner Stephen F.³³^ORCID,Doumbia Seydou³¹^ORCID,Mandanda Sheila M.¹⁸¹⁹,Aryeetey Sherihane¹²²,Ahmed Shymaa S.¹²²^ORCID,Elhamoumi Siham³³,Andriamandimby Soafy⁴⁴,Tope Sobajo¹⁴,Lekana-Douki Sonia⁸²,Prosolek Sophie²⁶^ORCID,Ouangraoua Soumeya¹²³¹²⁴^ORCID,Mundeke Steve A.¹⁸¹⁹,Rudder Steven²⁶,Panji Sumir¹¹¹^ORCID,Pillay Sureshnee¹^ORCID,Engelbrecht Susan⁴¹⁷²^ORCID,Nabadda Susan⁷⁶,Behillil Sylvie¹²⁵^ORCID,Budiaki Sylvie L.⁹⁴,van der Werf Sylvie¹²⁵^ORCID,Mashe Tapfumanei⁶⁵,Aanniz Tarik³⁸,Mohale Thabo³⁵^ORCID,Le-Viet Thanh²⁶^ORCID,Schindler Tobias⁴⁹⁹⁶^ORCID,Anyaneji Ugochukwu J.¹^ORCID,Chinedu Ugwu¹⁴^ORCID,Ramphal Upasana¹⁶⁹¹²⁶^ORCID,Jessica Uwanibe¹⁴,George Uwem¹⁴^ORCID,Fonseca Vagner¹⁴¹²⁷^ORCID,Enouf Vincent¹²⁵^ORCID,Gorova Vivianne¹²⁸¹²⁹,Roshdy Wael H.¹²²^ORCID,Ampofo William K.⁵⁰,Preiser Wolfgang⁴¹⁷²^ORCID,Choga Wonderful T.⁵⁴¹³⁰,Bediako Yaw⁵⁰^ORCID,Naidoo Yeshnee¹^ORCID,Butera Yvan¹⁰⁷¹³¹¹³²,de Laurent Zaydah R.³⁴^ORCID,Sall Amadou A.³⁰,Rebai Ahmed³²,von Gottberg Anne³⁵¹³³^ORCID,Kouriba Bourema¹²^ORCID,Williamson Carolyn⁷⁶⁹¹¹⁰^ORCID,Bridges Daniel J.¹⁰⁴^ORCID,Chikwe Ihekweazu⁹⁸,Bhiman Jinal N.³⁵¹³³^ORCID,Mine Madisa¹³⁴,Cotten Matthew⁴⁰¹³⁵^ORCID,Moyo Sikhulile⁵⁴¹³⁶^ORCID,Gaseitsiwe Simani⁵⁴¹³⁶,Saasa Ngonda⁵⁵^ORCID,Sabeti Pardis C.³³^ORCID,Kaleebu Pontiano⁴⁰,Tebeje Yenew K.²¹,Tessema Sofonias K.²¹,Happi Christian¹⁴,Nkengasong John²¹,de Oliveira Tulio¹²⁶⁹¹³⁷

Affiliation:

1. KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.

2. Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.

3. Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.

4. Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.

5. Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA.

6. Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa.

7. Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.

8. Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.

9. Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.

10. Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt.

11. Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali.

12. Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso.

13. MRCG at LSHTM Genomics Lab, Fajara, Gambia.

14. African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria.

15. Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria.

16. Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria.

17. CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia.

18. Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo.

19. Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo.

20. Genomics Research Program, Children’s Cancer Hospital, Cairo, Egypt.

21. Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia.

22. Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia.

23. Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia.

24. Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.

25. Irrua Specialist Teaching Hospital, Irrua, Nigeria.

26. Quadram Institute Bioscience, Norwich, UK.

27. World Health Organization, Africa Region, Brazzaville Congo.

28. Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea.

29. TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France.

30. Virology Department, Institut Pasteur de Dakar, Dakar, Senegal.

31. Mali-University Clinical Research Center (UCRC), Bamako, Mali.

32. Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.

33. Broad Insitute of Harvard and MIT, Cambridge, MA, USA.

34. KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya.

35. National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.

36. The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria

37. Institute of Virology, Charité – Universitätsmedizin, Berlin, Germany.

38. Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco.

39. Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria.

40. MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.

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

42. The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon.

43. Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.

44. Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.

45. University of Nebraska Medical Center (UNMC), Omaha, NE, USA.

46. Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.

47. CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire.

48. School of Public Health, Pwani University, Kilifi, Kenya.

49. Swiss Tropical and Public Health Institute, Basel, Switzerland.

50. West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana.

51. School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK.

52. Uganda Virus Research Institute, Entebbe, Uganda.

53. Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa.

54. Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.

55. University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia.

56. African Society for Laboratory Medicine, Addis Ababa, Ethiopia.

57. Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco.

58. Rwanda National Reference Laboratory, Kigali, Rwanda.

59. Robert Koch-Institute, Berlin, Germany.

60. G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France.

61. Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia.

62. Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria.

63. Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia.

64. Faculty of Pharmacy of Monastir, Monastir, Tunisia.

65. National Microbiology Reference Laboratory, Harare, Zimbabwe.

66. National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria.

67. Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria.

68. Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK.

69. Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.

70. Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa.

71. Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.

72. National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa.

73. Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini.

74. Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco.

75. Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.

76. Central Public Health Laboratories (CPHL), Kampala, Uganda.

77. Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt.

78. Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia.

79. Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia.

80. Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel.

81. Namibia Institute of Pathology, Windhoek, Namibia.

82. Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon.

83. Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.

84. Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA.

85. UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana.

86. Rollins School of Public Health, Emory University, Atlanta, GA, USA.

87. Anoual Laboratory, Casablanca, Morocco.

88. Botswana Institute for Technology Research and Innovation, Gaborone, Botswana.

89. New York University Grossman School of Medicine, New York City, NY, USA.

90. Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius.

91. Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt.

92. Ministry of Health and Wellness, Gaborone, Botswana.

93. Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.

94. National Reference Laboratory Lesotho, Maseru, Lesotho.

95. Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya.

96. Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea.

97. Ifakara Health Institute, Dar-es-Salaam, Tanzania.

98. Nigeria Centre for Disease Control, Abuja, Nigeria.

99. Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.

100. Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria.

101. Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt.

102. King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia.

103. Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt.

104. PATH, Lusaka, Zambia.

105. Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia.

106. Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco.

107. Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda.

108. School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.

109. Instituto Nacional de Saude (INS), Maputo, Mozambique.

110. National Health Laboratory Service (NHLS), Cape Town, South Africa.

111. Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa.

112. Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.

113. Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria.

114. Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.

115. Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria.

116. Mayotte Hospital Center, Mayotte, France.

117. Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon.

118. Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.

119. Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco.

120. Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia.

121. CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia.

122. Central Public Health Laboratories (CPHL), Cairo, Egypt.

123. Centre MURAZ, Ouagadougou, Burkina Faso.

124. National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso.

125. National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France.

126. Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa.

127. Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil.

128. World Health Organization, WHO Lesotho, Maseru, Lesotho.

129. Med24 Medical Centre, Ruwa, Zimbabwe.

130. Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa.

131. Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.

132. Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium.

133. School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa.

134. National Health Laboratory, Gaborone, Botswana.

135. MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.

136. Harvard T.H. Chan School of Public Health, Boston, MA, USA.

137. Department of Global Health, University of Washington, Seattle, WA, USA.

Abstract

SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference41 articles.

1. A novel coronavirus outbreak of global health concern

2. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

3. Seroprevalence of anti–SARS-CoV-2 IgG antibodies in Kenyan blood donors

4. Covid-19 deaths in Africa: prospective systematic postmortem surveillance study

5. The first and second waves of the COVID-19 pandemic in Africa: a cross-sectional study

Cited by 152 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. Cellular immune response to SARS-CoV-2 and clinical presentation in individuals exposed to endemic malaria;Cell Reports;2024-08

2. The nuts and bolts of recombination in the generation of SARS-CoV-2 variants; from XA to XBB;Letters in Applied Microbiology;2024-07-30

3. An amplicon-based sequencing approach for Usutu virus characterization;Virology Journal;2024-07-23

4. Understanding the Transmission Dynamics of the Chikungunya Virus in Africa;Pathogens;2024-07-22

5. SARS-CoV-2 genomic surveillance of migrants arriving to Europe through the Mediterranean routes;Journal of Global Health;2024-07-05