학술논문

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Document Type
Academic Journal
Author
Viana R; Lancet Laboratories, Johannesburg, South Africa.; Moyo S; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.; Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.; Amoako DG; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Tegally H; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Scheepers C; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; Althaus CL; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.; Anyaneji UJ; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Bester PA; Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa.; Division of Virology, University of the Free State, Bloemfontein, South Africa.; Boni MF; Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.; Chand M; Diagnofirm Medical Laboratories, Gaborone, Botswana.; Choga WT; Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Colquhoun R; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.; Davids M; Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.; Deforche K; Emweb, Herent, Belgium.; Doolabh D; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; du Plessis L; Department of Zoology, University of Oxford, Oxford, UK.; Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland.; Engelbrecht S; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.; Everatt J; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Giandhari J; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Giovanetti M; Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.; Hardie D; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.; Hill V; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.; Hsiao NY; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.; Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.; Iranzadeh A; Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Ismail A; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Joseph C; Diagnofirm Medical Laboratories, Gaborone, Botswana.; Joseph R; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Koopile L; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.; Kosakovsky Pond SL; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.; Kraemer MUG; Department of Zoology, University of Oxford, Oxford, UK.; Kuate-Lere L; Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.; Laguda-Akingba O; NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa.; Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa.; Lesetedi-Mafoko O; Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana.; Lessells RJ; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Lockman S; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Lucaci AG; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.; Maharaj A; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Mahlangu B; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Maponga T; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.; Mahlakwane K; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.; NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa.; Makatini Z; Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.; Marais G; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.; Maruapula D; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.; Masupu K; Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.; Matshaba M; Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.; Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.; Baylor College of Medicine, Houston, TX, USA.; Mayaphi S; Department of Medical Virology, University of Pretoria, Pretoria, South Africa.; Mbhele N; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Mbulawa MB; National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.; Mendes A; Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.; Mlisana K; National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.; Mnguni A; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Mohale T; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Moir M; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.; Moruisi K; Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.; Mosepele M; Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.; Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana.; Motsatsi G; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Motswaledi MS; Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.; Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana.; Mphoyakgosi T; National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.; Msomi N; Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa.; Mwangi PN; Division of Virology, University of the Free State, Bloemfontein, South Africa.; Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.; Naidoo Y; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Ntuli N; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Nyaga M; Division of Virology, University of the Free State, Bloemfontein, South Africa.; Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.; Olubayo L; Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.; Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Pillay S; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Radibe B; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.; Ramphal Y; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Ramphal U; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; San JE; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Scott L; Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.; Shapiro R; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Singh L; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Smith-Lawrence P; Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.; Stevens W; Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.; Strydom A; Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.; Subramoney K; Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.; Tebeila N; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Tshiabuila D; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.; Tsui J; Department of Zoology, University of Oxford, Oxford, UK.; van Wyk S; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.; Weaver S; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.; Wibmer CK; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; Wilkinson E; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.; Wolter N; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; Zarebski AE; Department of Zoology, University of Oxford, Oxford, UK.; Zuze B; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.; Goedhals D; Division of Virology, University of the Free State, Bloemfontein, South Africa.; PathCare Vermaak, Pretoria, South Africa.; Preiser W; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.; NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa.; Treurnicht F; Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.; Venter M; Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.; Williamson C; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.; Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.; Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.; Pybus OG; Department of Zoology, University of Oxford, Oxford, UK.; Bhiman J; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; Glass A; Lancet Laboratories, Johannesburg, South Africa.; Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; Martin DP; Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.; Rambaut A; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.; Gaseitsiwe S; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.; Harvard T.H. Chan School of Public Health, Boston, MA, USA.; von Gottberg A; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; de Oliveira T; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. tulio@sun.ac.za.; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa. tulio@sun.ac.za.; Department of Global Health, University of Washington, Seattle, WA, USA. tulio@sun.ac.za.
Source
Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE
Subject
Language
English
Abstract
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively 1-3 . In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function 4 . Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
(© 2022. The Author(s).)