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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Viana, Raquel; Moyo, Sikhulile; Amoako, Daniel G; Tegally, Houriiyah; Scheepers, Cathrine; Althaus, Christian L; Anyaneji, Ugochukwu J; Bester, Phillip A; Boni, Maciej F; Chand, Mohammed; Choga, Wonderful T; Colquhoun, Rachel; Davids, Michaela; Deforche, Koen; Doolabh, Deelan; du Plessis, Louis; Engelbrecht, Susan; Everatt, Josie; Giandhari, Jennifer; Giovanetti, Marta; Hardie, Diana; Hill, Verity; Hsiao, Nei-Yuan; Iranzadeh, Arash; Ismail, Arshad; Joseph, Charity; Joseph, Rageema; Koopile, Legodile; Kosakovsky Pond, Sergei L; Kraemer, Moritz U G; Kuate-Lere, Lesego; Laguda-Akingba, Oluwakemi; Lesetedi-Mafoko, Onalethatha; Lessells, Richard J; Lockman, Shahin; Lucaci, Alexander G; Maharaj, Arisha; Mahlangu, Boitshoko; Maponga, Tongai; Mahlakwane, Kamela; Makatini, Zinhle; Marais, Gert; Maruapula, Dorcas; Masupu, Kereng; Matshaba, Mogomotsi; Mayaphi, Simnikiwe; Mbhele, Nokuzola; Mbulawa, Mpaphi B; Mendes, Adriano; Mlisana, Koleka.
  • Viana R; Lancet Laboratories, Johannesburg, South Africa.
  • Moyo S; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
  • Amoako DG; Harvard T.H. Chan School of Public Health, Boston, MA, USA.
  • Tegally H; Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.
  • Scheepers C; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
  • Althaus CL; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Anyaneji UJ; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
  • Bester PA; South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
  • Boni MF; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
  • Chand M; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Choga WT; Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa.
  • Colquhoun R; Division of Virology, University of the Free State, Bloemfontein, South Africa.
  • Davids M; Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
  • Deforche K; Diagnofirm Medical Laboratories, Gaborone, Botswana.
  • Doolabh D; Harvard T.H. Chan School of Public Health, Boston, MA, USA.
  • du Plessis L; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Engelbrecht S; Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
  • Everatt J; Emweb, Herent, Belgium.
  • Giandhari J; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
  • Giovanetti M; Department of Zoology, University of Oxford, Oxford, UK.
  • Hardie D; Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland.
  • Hill V; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
  • Hsiao NY; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
  • Iranzadeh A; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Ismail A; Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
  • Joseph C; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
  • Joseph R; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
  • Koopile L; Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.
  • Kosakovsky Pond SL; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Kraemer MUG; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
  • Kuate-Lere L; Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.
  • Laguda-Akingba O; Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.
  • Lesetedi-Mafoko O; Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
  • Lessells RJ; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
  • Lockman S; Diagnofirm Medical Laboratories, Gaborone, Botswana.
  • Lucaci AG; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
  • Maharaj A; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
  • Mahlangu B; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.
  • Maponga T; Department of Zoology, University of Oxford, Oxford, UK.
  • Mahlakwane K; Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
  • Makatini Z; NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa.
  • Marais G; Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa.
  • Maruapula D; Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana.
  • Masupu K; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Matshaba M; Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
  • Mayaphi S; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
  • Mbhele N; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.
  • Mbulawa MB; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Mendes A; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
  • Mlisana K; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
Nature ; 603(7902): 679-686, 2022 03.
Article in English | MEDLINE | ID: covidwho-1638766
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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, respectively1-3. 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 function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Immune Evasion / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Africa Language: English Journal: Nature Year: 2022 Document Type: Article Affiliation country: S41586-022-04411-y

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Immune Evasion / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: Africa Language: English Journal: Nature Year: 2022 Document Type: Article Affiliation country: S41586-022-04411-y