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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Raquel Viana; Sikhulile Moyo; Daniel Gyamfi Amoako; Houriiyah Tegally; Cathrine Scheepers; Richard J Lessells; Jennifer Giandhari; Nicole Wolter; Josie Everatt; Andrew Rambaut; Christian Althaus; Eduan Wilkinson; Adriano Mendes; Amy Strydom; Michaela Davids; Simnikiwe Mayaphi; Simani Gaseitsiwe; Wonderful T Choga; Dorcas Maruapula; Boitumelo Zuze; Botshelo Radibe; Legodile Koopile; Roger Shapiro; Shahin Lockman; Mpaphi B. Mbulawa; Thongbotho Mphoyakgosi; Pamela Smith-Lawrence; Mosepele Mosepele; Mogomotsi Matshaba; Kereng Masupu; Mohammed Chand; Charity Joseph; Lesego Kuate-Lere; Onalethatha Lesetedi-Mafoko; Kgomotso Moruisi; Lesley Scott; Wendy Stevens; Constantinos Kurt Wibmer; Anele Mnguni; Arshad Ismail; Boitshoko Mahlangu; Darren P. Martin; Verity Hill; Rachel Colquhoun; Modisa S. Motswaledi; James Emmanuel San; Noxolo Ntuli; Gerald Motsatsi; Sureshnee Pillay; Thabo Mohale; Upasana Ramphal; Yeshnee Naidoo; Naume Tebeila; Marta Giovanetti; Koleka Mlisana; Carolyn Williamson; Nei-yuan Hsiao; Nokukhanya Msomi; Kamela Mahlakwane; Susan Engelbrecht; Tongai Maponga; Wolfgang Preiser; Zinhle Makatini; Oluwakemi Laguda-Akingba; Lavanya Singh; Ugochukwu J. Anyaneji; Monika Moir; Stephanie van Wyk; Derek Tshiabuila; Yajna Ramphal; Arisha Maharaj; Sergei Pond; Alexander G Lucaci; Steven Weaver; Maciej F Boni; Koen Deforche; Kathleen Subramoney; Diana Hardie; Gert Marais; Deelan Doolabh; Rageema Joseph; Nokuzola Mbhele; Luicer Olubayo; Arash Iranzadeh; Alexander E Zarebski; Joseph Tsui; Moritz UG Kraemer; Oliver G Pybus; Dominique Goedhals; Phillip Armand Bester; Martin M Nyaga; Peter N Mwangi; Allison Glass; Florette Treurnicht; Marietjie Venter; Jinal N. Bhiman; Anne von Gottberg; Tulio de Oliveira.
Affiliation
  • Raquel Viana; Lancet Laboratories, Johannesburg, South Africa
  • Sikhulile Moyo; Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana Harvard T.H. Chan School of Public health, Boston, Ma
  • Daniel Gyamfi Amoako; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Houriiyah Tegally; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa Centre
  • Cathrine Scheepers; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Richard J Lessells; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa Centre
  • Jennifer Giandhari; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
  • Nicole Wolter; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Josie Everatt; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Andrew Rambaut; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Christian Althaus; University of Bern
  • Eduan Wilkinson; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
  • Adriano Mendes; Zoonotic arbo and Resiratory virus program, Department Medical Virology, University of Pretoria, Pretoria, South Africa
  • Amy Strydom; Zoonotic arbo and Resiratory virus program, Department Medical Virology, University of Pretoria, Pretoria, South Africa
  • Michaela Davids; Zoonotic arbo and Resiratory virus program, Department Medical Virology, University of Pretoria, Pretoria, South Africa
  • Simnikiwe Mayaphi; Department Medical Virology University of Pretoria, Pretoria, South Africa National Health Laboratory Services, Thswane Academic Devision, Pretoria, South Afric
  • Simani Gaseitsiwe; Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana Department of Immunology and Infectious Diseases, Har
  • Wonderful T Choga; Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
  • Dorcas Maruapula; Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
  • Boitumelo Zuze; Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
  • Botshelo Radibe; Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
  • Legodile Koopile; Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
  • Roger Shapiro; Botswana Harvard AIDS Institite Partnership, Gaborone, Botswana Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Bos
  • Shahin Lockman; Botswana Harvard AIDS Institite Partnership, Gaborone, Botswana Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Bos
  • Mpaphi B. Mbulawa; National Health Laboratory, Gaborone, Botswana
  • Thongbotho Mphoyakgosi; National Health Laboratory, Gaborone, Botswana
  • Pamela Smith-Lawrence; Health Services, Ministry of Health and Wellness, Gaborone, Botswana
  • Mosepele Mosepele; Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana Botswana Pr
  • Mogomotsi Matshaba; Botswana-Baylor Children's Clinical Centre of E cellence Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana Botswana Presidential COVID-19 Taskforce
  • Kereng Masupu; Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
  • Mohammed Chand; Diagnofirm Medical Laboratories, Gaborone, Botswana
  • Charity Joseph; Diagnofirm Medical Laboratories, Gaborone, Botswana
  • Lesego Kuate-Lere; Ministry of Health and Wellness, Gaborone, Botswana
  • Onalethatha Lesetedi-Mafoko; Ministry of Health and Wellness, Gaborone, Botswana
  • Kgomotso Moruisi; Ministry of Health and Wellness, Gaborone, Botswana
  • Lesley Scott; University of the Witwatersrand
  • Wendy Stevens; University of the Witwatersrand
  • Constantinos Kurt Wibmer; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Anele Mnguni; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Arshad Ismail; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Boitshoko Mahlangu; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Darren P. Martin; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Af
  • Verity Hill; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Rachel Colquhoun; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Modisa S. Motswaledi; Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana,Gaborone, Botswana
  • James Emmanuel San; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
  • Noxolo Ntuli; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Gerald Motsatsi; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Sureshnee Pillay; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
  • Thabo Mohale; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Upasana Ramphal; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
  • Yeshnee Naidoo; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
  • Naume Tebeila; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa Department of Veterinary Tropic
  • Marta Giovanetti; FioCruz Foundation
  • Koleka Mlisana; National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  • Carolyn Williamson; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service (NHLS),South Africa
  • Nei-yuan Hsiao; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa National Healt
  • Nokukhanya Msomi; National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  • Kamela Mahlakwane; National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  • Susan Engelbrecht; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa;
  • Tongai Maponga; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa;
  • Wolfgang Preiser; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa; National Health Laboratory S
  • Zinhle Makatini; National Health Laboratory Service (NHLS), Johannesburg, South Africa National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Oluwakemi Laguda-Akingba; National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa
  • Lavanya Singh; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
  • Ugochukwu J. Anyaneji; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
  • Monika Moir; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
  • Stephanie van Wyk; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
  • Derek Tshiabuila; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
  • Yajna Ramphal; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
  • Arisha Maharaj; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
  • Sergei Pond; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
  • Alexander G Lucaci; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
  • Steven Weaver; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
  • Maciej F Boni; Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
  • Koen Deforche; Emweb bv, Herent, Belgium
  • Kathleen Subramoney; National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Diana Hardie; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
  • Gert Marais; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa
  • Deelan Doolabh; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
  • Rageema Joseph; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
  • Nokuzola Mbhele; Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
  • Luicer Olubayo; Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa) Division of Computational Biology, Faculty of Health Sciences, Unversity of Cape Town
  • Arash Iranzadeh; Division of Computational Biology, Faculty of Health Sciences, Unversity of Cape Town
  • Alexander E Zarebski; Department of Zoology, University of Oxford, Mansfield Road, Oxford, Oxford OX1 3SZ, UK
  • Joseph Tsui; Department of Zoology, University of Oxford, Mansfield Road, Oxford, Oxford OX1 3SZ, UK
  • Moritz UG Kraemer; Department of Zoology, University of Oxford, Mansfield Road, Oxford, Oxford OX1 3SZ, UK
  • Oliver G Pybus; Department of Zoology, University of Oxford, Mansfield Road, Oxford, Oxford OX1 3SZ, UK
  • Dominique Goedhals; PathCare Vermaak, Pretoria, South Africa Division of Virology, University of the Free State, Bloemfontein, South Africa
  • Phillip Armand Bester; Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa Division of Virology, University of the Free State, Bloemfontein, South Afr
  • Martin M Nyaga; Next Generation Sequencing Unit, University of the Free State, Bloemfontein, South Africa Division of Virology, University of the Free State, Bloemfontein, Sout
  • Peter N Mwangi; Next Generation Sequencing Unit, University of the Free State, Bloemfontein, South Africa Division of Virology, University of the Free State, Bloemfontein, Sout
  • Allison Glass; Lancet Laboratories, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  • Florette Treurnicht; National Health Laboratory Service (NHLS), Johannesburg, South Africa
  • Marietjie Venter; Zoonotic arbo and Respiratory virus research programme, Department Medical Virology, University of Pretoria;
  • Jinal N. Bhiman; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, Uni
  • Anne von Gottberg; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, Uni
  • Tulio de Oliveira; University of KwaZulu-Natal
Preprint in English | medRxiv | ID: ppmedrxiv-21268028
Journal article
A scientific journal published article is available and is probably based on this preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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ABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta 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) 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, 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: Preprints Database: medRxiv Type of study: Prognostic study Language: English Year: 2021 Document type: Preprint
Fulltext
Add to My VHL
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Full text: Available Collection: Preprints Database: medRxiv Type of study: Prognostic study Language: English Year: 2021 Document type: Preprint