Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana; Sikhulile Moyo; Daniel G Amoako; Houriiyah Tegally; Cathrine Scheepers; Christian L Althaus; Ugochukwu J Anyaneji; Phillip A Bester; Maciej F Boni; Mohammed Chand; Wonderful T Choga; Rachel Colquhoun; Michaela Davids; Koen Deforche; Deelan Doolabh; Louis du Plessis; Susan Engelbrecht; Josie Everatt; Jennifer Giandhari; Marta Giovanetti; Diana Hardie; Verity Hill; Nei-Yuan Hsiao; Arash Iranzadeh; Arshad Ismail; Charity Joseph; Rageema Joseph; Legodile Koopile; Sergei L Kosakovsky Pond; Moritz U G Kraemer; Lesego Kuate-Lere; Oluwakemi Laguda-Akingba; Onalethatha Lesetedi-Mafoko; Richard J Lessells; Shahin Lockman; Alexander G Lucaci; Arisha Maharaj; Boitshoko Mahlangu; Tongai Maponga; Kamela Mahlakwane; Zinhle Makatini; Gert Marais; Dorcas Maruapula; Kereng Masupu; Mogomotsi Matshaba; Simnikiwe Mayaphi; Nokuzola Mbhele; Mpaphi B Mbulawa; Adriano Mendes; Koleka Mlisana; Anele Mnguni; Thabo Mohale; Monika Moir; Kgomotso Moruisi; Mosepele Mosepele; Gerald Motsatsi; Modisa S Motswaledi; Thongbotho Mphoyakgosi; Nokukhanya Msomi; Peter N Mwangi; Yeshnee Naidoo; Noxolo Ntuli; Martin Nyaga; Lucier Olubayo; Sureshnee Pillay; Botshelo Radibe; Yajna Ramphal; Upasana Ramphal; James E San; Lesley Scott; Roger Shapiro; Lavanya Singh; Pamela Smith-Lawrence; Wendy Stevens; Amy Strydom; Kathleen Subramoney; Naume Tebeila; Derek Tshiabuila; Joseph Tsui; Stephanie van Wyk; Steven Weaver; Constantinos K Wibmer; Eduan Wilkinson; Nicole Wolter; Alexander E Zarebski; Boitumelo Zuze; Dominique Goedhals; Wolfgang Preiser; Florette Treurnicht; Marietje Venter; Carolyn Williamson; Oliver G Pybus; Jinal Bhiman; Allison Glass; Darren P Martin; Andrew Rambaut; Simani Gaseitsiwe; Anne von Gottberg; Tulio de Oliveira

doi:10.1038/s41586-022-04411-y

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Nature. 2022 Mar;603(7902):679-686. doi: 10.1038/s41586-022-04411-y. Epub 2022 Jan 7.

Authors

Raquel Viana^#¹, Sikhulile Moyo^#^{2

3

4}, Daniel G Amoako^#⁵, Houriiyah Tegally^#⁶, Cathrine Scheepers^#^{5

7}, Christian L Althaus⁸, Ugochukwu J Anyaneji⁶, Phillip A Bester^{9

10}, Maciej F Boni¹¹, Mohammed Chand¹², Wonderful T Choga³, Rachel Colquhoun¹³, Michaela Davids¹⁴, Koen Deforche¹⁵, Deelan Doolabh¹⁶, Louis du Plessis^{17

18}, Susan Engelbrecht¹⁹, Josie Everatt⁵, Jennifer Giandhari⁶, Marta Giovanetti^{20

21}, Diana Hardie^{16

22}, Verity Hill¹³, Nei-Yuan Hsiao^{16

22

23}, Arash Iranzadeh²⁴, Arshad Ismail⁵, Charity Joseph¹², Rageema Joseph¹⁶, Legodile Koopile², Sergei L Kosakovsky Pond²⁵, Moritz U G Kraemer¹⁷, Lesego Kuate-Lere²⁶, Oluwakemi Laguda-Akingba^{27

28}, Onalethatha Lesetedi-Mafoko²⁹, Richard J Lessells⁶, Shahin Lockman^{2

30}, Alexander G Lucaci²⁵, Arisha Maharaj⁶, Boitshoko Mahlangu⁵, Tongai Maponga¹⁹, Kamela Mahlakwane^{19

31}, Zinhle Makatini³², Gert Marais^{16

22}, Dorcas Maruapula², Kereng Masupu⁴, Mogomotsi Matshaba^{4

33

34}, Simnikiwe Mayaphi³⁵, Nokuzola Mbhele¹⁶, Mpaphi B Mbulawa³⁶, Adriano Mendes¹⁴, Koleka Mlisana^{37

38}, Anele Mnguni⁵, Thabo Mohale⁵, Monika Moir³⁹, Kgomotso Moruisi²⁶, Mosepele Mosepele^{4

40}, Gerald Motsatsi⁵, Modisa S Motswaledi^{4

41}, Thongbotho Mphoyakgosi³⁶, Nokukhanya Msomi⁴², Peter N Mwangi^{10

43}, Yeshnee Naidoo⁶, Noxolo Ntuli⁵, Martin Nyaga^{10

43}, Lucier Olubayo^{23

24}, Sureshnee Pillay⁶, Botshelo Radibe², Yajna Ramphal⁶, Upasana Ramphal⁶, James E San⁶, Lesley Scott⁴⁴, Roger Shapiro^{2

30}, Lavanya Singh⁶, Pamela Smith-Lawrence²⁶, Wendy Stevens⁴⁴, Amy Strydom¹⁴, Kathleen Subramoney³², Naume Tebeila⁵, Derek Tshiabuila⁶, Joseph Tsui¹⁷, Stephanie van Wyk³⁹, Steven Weaver²⁵, Constantinos K Wibmer⁵, Eduan Wilkinson³⁹, Nicole Wolter^{5

45}, Alexander E Zarebski¹⁷, Boitumelo Zuze², Dominique Goedhals^{10

46}, Wolfgang Preiser^{19

31}, Florette Treurnicht³², Marietje Venter¹⁴, Carolyn Williamson^{16

22

23

47}, Oliver G Pybus¹⁷, Jinal Bhiman^{5

7}, Allison Glass^{1

48}, Darren P Martin^{23

47}, Andrew Rambaut¹³, Simani Gaseitsiwe^{2

3}, Anne von Gottberg^{5

45}, Tulio de Oliveira^{49

50

51}

Affiliations

¹ Lancet Laboratories, Johannesburg, South Africa.
² Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana.
³ Harvard T.H. Chan School of Public Health, Boston, MA, USA.
⁴ Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana.
⁵ National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
⁶ KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
⁷ South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁸ Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
⁹ Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa.
¹⁰ Division of Virology, University of the Free State, Bloemfontein, South Africa.
¹¹ Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
¹² Diagnofirm Medical Laboratories, Gaborone, Botswana.
¹³ Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
¹⁴ Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
¹⁵ Emweb, Herent, Belgium.
¹⁶ Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
¹⁷ Department of Zoology, University of Oxford, Oxford, UK.
¹⁸ Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland.
¹⁹ Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
²⁰ Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
²¹ Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
²² Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa.
²³ Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa.
²⁴ Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
²⁵ Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.
²⁶ Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
²⁷ NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa.
²⁸ Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa.
²⁹ Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana.
³⁰ Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
³¹ NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa.
³² Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa.
³³ Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.
³⁴ Baylor College of Medicine, Houston, TX, USA.
³⁵ Department of Medical Virology, University of Pretoria, Pretoria, South Africa.
³⁶ National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana.
³⁷ National Health Laboratory Service (NHLS), Johannesburg, South Africa.
³⁸ Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
³⁹ Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
⁴⁰ Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana.
⁴¹ Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana.
⁴² Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa.
⁴³ Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
⁴⁴ Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.
⁴⁵ School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁴⁶ PathCare Vermaak, Pretoria, South Africa.
⁴⁷ Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
⁴⁸ Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁴⁹ 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.
⁵⁰ Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa. tulio@sun.ac.za.
⁵¹ Department of Global Health, University of Washington, Seattle, WA, USA. tulio@sun.ac.za.

^# Contributed equally.

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 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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Antibodies, Neutralizing / immunology
Botswana / epidemiology
COVID-19 / epidemiology*
COVID-19 / immunology
COVID-19 / transmission
COVID-19 / virology*
Humans
Immune Evasion*
Models, Molecular
Mutation
Phylogeny
Recombination, Genetic
SARS-CoV-2 / classification
SARS-CoV-2 / immunology
SARS-CoV-2 / isolation & purification*
South Africa / epidemiology
Spike Glycoprotein, Coronavirus / genetics
Spike Glycoprotein, Coronavirus / immunology

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

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