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

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 GiovanettiDiana 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

Research output: Contribution to journal › Article › peer-review

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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, 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.

Original language	English (US)
Pages (from-to)	679-686
Number of pages	8
Journal	Nature
Volume	603
Issue number	7902
DOIs	https://doi.org/10.1038/s41586-022-04411-y
State	Published - Mar 24 2022

All Science Journal Classification (ASJC) codes

General

Access to Document

10.1038/s41586-022-04411-y

Cite this

Viana, R., Moyo, S., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., Choga, W. T., Colquhoun, R., Davids, M., Deforche, K., Doolabh, D., du Plessis, L., Engelbrecht, S., Everatt, J., Giandhari, J., ... de Oliveira, T. (2022). Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature, 603(7902), 679-686. https://doi.org/10.1038/s41586-022-04411-y

@article{8b72048da7494330bd9786d9918f9941,

title = "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa",

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.",

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

note = "Funding Information: Acknowledgements We thank L. de Gouveia, A. Buys, C. Fourie, N. Duma, M. Ndlovu and other members of the NICD Centre for Respiratory Diseases and Meningitis and Sequencing Core Facility; N. Govender, G. Ntshoe, A. Moipone Shonhiwa, D. Muganhiri, I. Matiea, E. Mathatha, F. Gavhi, T. Mashudu Lamola, M. Makhubele, M. Matjokotja, S. Mdleleni, M. Makhubela from the national SARS-CoV-2 NICD surveillance team for NMCSS case data; F. Mckenna, T. Graham Bell, N. Munava, S. Kwenda, M. Raza Bano and J. Khosa from NICD IT for NMCSS case and test data (in particular, SGTF data); and the following people from the diagnostic laboratories for their assistance: K. Reddy, L. Gounder and C. Naicker from NHLS Inkosi Albert Luthuli Central Hospital Laboratory, S. Korsman from the NHLS Groote Schuur Laboratory, and A. Enoch at NHLS Green Point Laboratory; the staff at the global laboratories who generated and made public the SARS-CoV-2 sequences (through GISAID) used as reference dataset in this study (a complete list of individual contributors of sequences is provided in Supplementary Table 1). The research reported in this publication was supported by the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council, with funds received from the South African Department of Science and Innovation. Sequencing activities at KRISP and CERI were supported in part by the WHO, the National Institutes of Health (NIH) (U01 AI151698) for the United World Antivirus Research Network (UWARN), and the Rockefeller Foundation (grants 2021 HTH 017 and 2020 HTH 062). C.L.A. received funding from the European Union{\textquoteright}s Horizon 2020 research and innovation programme, project EpiPose (no. 101003688). D.P.M. was funded by the Wellcome Trust (222574/Z/21/Z). R.C. and A.R. acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z, ARTIC network) and A.R. from the European Research Council (no. 725422, ReservoirDOCS). V.H. was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant no. BB/M010996/1). A.E.Z., J.T., M.U.G.K. and O.G.P. acknowledge support from the Oxford Martin School. M.U.G.K. acknowledges support from the Rockefeller Foundation, Google.org, and the European Horizon 2020 programme MOOD (no. 874850). M.V. and the members of the Zoonotic Arbo and Respiratory Virus Program, UP was funded through the ANDEMIA G7 Global Health Concept: contributions to improvement of International Health, COVID-19 funds through the Robert Koch Institute. The genomic sequencing at UCT/NHLS is funded from the South African Medical Research Council and Department of Science and Innovation; and by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). C.W. and J.B. are funded by the EDCTP (RADIATES Consortium; RIA2020EF-3030). Sequencing activities at the NICD were supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (no. 5U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a subaward from the Bill and Melinda Gates Foundation grant no. INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (no. 221003/Z/20/Z); the South African Medical Research Council (SHIPNCD 76756); the UK Department of Health and Social Care, managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. The genomic sequencing in Botswana was supported by the Foundation for Innovative New Diagnostics and Fogarty International Center (5D43TW009610), NIH (5K24AI131924-04; 5K24AI131928-05) and support from the Botswana government through the Ministry of Health & Wellness and Presidential COVID-19 Task Force. S. Moyo. was supported in part by the Bill & Melinda Gates Foundation (036530). Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. Funding Information: We thank L. de Gouveia, A. Buys, C. Fourie, N. Duma, M. Ndlovu and other members of the NICD Centre for Respiratory Diseases and Meningitis and Sequencing Core Facility; N. Govender, G. Ntshoe, A. Moipone Shonhiwa, D. Muganhiri, I. Matiea, E. Mathatha, F. Gavhi, T. Mashudu Lamola, M. Makhubele, M. Matjokotja, S. Mdleleni, M. Makhubela from the national SARS-CoV-2 NICD surveillance team for NMCSS case data; F. Mckenna, T. Graham Bell, N. Munava, S. Kwenda, M. Raza Bano and J. Khosa from NICD IT for NMCSS case and test data (in particular, SGTF data); and the following people from the diagnostic laboratories for their assistance: K. Reddy, L. Gounder and C. Naicker from NHLS Inkosi Albert Luthuli Central Hospital Laboratory, S. Korsman from the NHLS Groote Schuur Laboratory, and A. Enoch at NHLS Green Point Laboratory; the staff at the global laboratories who generated and made public the SARS-CoV-2 sequences (through GISAID) used as reference dataset in this study (a complete list of individual contributors of sequences is provided in Supplementary Table 1). The research reported in this publication was supported by the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council, with funds received from the South African Department of Science and Innovation. Sequencing activities at KRISP and CERI were supported in part by the WHO, the National Institutes of Health (NIH) (U01 AI151698) for the United World Antivirus Research Network (UWARN), and the Rockefeller Foundation (grants 2021 HTH 017 and 2020 HTH 062).?C.L.A. received funding from the European Union?s Horizon 2020 research and innovation programme, project EpiPose (no. 101003688). D.P.M. was funded by the Wellcome Trust (222574/Z/21/Z). R.C. and A.R. acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z, ARTIC network) and A.R. from the European Research Council (no. 725422, ReservoirDOCS). V.H. was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant no. BB/M010996/1). A.E.Z., J.T., M.U.G.K. and O.G.P. acknowledge support from the Oxford Martin School. M.U.G.K. acknowledges support from the Rockefeller Foundation, Google.org, and the European Horizon 2020 programme MOOD (no. 874850). M.V. and the members of the Zoonotic Arbo and Respiratory Virus Program, UP was funded through the ANDEMIA G7 Global Health Concept: contributions to improvement of International Health, COVID-19 funds through the Robert Koch Institute. The genomic sequencing at UCT/NHLS is funded from the South African Medical Research Council and Department of Science and Innovation; and by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). C.W. and J.B. are funded by the EDCTP (RADIATES Consortium; RIA2020EF-3030). Sequencing activities at the NICD were supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (no. 5U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a subaward from the Bill and Melinda Gates Foundation grant no. INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (no. 221003/Z/20/Z); the South African Medical Research Council (SHIPNCD 76756); the UK Department of Health and Social Care, managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. The genomic sequencing in Botswana was supported by the Foundation for Innovative New Diagnostics and Fogarty International Center (5D43TW009610), NIH (5K24AI131924-04; 5K24AI131928-05) and support from the Botswana government through the Ministry of Health & Wellness and Presidential COVID-19 Task Force. S.?Moyo. was supported in part by the Bill & Melinda Gates Foundation (036530).?Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = mar,

day = "24",

doi = "10.1038/s41586-022-04411-y",

language = "English (US)",

volume = "603",

pages = "679--686",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7902",

}

Viana, R, Moyo, S, Amoako, DG, Tegally, H, Scheepers, C, Althaus, CL, Anyaneji, UJ, Bester, PA, Boni, MF, Chand, M, Choga, WT, Colquhoun, R, Davids, M, Deforche, K, Doolabh, D, du Plessis, L, Engelbrecht, S, Everatt, J, Giandhari, J, Giovanetti, M, Hardie, D, Hill, V, Hsiao, NY, Iranzadeh, A, Ismail, A, Joseph, C, Joseph, R, Koopile, L, Kosakovsky Pond, SL, Kraemer, MUG, Kuate-Lere, L, Laguda-Akingba, O, Lesetedi-Mafoko, O, Lessells, RJ, Lockman, S, Lucaci, AG, Maharaj, A, Mahlangu, B, Maponga, T, Mahlakwane, K, Makatini, Z, Marais, G, Maruapula, D, Masupu, K, Matshaba, M, Mayaphi, S, Mbhele, N, Mbulawa, MB, Mendes, A, Mlisana, K, Mnguni, A, Mohale, T, Moir, M, Moruisi, K, Mosepele, M, Motsatsi, G, Motswaledi, MS, Mphoyakgosi, T, Msomi, N, Mwangi, PN, Naidoo, Y, Ntuli, N, Nyaga, M, Olubayo, L, Pillay, S, Radibe, B, Ramphal, Y, Ramphal, U, San, JE, Scott, L, Shapiro, R, Singh, L, Smith-Lawrence, P, Stevens, W, Strydom, A, Subramoney, K, Tebeila, N, Tshiabuila, D, Tsui, J, van Wyk, S, Weaver, S, Wibmer, CK, Wilkinson, E, Wolter, N, Zarebski, AE, Zuze, B, Goedhals, D, Preiser, W, Treurnicht, F, Venter, M, Williamson, C, Pybus, OG, Bhiman, J, Glass, A, Martin, DP, Rambaut, A, Gaseitsiwe, S, von Gottberg, A & de Oliveira, T 2022, 'Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa', Nature, vol. 603, no. 7902, pp. 679-686. https://doi.org/10.1038/s41586-022-04411-y

TY - JOUR

T1 - Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

AU - Viana, Raquel

AU - Moyo, Sikhulile

AU - Amoako, Daniel G.

AU - Tegally, Houriiyah

AU - Scheepers, Cathrine

AU - Althaus, Christian L.

AU - Anyaneji, Ugochukwu J.

AU - Bester, Phillip A.

AU - Boni, Maciej F.

AU - Chand, Mohammed

AU - Choga, Wonderful T.

AU - Colquhoun, Rachel

AU - Davids, Michaela

AU - Deforche, Koen

AU - Doolabh, Deelan

AU - du Plessis, Louis

AU - Engelbrecht, Susan

AU - Everatt, Josie

AU - Giandhari, Jennifer

AU - Giovanetti, Marta

AU - Hardie, Diana

AU - Hill, Verity

AU - Hsiao, Nei Yuan

AU - Iranzadeh, Arash

AU - Ismail, Arshad

AU - Joseph, Charity

AU - Joseph, Rageema

AU - Koopile, Legodile

AU - Kosakovsky Pond, Sergei L.

AU - Kraemer, Moritz U.G.

AU - Kuate-Lere, Lesego

AU - Laguda-Akingba, Oluwakemi

AU - Lesetedi-Mafoko, Onalethatha

AU - Lessells, Richard J.

AU - Lockman, Shahin

AU - Lucaci, Alexander G.

AU - Maharaj, Arisha

AU - Mahlangu, Boitshoko

AU - Maponga, Tongai

AU - Mahlakwane, Kamela

AU - Makatini, Zinhle

AU - Marais, Gert

AU - Maruapula, Dorcas

AU - Masupu, Kereng

AU - Matshaba, Mogomotsi

AU - Mayaphi, Simnikiwe

AU - Mbhele, Nokuzola

AU - Mbulawa, Mpaphi B.

AU - Mendes, Adriano

AU - Mlisana, Koleka

AU - Mnguni, Anele

AU - Mohale, Thabo

AU - Moir, Monika

AU - Moruisi, Kgomotso

AU - Mosepele, Mosepele

AU - Motsatsi, Gerald

AU - Motswaledi, Modisa S.

AU - Mphoyakgosi, Thongbotho

AU - Msomi, Nokukhanya

AU - Mwangi, Peter N.

AU - Naidoo, Yeshnee

AU - Ntuli, Noxolo

AU - Nyaga, Martin

AU - Olubayo, Lucier

AU - Pillay, Sureshnee

AU - Radibe, Botshelo

AU - Ramphal, Yajna

AU - Ramphal, Upasana

AU - San, James E.

AU - Scott, Lesley

AU - Shapiro, Roger

AU - Singh, Lavanya

AU - Smith-Lawrence, Pamela

AU - Stevens, Wendy

AU - Strydom, Amy

AU - Subramoney, Kathleen

AU - Tebeila, Naume

AU - Tshiabuila, Derek

AU - Tsui, Joseph

AU - van Wyk, Stephanie

AU - Weaver, Steven

AU - Wibmer, Constantinos K.

AU - Wilkinson, Eduan

AU - Wolter, Nicole

AU - Zarebski, Alexander E.

AU - Zuze, Boitumelo

AU - Goedhals, Dominique

AU - Preiser, Wolfgang

AU - Treurnicht, Florette

AU - Venter, Marietje

AU - Williamson, Carolyn

AU - Pybus, Oliver G.

AU - Bhiman, Jinal

AU - Glass, Allison

AU - Martin, Darren P.

AU - Rambaut, Andrew

AU - Gaseitsiwe, Simani

AU - von Gottberg, Anne

AU - de Oliveira, Tulio

N1 - Funding Information: Acknowledgements We thank L. de Gouveia, A. Buys, C. Fourie, N. Duma, M. Ndlovu and other members of the NICD Centre for Respiratory Diseases and Meningitis and Sequencing Core Facility; N. Govender, G. Ntshoe, A. Moipone Shonhiwa, D. Muganhiri, I. Matiea, E. Mathatha, F. Gavhi, T. Mashudu Lamola, M. Makhubele, M. Matjokotja, S. Mdleleni, M. Makhubela from the national SARS-CoV-2 NICD surveillance team for NMCSS case data; F. Mckenna, T. Graham Bell, N. Munava, S. Kwenda, M. Raza Bano and J. Khosa from NICD IT for NMCSS case and test data (in particular, SGTF data); and the following people from the diagnostic laboratories for their assistance: K. Reddy, L. Gounder and C. Naicker from NHLS Inkosi Albert Luthuli Central Hospital Laboratory, S. Korsman from the NHLS Groote Schuur Laboratory, and A. Enoch at NHLS Green Point Laboratory; the staff at the global laboratories who generated and made public the SARS-CoV-2 sequences (through GISAID) used as reference dataset in this study (a complete list of individual contributors of sequences is provided in Supplementary Table 1). The research reported in this publication was supported by the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council, with funds received from the South African Department of Science and Innovation. Sequencing activities at KRISP and CERI were supported in part by the WHO, the National Institutes of Health (NIH) (U01 AI151698) for the United World Antivirus Research Network (UWARN), and the Rockefeller Foundation (grants 2021 HTH 017 and 2020 HTH 062). C.L.A. received funding from the European Union’s Horizon 2020 research and innovation programme, project EpiPose (no. 101003688). D.P.M. was funded by the Wellcome Trust (222574/Z/21/Z). R.C. and A.R. acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z, ARTIC network) and A.R. from the European Research Council (no. 725422, ReservoirDOCS). V.H. was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant no. BB/M010996/1). A.E.Z., J.T., M.U.G.K. and O.G.P. acknowledge support from the Oxford Martin School. M.U.G.K. acknowledges support from the Rockefeller Foundation, Google.org, and the European Horizon 2020 programme MOOD (no. 874850). M.V. and the members of the Zoonotic Arbo and Respiratory Virus Program, UP was funded through the ANDEMIA G7 Global Health Concept: contributions to improvement of International Health, COVID-19 funds through the Robert Koch Institute. The genomic sequencing at UCT/NHLS is funded from the South African Medical Research Council and Department of Science and Innovation; and by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). C.W. and J.B. are funded by the EDCTP (RADIATES Consortium; RIA2020EF-3030). Sequencing activities at the NICD were supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (no. 5U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a subaward from the Bill and Melinda Gates Foundation grant no. INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (no. 221003/Z/20/Z); the South African Medical Research Council (SHIPNCD 76756); the UK Department of Health and Social Care, managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. The genomic sequencing in Botswana was supported by the Foundation for Innovative New Diagnostics and Fogarty International Center (5D43TW009610), NIH (5K24AI131924-04; 5K24AI131928-05) and support from the Botswana government through the Ministry of Health & Wellness and Presidential COVID-19 Task Force. S. Moyo. was supported in part by the Bill & Melinda Gates Foundation (036530). Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. Funding Information: We thank L. de Gouveia, A. Buys, C. Fourie, N. Duma, M. Ndlovu and other members of the NICD Centre for Respiratory Diseases and Meningitis and Sequencing Core Facility; N. Govender, G. Ntshoe, A. Moipone Shonhiwa, D. Muganhiri, I. Matiea, E. Mathatha, F. Gavhi, T. Mashudu Lamola, M. Makhubele, M. Matjokotja, S. Mdleleni, M. Makhubela from the national SARS-CoV-2 NICD surveillance team for NMCSS case data; F. Mckenna, T. Graham Bell, N. Munava, S. Kwenda, M. Raza Bano and J. Khosa from NICD IT for NMCSS case and test data (in particular, SGTF data); and the following people from the diagnostic laboratories for their assistance: K. Reddy, L. Gounder and C. Naicker from NHLS Inkosi Albert Luthuli Central Hospital Laboratory, S. Korsman from the NHLS Groote Schuur Laboratory, and A. Enoch at NHLS Green Point Laboratory; the staff at the global laboratories who generated and made public the SARS-CoV-2 sequences (through GISAID) used as reference dataset in this study (a complete list of individual contributors of sequences is provided in Supplementary Table 1). The research reported in this publication was supported by the Strategic Health Innovation Partnerships Unit of the South African Medical Research Council, with funds received from the South African Department of Science and Innovation. Sequencing activities at KRISP and CERI were supported in part by the WHO, the National Institutes of Health (NIH) (U01 AI151698) for the United World Antivirus Research Network (UWARN), and the Rockefeller Foundation (grants 2021 HTH 017 and 2020 HTH 062).?C.L.A. received funding from the European Union?s Horizon 2020 research and innovation programme, project EpiPose (no. 101003688). D.P.M. was funded by the Wellcome Trust (222574/Z/21/Z). R.C. and A.R. acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z, ARTIC network) and A.R. from the European Research Council (no. 725422, ReservoirDOCS). V.H. was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant no. BB/M010996/1). A.E.Z., J.T., M.U.G.K. and O.G.P. acknowledge support from the Oxford Martin School. M.U.G.K. acknowledges support from the Rockefeller Foundation, Google.org, and the European Horizon 2020 programme MOOD (no. 874850). M.V. and the members of the Zoonotic Arbo and Respiratory Virus Program, UP was funded through the ANDEMIA G7 Global Health Concept: contributions to improvement of International Health, COVID-19 funds through the Robert Koch Institute. The genomic sequencing at UCT/NHLS is funded from the South African Medical Research Council and Department of Science and Innovation; and by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). C.W. and J.B. are funded by the EDCTP (RADIATES Consortium; RIA2020EF-3030). Sequencing activities at the NICD were supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (no. 5U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a subaward from the Bill and Melinda Gates Foundation grant no. INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (no. 221003/Z/20/Z); the South African Medical Research Council (SHIPNCD 76756); the UK Department of Health and Social Care, managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. The genomic sequencing in Botswana was supported by the Foundation for Innovative New Diagnostics and Fogarty International Center (5D43TW009610), NIH (5K24AI131924-04; 5K24AI131928-05) and support from the Botswana government through the Ministry of Health & Wellness and Presidential COVID-19 Task Force. S.?Moyo. was supported in part by the Bill & Melinda Gates Foundation (036530).?Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission. Publisher Copyright: © 2022, The Author(s).

PY - 2022/3/24

Y1 - 2022/3/24

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85122882393&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85122882393&partnerID=8YFLogxK

U2 - 10.1038/s41586-022-04411-y

DO - 10.1038/s41586-022-04411-y

M3 - Article

C2 - 35042229

AN - SCOPUS:85122882393

SN - 0028-0836

VL - 603

SP - 679

EP - 686

JO - Nature

JF - Nature

IS - 7902

ER -

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

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