@article{Viana2021,
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 respectively[1][1]–[3][2]. 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 function[4][3]. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest. {\#}{\#}{\#} Funding Statement 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. CA received funding from the European Union Horizon 2020 research and innovation programme project EpiPose (No 101003688). DPM was funded by the Wellcome Trust (222574/Z/21/Z). RC {\&} AR acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z ARTIC network) and AR from the European Research Council (grant agreement number 725422 ReservoirDOCS). VH was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant number BB/M010996/1). AEZ, JT, MUGK, OGP acknowledge support from the Oxford Martin School. MUGK acknowledges support from the Rockefeller Foundation, Google.org, and the European Horizon 2020 programme MOOD ({\#}874850). MV and the ZARV members, UP was funded through the ANDEMIA G7 Global Health Concept: contributions to improvement of International Health, COVID19 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]. CW and JNB 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 (grant number 5 U01IP001048 05 00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub award from the Bill and Melinda Gates Foundation grant number INV 018978; the UK Foreign, Commonwealth and Development Office and Wellcome (Grant no 221003/Z/20/Z); the South African Medical Research Council (Reference number 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), as well in kind support from the Botswana government through the Ministry of Health {\&} Wellness and Presidential COVID 19 Task Force. SM was supported in part by the Bill {\&} Melinda Gates Foundation [036530]. {\#}{\#}{\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The genomic surveillance in South Africa was approved by the University of KwaZulu Natal Biomedical Research Ethics Committee (BREC/00001510/2020), the University of the Witwatersrand Human Research Ethics Committee (HREC) (M180832), Stellenbosch University HREC (N20/04/008{\_}COVID-19), University of Cape Town HREC (383/2020), University of Pretoria HREC (H101/17) and the University of the Free State Health Sciences Research Ethics Committee (UFS HSD2020/1860/2710). The genomic sequencing in Botswana was conductedas part of the national vaccine roll-out plan and was approved by the Health Research and Development Committee (Health Research Ethics body, HRDC{\#}00948 and HRDC{\#}00904). Individual participant consent was not required for the genomic surveillance. This requirement was waived by the Research Ethics Committees. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All genomes generated in this research at public available at GISAID. The short reads are public available at the Short Read Archives of NCBI. [1]: {\#}ref-1 [2]: {\#}ref-3 [3]: {\#}ref-4},
author = {Viana, Raquel and Moyo, Sikhulile and Amoako, Daniel G and Tegally, Houriiyah and Scheepers, Cathrine and Althaus, Christian L and Anyaneji, Ugochukwu J and Bester, Phillip A and Boni, Maciej F and Chand, Mohammed and Choga, Wonderful T and Colquhoun, Rachel and Davids, Michaela and Deforche, Koen and Doolabh, Deelan and Engelbrecht, Susan and Everatt, Josie and Giandhari, Jennifer and Giovanetti, Marta and Hardie, Diana and Hill, Verity and Hsiao, Nei-Yuan and Iranzadeh, Arash and Ismail, Arshad and Joseph, Charity and Joseph, Rageema and Koopile, Legodile and Pond, Sergei L Kosakovsky and Kraemer, Moritz U G and Kuate-Lere, Lesego and Laguda-Akingba, Oluwakemi and Lesetedi-Mafoko, Onalethatha and Lessells, Richard J and Lockman, Shahin and Lucaci, Alexander G and Maharaj, Arisha and Mahlangu, Boitshoko and Maponga, Tongai and Mahlakwane, Kamela and Makatini, Zinhle and Marais, Gert and Maruapula, Dorcas and Masupu, Kereng and Matshaba, Mogomotsi and Mayaphi, Simnikiwe and Mbhele, Nokuzola and Mbulawa, Mpaphi B and Mendes, Adriano and Mlisana, Koleka and Mnguni, Anele and Mohale, Thabo and Moir, Monika and Moruisi, Kgomotso and Mosepele, Mosepele and Motsatsi, Gerald and Motswaledi, Modisa S and Mphoyakgosi, Thongbotho and Msomi, Nokukhanya and Mwangi, Peter N and Naidoo, Yeshnee and Ntuli, Noxolo and Nyaga, Martin and Olubayo, Lucier and Pillay, Sureshnee and Radibe, Botshelo and Ramphal, Yajna and Ramphal, Upasana and San, James E and Scott, Lesley and Shapiro, Roger and Singh, Lavanya and Smith-Lawrence, Pamela and Stevens, Wendy and Strydom, Amy and Subramoney, Kathleen and Tebeila, Naume and Tshiabuila, Derek and Tsui, Joseph and van Wyk, Stephanie and Weaver, Steven and Wibmer, Constantinos K and Wilkinson, Eduan and Wolter, Nicole and Zarebski, Alexander E and Zuze, Boitumelo and Goedhals, Dominique and Preiser, Wolfgang and Treurnicht, Florette and Venter, Marietje and Williamson, Carolyn and Pybus, Oliver G and Bhiman, Jinal and Glass, Allison and Martin, Darren P and Rambaut, Andrew and Gaseitsiwe, Simani and von Gottberg, Anne and de Oliveira, Tulio},
doi = {10.1101/2021.12.19.21268028},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Viana et al. - 2021 - Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.pdf:pdf},
journal = {medRxiv},
keywords = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
month = {dec},
pages = {2021.12.19.21268028},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa}},
url = {https://www.medrxiv.org/content/10.1101/2021.12.19.21268028v1 https://www.medrxiv.org/content/10.1101/2021.12.19.21268028v1.abstract},
year = {2021}
}

{"_id":"spwZaRW2j73Po787t","bibbaseid":"viana-moyo-amoako-tegally-scheepers-althaus-anyaneji-bester-etal-rapidepidemicexpansionofthesarscov2omicronvariantinsouthernafrica-2021","author_short":["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.","Engelbrecht, S.","Everatt, J.","Giandhari, J.","Giovanetti, M.","Hardie, D.","Hill, V.","Hsiao, N.","Iranzadeh, A.","Ismail, A.","Joseph, C.","Joseph, R.","Koopile, L.","Pond, S. L K.","Kraemer, M. U G","Kuate-Lere, L.","Laguda-Akingba, O.","Lesetedi-Mafoko, O.","Lessells, R. J","Lockman, S.","Lucaci, A. G","Maharaj, A.","Mahlangu, B.","Maponga, T.","Mahlakwane, K.","Makatini, Z.","Marais, G.","Maruapula, D.","Masupu, K.","Matshaba, M.","Mayaphi, S.","Mbhele, N.","Mbulawa, M. B","Mendes, A.","Mlisana, K.","Mnguni, A.","Mohale, T.","Moir, M.","Moruisi, K.","Mosepele, M.","Motsatsi, G.","Motswaledi, M. S","Mphoyakgosi, T.","Msomi, N.","Mwangi, P. N","Naidoo, Y.","Ntuli, N.","Nyaga, M.","Olubayo, L.","Pillay, S.","Radibe, B.","Ramphal, Y.","Ramphal, U.","San, J. E","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, C. K","Wilkinson, E.","Wolter, N.","Zarebski, A. E","Zuze, B.","Goedhals, D.","Preiser, W.","Treurnicht, F.","Venter, M.","Williamson, C.","Pybus, O. G","Bhiman, J.","Glass, A.","Martin, D. P","Rambaut, A.","Gaseitsiwe, S.","von Gottberg, A.","de Oliveira, T."],"bibdata":{"bibtype":"article","type":"article","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 respectively[1][1]–[3][2]. 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 function[4][3]. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement 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. CA received funding from the European Union Horizon 2020 research and innovation programme project EpiPose (No 101003688). DPM was funded by the Wellcome Trust (222574/Z/21/Z). RC & AR acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z ARTIC network) and AR from the European Research Council (grant agreement number 725422 ReservoirDOCS). VH was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant number BB/M010996/1). AEZ, JT, MUGK, OGP acknowledge support from the Oxford Martin School. MUGK acknowledges support from the Rockefeller Foundation, Google.org, and the European Horizon 2020 programme MOOD (#874850). MV and the ZARV members, UP was funded through the ANDEMIA G7 Global Health Concept: contributions to improvement of International Health, COVID19 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]. CW and JNB 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 (grant number 5 U01IP001048 05 00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub award from the Bill and Melinda Gates Foundation grant number INV 018978; the UK Foreign, Commonwealth and Development Office and Wellcome (Grant no 221003/Z/20/Z); the South African Medical Research Council (Reference number 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), as well in kind support from the Botswana government through the Ministry of Health & Wellness and Presidential COVID 19 Task Force. SM was supported in part by the Bill & Melinda Gates Foundation [036530]. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The genomic surveillance in South Africa was approved by the University of KwaZulu Natal Biomedical Research Ethics Committee (BREC/00001510/2020), the University of the Witwatersrand Human Research Ethics Committee (HREC) (M180832), Stellenbosch University HREC (N20/04/008_COVID-19), University of Cape Town HREC (383/2020), University of Pretoria HREC (H101/17) and the University of the Free State Health Sciences Research Ethics Committee (UFS HSD2020/1860/2710). The genomic sequencing in Botswana was conductedas part of the national vaccine roll-out plan and was approved by the Health Research and Development Committee (Health Research Ethics body, HRDC#00948 and HRDC#00904). Individual participant consent was not required for the genomic surveillance. This requirement was waived by the Research Ethics Committees. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All genomes generated in this research at public available at GISAID. The short reads are public available at the Short Read Archives of NCBI. [1]: #ref-1 [2]: #ref-3 [3]: #ref-4","author":[{"propositions":[],"lastnames":["Viana"],"firstnames":["Raquel"],"suffixes":[]},{"propositions":[],"lastnames":["Moyo"],"firstnames":["Sikhulile"],"suffixes":[]},{"propositions":[],"lastnames":["Amoako"],"firstnames":["Daniel","G"],"suffixes":[]},{"propositions":[],"lastnames":["Tegally"],"firstnames":["Houriiyah"],"suffixes":[]},{"propositions":[],"lastnames":["Scheepers"],"firstnames":["Cathrine"],"suffixes":[]},{"propositions":[],"lastnames":["Althaus"],"firstnames":["Christian","L"],"suffixes":[]},{"propositions":[],"lastnames":["Anyaneji"],"firstnames":["Ugochukwu","J"],"suffixes":[]},{"propositions":[],"lastnames":["Bester"],"firstnames":["Phillip","A"],"suffixes":[]},{"propositions":[],"lastnames":["Boni"],"firstnames":["Maciej","F"],"suffixes":[]},{"propositions":[],"lastnames":["Chand"],"firstnames":["Mohammed"],"suffixes":[]},{"propositions":[],"lastnames":["Choga"],"firstnames":["Wonderful","T"],"suffixes":[]},{"propositions":[],"lastnames":["Colquhoun"],"firstnames":["Rachel"],"suffixes":[]},{"propositions":[],"lastnames":["Davids"],"firstnames":["Michaela"],"suffixes":[]},{"propositions":[],"lastnames":["Deforche"],"firstnames":["Koen"],"suffixes":[]},{"propositions":[],"lastnames":["Doolabh"],"firstnames":["Deelan"],"suffixes":[]},{"propositions":[],"lastnames":["Engelbrecht"],"firstnames":["Susan"],"suffixes":[]},{"propositions":[],"lastnames":["Everatt"],"firstnames":["Josie"],"suffixes":[]},{"propositions":[],"lastnames":["Giandhari"],"firstnames":["Jennifer"],"suffixes":[]},{"propositions":[],"lastnames":["Giovanetti"],"firstnames":["Marta"],"suffixes":[]},{"propositions":[],"lastnames":["Hardie"],"firstnames":["Diana"],"suffixes":[]},{"propositions":[],"lastnames":["Hill"],"firstnames":["Verity"],"suffixes":[]},{"propositions":[],"lastnames":["Hsiao"],"firstnames":["Nei-Yuan"],"suffixes":[]},{"propositions":[],"lastnames":["Iranzadeh"],"firstnames":["Arash"],"suffixes":[]},{"propositions":[],"lastnames":["Ismail"],"firstnames":["Arshad"],"suffixes":[]},{"propositions":[],"lastnames":["Joseph"],"firstnames":["Charity"],"suffixes":[]},{"propositions":[],"lastnames":["Joseph"],"firstnames":["Rageema"],"suffixes":[]},{"propositions":[],"lastnames":["Koopile"],"firstnames":["Legodile"],"suffixes":[]},{"propositions":[],"lastnames":["Pond"],"firstnames":["Sergei","L","Kosakovsky"],"suffixes":[]},{"propositions":[],"lastnames":["Kraemer"],"firstnames":["Moritz","U","G"],"suffixes":[]},{"propositions":[],"lastnames":["Kuate-Lere"],"firstnames":["Lesego"],"suffixes":[]},{"propositions":[],"lastnames":["Laguda-Akingba"],"firstnames":["Oluwakemi"],"suffixes":[]},{"propositions":[],"lastnames":["Lesetedi-Mafoko"],"firstnames":["Onalethatha"],"suffixes":[]},{"propositions":[],"lastnames":["Lessells"],"firstnames":["Richard","J"],"suffixes":[]},{"propositions":[],"lastnames":["Lockman"],"firstnames":["Shahin"],"suffixes":[]},{"propositions":[],"lastnames":["Lucaci"],"firstnames":["Alexander","G"],"suffixes":[]},{"propositions":[],"lastnames":["Maharaj"],"firstnames":["Arisha"],"suffixes":[]},{"propositions":[],"lastnames":["Mahlangu"],"firstnames":["Boitshoko"],"suffixes":[]},{"propositions":[],"lastnames":["Maponga"],"firstnames":["Tongai"],"suffixes":[]},{"propositions":[],"lastnames":["Mahlakwane"],"firstnames":["Kamela"],"suffixes":[]},{"propositions":[],"lastnames":["Makatini"],"firstnames":["Zinhle"],"suffixes":[]},{"propositions":[],"lastnames":["Marais"],"firstnames":["Gert"],"suffixes":[]},{"propositions":[],"lastnames":["Maruapula"],"firstnames":["Dorcas"],"suffixes":[]},{"propositions":[],"lastnames":["Masupu"],"firstnames":["Kereng"],"suffixes":[]},{"propositions":[],"lastnames":["Matshaba"],"firstnames":["Mogomotsi"],"suffixes":[]},{"propositions":[],"lastnames":["Mayaphi"],"firstnames":["Simnikiwe"],"suffixes":[]},{"propositions":[],"lastnames":["Mbhele"],"firstnames":["Nokuzola"],"suffixes":[]},{"propositions":[],"lastnames":["Mbulawa"],"firstnames":["Mpaphi","B"],"suffixes":[]},{"propositions":[],"lastnames":["Mendes"],"firstnames":["Adriano"],"suffixes":[]},{"propositions":[],"lastnames":["Mlisana"],"firstnames":["Koleka"],"suffixes":[]},{"propositions":[],"lastnames":["Mnguni"],"firstnames":["Anele"],"suffixes":[]},{"propositions":[],"lastnames":["Mohale"],"firstnames":["Thabo"],"suffixes":[]},{"propositions":[],"lastnames":["Moir"],"firstnames":["Monika"],"suffixes":[]},{"propositions":[],"lastnames":["Moruisi"],"firstnames":["Kgomotso"],"suffixes":[]},{"propositions":[],"lastnames":["Mosepele"],"firstnames":["Mosepele"],"suffixes":[]},{"propositions":[],"lastnames":["Motsatsi"],"firstnames":["Gerald"],"suffixes":[]},{"propositions":[],"lastnames":["Motswaledi"],"firstnames":["Modisa","S"],"suffixes":[]},{"propositions":[],"lastnames":["Mphoyakgosi"],"firstnames":["Thongbotho"],"suffixes":[]},{"propositions":[],"lastnames":["Msomi"],"firstnames":["Nokukhanya"],"suffixes":[]},{"propositions":[],"lastnames":["Mwangi"],"firstnames":["Peter","N"],"suffixes":[]},{"propositions":[],"lastnames":["Naidoo"],"firstnames":["Yeshnee"],"suffixes":[]},{"propositions":[],"lastnames":["Ntuli"],"firstnames":["Noxolo"],"suffixes":[]},{"propositions":[],"lastnames":["Nyaga"],"firstnames":["Martin"],"suffixes":[]},{"propositions":[],"lastnames":["Olubayo"],"firstnames":["Lucier"],"suffixes":[]},{"propositions":[],"lastnames":["Pillay"],"firstnames":["Sureshnee"],"suffixes":[]},{"propositions":[],"lastnames":["Radibe"],"firstnames":["Botshelo"],"suffixes":[]},{"propositions":[],"lastnames":["Ramphal"],"firstnames":["Yajna"],"suffixes":[]},{"propositions":[],"lastnames":["Ramphal"],"firstnames":["Upasana"],"suffixes":[]},{"propositions":[],"lastnames":["San"],"firstnames":["James","E"],"suffixes":[]},{"propositions":[],"lastnames":["Scott"],"firstnames":["Lesley"],"suffixes":[]},{"propositions":[],"lastnames":["Shapiro"],"firstnames":["Roger"],"suffixes":[]},{"propositions":[],"lastnames":["Singh"],"firstnames":["Lavanya"],"suffixes":[]},{"propositions":[],"lastnames":["Smith-Lawrence"],"firstnames":["Pamela"],"suffixes":[]},{"propositions":[],"lastnames":["Stevens"],"firstnames":["Wendy"],"suffixes":[]},{"propositions":[],"lastnames":["Strydom"],"firstnames":["Amy"],"suffixes":[]},{"propositions":[],"lastnames":["Subramoney"],"firstnames":["Kathleen"],"suffixes":[]},{"propositions":[],"lastnames":["Tebeila"],"firstnames":["Naume"],"suffixes":[]},{"propositions":[],"lastnames":["Tshiabuila"],"firstnames":["Derek"],"suffixes":[]},{"propositions":[],"lastnames":["Tsui"],"firstnames":["Joseph"],"suffixes":[]},{"propositions":["van"],"lastnames":["Wyk"],"firstnames":["Stephanie"],"suffixes":[]},{"propositions":[],"lastnames":["Weaver"],"firstnames":["Steven"],"suffixes":[]},{"propositions":[],"lastnames":["Wibmer"],"firstnames":["Constantinos","K"],"suffixes":[]},{"propositions":[],"lastnames":["Wilkinson"],"firstnames":["Eduan"],"suffixes":[]},{"propositions":[],"lastnames":["Wolter"],"firstnames":["Nicole"],"suffixes":[]},{"propositions":[],"lastnames":["Zarebski"],"firstnames":["Alexander","E"],"suffixes":[]},{"propositions":[],"lastnames":["Zuze"],"firstnames":["Boitumelo"],"suffixes":[]},{"propositions":[],"lastnames":["Goedhals"],"firstnames":["Dominique"],"suffixes":[]},{"propositions":[],"lastnames":["Preiser"],"firstnames":["Wolfgang"],"suffixes":[]},{"propositions":[],"lastnames":["Treurnicht"],"firstnames":["Florette"],"suffixes":[]},{"propositions":[],"lastnames":["Venter"],"firstnames":["Marietje"],"suffixes":[]},{"propositions":[],"lastnames":["Williamson"],"firstnames":["Carolyn"],"suffixes":[]},{"propositions":[],"lastnames":["Pybus"],"firstnames":["Oliver","G"],"suffixes":[]},{"propositions":[],"lastnames":["Bhiman"],"firstnames":["Jinal"],"suffixes":[]},{"propositions":[],"lastnames":["Glass"],"firstnames":["Allison"],"suffixes":[]},{"propositions":[],"lastnames":["Martin"],"firstnames":["Darren","P"],"suffixes":[]},{"propositions":[],"lastnames":["Rambaut"],"firstnames":["Andrew"],"suffixes":[]},{"propositions":[],"lastnames":["Gaseitsiwe"],"firstnames":["Simani"],"suffixes":[]},{"propositions":["von"],"lastnames":["Gottberg"],"firstnames":["Anne"],"suffixes":[]},{"propositions":["de"],"lastnames":["Oliveira"],"firstnames":["Tulio"],"suffixes":[]}],"doi":"10.1101/2021.12.19.21268028","file":":C$\\$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Viana et al. - 2021 - Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.pdf:pdf","journal":"medRxiv","keywords":"OA,fund_ack,genomics_fund_ack,original","mendeley-tags":"OA,fund_ack,genomics_fund_ack,original","month":"dec","pages":"2021.12.19.21268028","publisher":"Cold Spring Harbor Laboratory Press","title":"Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa","url":"https://www.medrxiv.org/content/10.1101/2021.12.19.21268028v1 https://www.medrxiv.org/content/10.1101/2021.12.19.21268028v1.abstract","year":"2021","bibtex":"@article{Viana2021,\r\nabstract = {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 respectively[1][1]–[3][2]. 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 function[4][3]. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity. {\\#}{\\#}{\\#} Competing Interest Statement The authors have declared no competing interest. {\\#}{\\#}{\\#} Funding Statement 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. CA received funding from the European Union Horizon 2020 research and innovation programme project EpiPose (No 101003688). DPM was funded by the Wellcome Trust (222574/Z/21/Z). RC {\\&} AR acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z ARTIC network) and AR from the European Research Council (grant agreement number 725422 ReservoirDOCS). VH was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant number BB/M010996/1). AEZ, JT, MUGK, OGP acknowledge support from the Oxford Martin School. MUGK acknowledges support from the Rockefeller Foundation, Google.org, and the European Horizon 2020 programme MOOD ({\\#}874850). MV and the ZARV members, UP was funded through the ANDEMIA G7 Global Health Concept: contributions to improvement of International Health, COVID19 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]. CW and JNB 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 (grant number 5 U01IP001048 05 00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub award from the Bill and Melinda Gates Foundation grant number INV 018978; the UK Foreign, Commonwealth and Development Office and Wellcome (Grant no 221003/Z/20/Z); the South African Medical Research Council (Reference number 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), as well in kind support from the Botswana government through the Ministry of Health {\\&} Wellness and Presidential COVID 19 Task Force. SM was supported in part by the Bill {\\&} Melinda Gates Foundation [036530]. {\\#}{\\#}{\\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The genomic surveillance in South Africa was approved by the University of KwaZulu Natal Biomedical Research Ethics Committee (BREC/00001510/2020), the University of the Witwatersrand Human Research Ethics Committee (HREC) (M180832), Stellenbosch University HREC (N20/04/008{\\_}COVID-19), University of Cape Town HREC (383/2020), University of Pretoria HREC (H101/17) and the University of the Free State Health Sciences Research Ethics Committee (UFS HSD2020/1860/2710). The genomic sequencing in Botswana was conductedas part of the national vaccine roll-out plan and was approved by the Health Research and Development Committee (Health Research Ethics body, HRDC{\\#}00948 and HRDC{\\#}00904). Individual participant consent was not required for the genomic surveillance. This requirement was waived by the Research Ethics Committees. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All genomes generated in this research at public available at GISAID. The short reads are public available at the Short Read Archives of NCBI. [1]: {\\#}ref-1 [2]: {\\#}ref-3 [3]: {\\#}ref-4},\r\nauthor = {Viana, Raquel and Moyo, Sikhulile and Amoako, Daniel G and Tegally, Houriiyah and Scheepers, Cathrine and Althaus, Christian L and Anyaneji, Ugochukwu J and Bester, Phillip A and Boni, Maciej F and Chand, Mohammed and Choga, Wonderful T and Colquhoun, Rachel and Davids, Michaela and Deforche, Koen and Doolabh, Deelan and Engelbrecht, Susan and Everatt, Josie and Giandhari, Jennifer and Giovanetti, Marta and Hardie, Diana and Hill, Verity and Hsiao, Nei-Yuan and Iranzadeh, Arash and Ismail, Arshad and Joseph, Charity and Joseph, Rageema and Koopile, Legodile and Pond, Sergei L Kosakovsky and Kraemer, Moritz U G and Kuate-Lere, Lesego and Laguda-Akingba, Oluwakemi and Lesetedi-Mafoko, Onalethatha and Lessells, Richard J and Lockman, Shahin and Lucaci, Alexander G and Maharaj, Arisha and Mahlangu, Boitshoko and Maponga, Tongai and Mahlakwane, Kamela and Makatini, Zinhle and Marais, Gert and Maruapula, Dorcas and Masupu, Kereng and Matshaba, Mogomotsi and Mayaphi, Simnikiwe and Mbhele, Nokuzola and Mbulawa, Mpaphi B and Mendes, Adriano and Mlisana, Koleka and Mnguni, Anele and Mohale, Thabo and Moir, Monika and Moruisi, Kgomotso and Mosepele, Mosepele and Motsatsi, Gerald and Motswaledi, Modisa S and Mphoyakgosi, Thongbotho and Msomi, Nokukhanya and Mwangi, Peter N and Naidoo, Yeshnee and Ntuli, Noxolo and Nyaga, Martin and Olubayo, Lucier and Pillay, Sureshnee and Radibe, Botshelo and Ramphal, Yajna and Ramphal, Upasana and San, James E and Scott, Lesley and Shapiro, Roger and Singh, Lavanya and Smith-Lawrence, Pamela and Stevens, Wendy and Strydom, Amy and Subramoney, Kathleen and Tebeila, Naume and Tshiabuila, Derek and Tsui, Joseph and van Wyk, Stephanie and Weaver, Steven and Wibmer, Constantinos K and Wilkinson, Eduan and Wolter, Nicole and Zarebski, Alexander E and Zuze, Boitumelo and Goedhals, Dominique and Preiser, Wolfgang and Treurnicht, Florette and Venter, Marietje and Williamson, Carolyn and Pybus, Oliver G and Bhiman, Jinal and Glass, Allison and Martin, Darren P and Rambaut, Andrew and Gaseitsiwe, Simani and von Gottberg, Anne and de Oliveira, Tulio},\r\ndoi = {10.1101/2021.12.19.21268028},\r\nfile = {:C$\\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Viana et al. - 2021 - Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.pdf:pdf},\r\njournal = {medRxiv},\r\nkeywords = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmendeley-tags = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmonth = {dec},\r\npages = {2021.12.19.21268028},\r\npublisher = {Cold Spring Harbor Laboratory Press},\r\ntitle = {{Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa}},\r\nurl = {https://www.medrxiv.org/content/10.1101/2021.12.19.21268028v1 https://www.medrxiv.org/content/10.1101/2021.12.19.21268028v1.abstract},\r\nyear = {2021}\r\n}\r\n","author_short":["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.","Engelbrecht, S.","Everatt, J.","Giandhari, J.","Giovanetti, M.","Hardie, D.","Hill, V.","Hsiao, N.","Iranzadeh, A.","Ismail, A.","Joseph, C.","Joseph, R.","Koopile, L.","Pond, S. L K.","Kraemer, M. U G","Kuate-Lere, L.","Laguda-Akingba, O.","Lesetedi-Mafoko, O.","Lessells, R. J","Lockman, S.","Lucaci, A. G","Maharaj, A.","Mahlangu, B.","Maponga, T.","Mahlakwane, K.","Makatini, Z.","Marais, G.","Maruapula, D.","Masupu, K.","Matshaba, M.","Mayaphi, S.","Mbhele, N.","Mbulawa, M. B","Mendes, A.","Mlisana, K.","Mnguni, A.","Mohale, T.","Moir, M.","Moruisi, K.","Mosepele, M.","Motsatsi, G.","Motswaledi, M. S","Mphoyakgosi, T.","Msomi, N.","Mwangi, P. N","Naidoo, Y.","Ntuli, N.","Nyaga, M.","Olubayo, L.","Pillay, S.","Radibe, B.","Ramphal, Y.","Ramphal, U.","San, J. E","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, C. K","Wilkinson, E.","Wolter, N.","Zarebski, A. E","Zuze, B.","Goedhals, D.","Preiser, W.","Treurnicht, F.","Venter, M.","Williamson, C.","Pybus, O. G","Bhiman, J.","Glass, A.","Martin, D. P","Rambaut, A.","Gaseitsiwe, S.","von Gottberg, A.","de Oliveira, T."],"key":"Viana2021","id":"Viana2021","bibbaseid":"viana-moyo-amoako-tegally-scheepers-althaus-anyaneji-bester-etal-rapidepidemicexpansionofthesarscov2omicronvariantinsouthernafrica-2021","role":"author","urls":{"Paper":"https://www.medrxiv.org/content/10.1101/2021.12.19.21268028v1 https://www.medrxiv.org/content/10.1101/2021.12.19.21268028v1.abstract"},"keyword":["OA","fund_ack","genomics_fund_ack","original"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://drive.google.com/uc?export=download&id=1-JLqZ7RwZ3VC2d6ErLGHAtOeMRS_7GCz","dataSources":["Krmt6gt9ktB2s6ARh","y6ojaHcuarkmc4yRQ"],"keywords":["oa","fund_ack","genomics_fund_ack","original"],"search_terms":["rapid","epidemic","expansion","sars","cov","omicron","variant","southern","africa","viana","moyo","amoako","tegally","scheepers","althaus","anyaneji","bester","boni","chand","choga","colquhoun","davids","deforche","doolabh","engelbrecht","everatt","giandhari","giovanetti","hardie","hill","hsiao","iranzadeh","ismail","joseph","joseph","koopile","pond","kraemer","kuate-lere","laguda-akingba","lesetedi-mafoko","lessells","lockman","lucaci","maharaj","mahlangu","maponga","mahlakwane","makatini","marais","maruapula","masupu","matshaba","mayaphi","mbhele","mbulawa","mendes","mlisana","mnguni","mohale","moir","moruisi","mosepele","motsatsi","motswaledi","mphoyakgosi","msomi","mwangi","naidoo","ntuli","nyaga","olubayo","pillay","radibe","ramphal","ramphal","san","scott","shapiro","singh","smith-lawrence","stevens","strydom","subramoney","tebeila","tshiabuila","tsui","van wyk","weaver","wibmer","wilkinson","wolter","zarebski","zuze","goedhals","preiser","treurnicht","venter","williamson","pybus","bhiman","glass","martin","rambaut","gaseitsiwe","von gottberg","de oliveira"],"title":"Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa","year":2021}