Rapid replacement of the Beta variant by the Delta variant in South Africa. Tegally, H., Wilkinson, E., Althaus, C. L, Giovanetti, M., San, J. E., Giandhari, J., Pillay, S., Naidoo, Y., Ramphal, U., Msomi, N., Mlisana, K., Amoako, D. G, Everatt, J., Mohale, T., Nguni, A., Mahlangu, B., Ntuli, N., Khumalo, Z. T, Makatini, Z., Wolter, N., Scheepers, C., Ismail, A., Doolabh, D., Joseph, R., Strydom, A., Mendes, A., Davis, M., Mayaphi, S. H, Ramphal, Y., Maharaj, A., Karim, W. A., Tshiabuila, D., Anyaneji, U. J, Singh, L., Engelbrecht, S., Fonseca, V., Marais, K., Korsman, S., Hardie, D., Hsiao, N., Maponga, T., van Zyl, G., Marais, G., Iranzadeh, A., Martin, D., Alcantara, L. C. J., Bester, P. A., Nyaga, M. M, Subramoney, K., Treurnicht, F. K, Venter, M., Goedhals, D., Preiser, W., Bhiman, J. N, von Gottberg, A., Williamson, C., Lessells, R. J, & de Oliveira, T. medRxiv, Cold Spring Harbor Laboratory Press, sep, 2021.
Rapid replacement of the Beta variant by the Delta variant in South Africa [link]Paper  doi  abstract   bibtex   
The Beta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in South Africa in late 2020 and rapidly became the dominant variant, causing over 95% of infections in the country during and after the second epidemic wave. Here we show rapid replacement of the Beta variant by the Delta variant, a highly transmissible variant of concern (VOC) that emerged in India and subsequently spread around the world. The Delta variant was imported to South Africa primarily from India, spread rapidly in large monophyletic clusters to all provinces, and became dominant within three months of introduction. This was associated with a resurgence in community transmission, leading to a third wave which was associated with a high number of deaths. We estimated a growth advantage for the Delta variant in South Africa of 0.089 (95% confidence interval [CI] 0.084-0.093) per day which corresponds to a transmission advantage of 46% (95% CI 44-48) compared to the Beta variant. These data provide additional support for the increased transmissibility of the Delta variant relative to other VOC and highlight how dynamic shifts in the distribution of variants contribute to the ongoing public health threat. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This 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 (DSI). Genomics Surveillance in South Africa was supported in part through National Institutes of Health USA grant U01 AI151698 for the United World Antiviral Research Network (UWARN) and by the Rockefeller Foundation (Prof. Tulio de Oliveira and Dr. Eduan Wilkinson). CERI and KRISP have received donations from Chan Soon-Shiong Family Foundation (CSSFF) and Illumina . CW is funded by the South African MRC; Wellcome Trust (2222574/Z/21/Z) and the EDCTP (RADIATES Consortium; RIA2020EF-3030) ### 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 was approved by the University of KwaZuluNatal Biomedical Research Ethics Committee (ref. BREC/00001510/2020), the University of the Witwatersrand Human Research Ethics Committee (HREC, ref. M180832, M210159, M210752), Stellenbosch University HREC (ref. N20/04/008_COVID19), and the University of Cape Town HREC (ref. 383/2020), the University of Pretoria HREC (100/2017), and the University of Free State Health Sciences Research Ethics Committee (ref. UFS HSD2020/1860/2710). Individual participant consent was not required for genomic surveillance, this requirement was waived by the Research Ethics Committees. Following sequencing, all consensus sequences are uploaded to GISAID33 and their use is subject to the database terms and conditions. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. 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 sequence data is public at GISAID. Short reads (i.e. FastQ files) are available at the Short Read Archive of the NCBI. [htts://www.ceri.org.za][1] [1]: https://www.ceri.org.za
@article{Tegally2021,
abstract = {The Beta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in South Africa in late 2020 and rapidly became the dominant variant, causing over 95{\%} of infections in the country during and after the second epidemic wave. Here we show rapid replacement of the Beta variant by the Delta variant, a highly transmissible variant of concern (VOC) that emerged in India and subsequently spread around the world. The Delta variant was imported to South Africa primarily from India, spread rapidly in large monophyletic clusters to all provinces, and became dominant within three months of introduction. This was associated with a resurgence in community transmission, leading to a third wave which was associated with a high number of deaths. We estimated a growth advantage for the Delta variant in South Africa of 0.089 (95{\%} confidence interval [CI] 0.084-0.093) per day which corresponds to a transmission advantage of 46{\%} (95{\%} CI 44-48) compared to the Beta variant. These data provide additional support for the increased transmissibility of the Delta variant relative to other VOC and highlight how dynamic shifts in the distribution of variants contribute to the ongoing public health threat. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest. {\#}{\#}{\#} Funding Statement This 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 (DSI). Genomics Surveillance in South Africa was supported in part through National Institutes of Health USA grant U01 AI151698 for the United World Antiviral Research Network (UWARN) and by the Rockefeller Foundation (Prof. Tulio de Oliveira and Dr. Eduan Wilkinson). CERI and KRISP have received donations from Chan Soon-Shiong Family Foundation (CSSFF) and Illumina . CW is funded by the South African MRC; Wellcome Trust (2222574/Z/21/Z) and the EDCTP (RADIATES Consortium; RIA2020EF-3030) {\#}{\#}{\#} 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 was approved by the University of KwaZuluNatal Biomedical Research Ethics Committee (ref. BREC/00001510/2020), the University of the Witwatersrand Human Research Ethics Committee (HREC, ref. M180832, M210159, M210752), Stellenbosch University HREC (ref. N20/04/008{\_}COVID19), and the University of Cape Town HREC (ref. 383/2020), the University of Pretoria HREC (100/2017), and the University of Free State Health Sciences Research Ethics Committee (ref. UFS HSD2020/1860/2710). Individual participant consent was not required for genomic surveillance, this requirement was waived by the Research Ethics Committees. Following sequencing, all consensus sequences are uploaded to GISAID33 and their use is subject to the database terms and conditions. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. 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 sequence data is public at GISAID. Short reads (i.e. FastQ files) are available at the Short Read Archive of the NCBI. [htts://www.ceri.org.za][1] [1]: https://www.ceri.org.za},
author = {Tegally, Houriiyah and Wilkinson, Eduan and Althaus, Christian L and Giovanetti, Marta and San, James Emmanuel and Giandhari, Jennifer and Pillay, Sureshnee and Naidoo, Yeshnee and Ramphal, Upasana and Msomi, Nokukhanya and Mlisana, Koleka and Amoako, Daniel G and Everatt, Josie and Mohale, Thabo and Nguni, Anele and Mahlangu, Boitshoko and Ntuli, Noxolo and Khumalo, Zamantungwa T and Makatini, Zinhle and Wolter, Nicole and Scheepers, Cathrine and Ismail, Arshad and Doolabh, Deelan and Joseph, Rageema and Strydom, Amy and Mendes, Adriano and Davis, Michaela and Mayaphi, Simnikiwe H and Ramphal, Yajna and Maharaj, Arisha and Karim, Wasim Abdool and Tshiabuila, Derek and Anyaneji, Ugochukwu J and Singh, Lavanya and Engelbrecht, Susan and Fonseca, Vagner and Marais, Kruger and Korsman, Stephen and Hardie, Diana and Hsiao, Nei-yuan and Maponga, Tongai and van Zyl, Gert and Marais, Gert and Iranzadeh, Arash and Martin, Darren and Alcantara, Luiz Carlos Junior and Bester, Phillip Armand and Nyaga, Martin M and Subramoney, Kathleen and Treurnicht, Florette K and Venter, Marietjie and Goedhals, Dominique and Preiser, Wolfgang and Bhiman, Jinal N and von Gottberg, Anne and Williamson, Carolyn and Lessells, Richard J and de Oliveira, Tulio},
doi = {10.1101/2021.09.23.21264018},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Tegally et al. - 2021 - Rapid replacement of the Beta variant by the Delta variant in South Africa.pdf:pdf},
journal = {medRxiv},
keywords = {OA,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,genomics{\_}fund{\_}ack,original},
month = {sep},
pages = {2021.09.23.21264018},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Rapid replacement of the Beta variant by the Delta variant in South Africa}},
url = {https://www.medrxiv.org/content/10.1101/2021.09.23.21264018v1 https://www.medrxiv.org/content/10.1101/2021.09.23.21264018v1.abstract},
year = {2021}
}
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