Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D. G, Baxter, C., Althaus, C. L, Anyaneji, U. J, Kekana, D., Viana, R., Giandhari, J., Lessells, R. J, Maponga, T., Maruapula, D., Choga, W., Matshaba, M., Mbulawa, M. B, Msomi, N., consortium , N., Naidoo, Y., Pillay, S., Sanko, T. J., San, J. E, Scott, L., Singh, L., Magini, N. A, Smith-Lawrence, P., Stevens, W., Dor, G., Tshiabuila, D., Wolter, N., Preiser, W., Treurnicht, F. K, Venter, M., Chiloane, G., McIntyre, C., O'Toole, A., Ruis, C., Peacock, T. P, Roemer, C., Pond, S. L K., Williamson, C., Pybus, O. G, Bhiman, J. N, Glass, A., Martin, D. P, Jackson, B., Rambaut, A., Laguda-Akingba, O., Gaseitsiwe, S., von Gottberg, A., & de Oliveira, T. Nature Medicine, 28(9):1785–1790, Nature Publishing Group, jun, 2022. ![Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern predominantly drove South Africa's fourth COVID-19 wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild type amino acid at Q493.The two lineages only differ outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature . BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimate growth advantages for BA.4 and BA.5 of 0.08 (95% CI: 0.08 - 0.09) and 0.10 (95% CI: 0.09 - 0.11) per day respectively over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.
@article{Tegally2022b,
abstract = {Three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern predominantly drove South Africa's fourth COVID-19 wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild type amino acid at Q493.The two lineages only differ outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature . BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50{\%} of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimate growth advantages for BA.4 and BA.5 of 0.08 (95{\%} CI: 0.08 - 0.09) and 0.10 (95{\%} CI: 0.09 - 0.11) per day respectively over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.},
author = {Tegally, Houriiyah and Moir, Monika and Everatt, Josie and Giovanetti, Marta and Scheepers, Cathrine and Wilkinson, Eduan and Subramoney, Kathleen and Makatini, Zinhle and Moyo, Sikhulile and Amoako, Daniel G and Baxter, Cheryl and Althaus, Christian L and Anyaneji, Ugochukwu J and Kekana, Dikeledi and Viana, Raquel and Giandhari, Jennifer and Lessells, Richard J and Maponga, Tongai and Maruapula, Dorcas and Choga, Wonderful and Matshaba, Mogomotsi and Mbulawa, Mpaphi B and Msomi, Nokukhanya and NGS-SA consortium and Naidoo, Yeshnee and Pillay, Sureshnee and Sanko, Tomasz Janusz and San, James E and Scott, Lesley and Singh, Lavanya and Magini, Nonkululeko A and Smith-Lawrence, Pamela and Stevens, Wendy and Dor, Graeme and Tshiabuila, Derek and Wolter, Nicole and Preiser, Wolfgang and Treurnicht, Florette K and Venter, Marietjie and Chiloane, Georginah and McIntyre, Caitlyn and O'Toole, Aine and Ruis, Christopher and Peacock, Thomas P and Roemer, Cornelius and Pond, Sergei L Kosakovsky and Williamson, Carolyn and Pybus, Oliver G and Bhiman, Jinal N and Glass, Allison and Martin, Darren P and Jackson, Ben and Rambaut, Andrew and Laguda-Akingba, Oluwakemi and Gaseitsiwe, Simani and von Gottberg, Anne and de Oliveira, Tulio},
doi = {10.1038/s41591-022-01911-2},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Tegally et al. - 2022 - Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa.pdf:pdf},
issn = {1546-170X},
journal = {Nature Medicine},
keywords = {Epidemiology,OA,Phylogeny,fund{\_}not{\_}ack,original},
mendeley-tags = {OA,fund{\_}not{\_}ack,original},
month = {jun},
number = {9},
pages = {1785--1790},
pmid = {35760080},
publisher = {Nature Publishing Group},
title = {{Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa}},
url = {https://www.nature.com/articles/s41591-022-01911-2},
volume = {28},
year = {2022}
}
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