- Published
- 27 June 2022
- Journal article
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
- Authors
-
- Source
- Nature Medicine
Abstract
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (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 similar to BA.2 except for the addition of 69–70 deletion (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 differ only 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 estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (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.
Rights
This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Cite as
Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D., Baxter, C., Althaus, C., Anyaneji, U., Kekana, D., Viana, R., Giandhari, J., Lessells, R., Maponga, T., Maruapula, D., Choga, W., Matshaba, M., Mbulawa, M., Msomi, N., NGS-SA Consortium, Naidoo, Y., Pillay, S., Sanko, T., San, J., Scott, L., Singh, L., Magini, N., Smith-Lawrence, P., Stevens, W., Dor, G., Tshiabuila, D., Wolter, N., Preiser, W., Treurnicht, F., Venter, M., Chiloane, G., McIntyre, C., O'Toole, Á., Ruis, C., Peacock, T., Roemer, C., Kosakovsky Pond, S., Williamson, C., Pybus, O., Bhiman, J., Glass, A., Martin, D., Jackson, B., Rambaut, A., Laguda-Akingba, O., Gaseitsiwe, S., von Gottberg, A. & De Oliveira, T. 2022, 'Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa', Nature Medicine. https://doi.org/10.1038/s41591-022-01911-2