@article{Tegally_H-2022_92702,
title = {Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa},
author = {Tegally, H. and Moir, M. and Everatt, J. and Giovanetti, M. and Scheepers, C. and Wilkinson, E. and Subramoney, K. and Makatini, Z. and Moyo, S. and Amoako, D. and Baxter, C. and Althaus, C. and Anyaneji, U. and Kekana, D. and Viana, R. and Giandhari, J. and Lessells, R. and Maponga, T. and Maruapula, D. and Choga, W. and Matshaba, M. and Mbulawa, M. and Msomi, N. and NGS-SA Consortium and Naidoo, Y. and Pillay, S. and Sanko, T. and San, J. and Scott, L. and Singh, L. and Magini, N. and Smith-Lawrence, P. and Stevens, W. and Dor, G. and Tshiabuila, D. and Wolter, N. and Preiser, W. and Treurnicht, F. and Venter, M. and Chiloane, G. and McIntyre, C. and O'Toole, Á. and Ruis, C. and Peacock, T. and Roemer, C. and Kosakovsky Pond, S. and Williamson, C. and Pybus, O. and Bhiman, J. and Glass, A. and Martin, D. and Jackson, B. and Rambaut, A. and Laguda-Akingba, O. and Gaseitsiwe, S. and von Gottberg, A. and De Oliveira, T.},
month = {jun},
year = {2022},
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.},
journal = {Nature Medicine},
publisher = {Springer Nature},
url = {https://doi.org/10.1038/s41591-022-01911-2},
}
