Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages
Author:
Tegally Houriiyah, Moir Monika, Everatt Josie, Giovanetti Marta, Scheepers Cathrine, Wilkinson Eduan, Subramoney Kathleen, Moyo Sikhulile, Amoako Daniel G., Baxter Cheryl, Althaus Christian L., Anyaneji Ugochukwu J., Kekana Dikeledi, Viana Raquel, Giandhari Jennifer, Lessells Richard J., Maponga Tongai, Maruapula Dorcas, Choga Wonderful, Matshaba Mogomotsi, Mayaphi Simnikiwe, Mbhele Nokuzola, Mbulawa Mpaphi B., Msomi Nokukhanya, Naidoo Yeshnee, Pillay Sureshnee, Sanko Tomasz Janusz, San James E., Scott Lesley, Singh Lavanya, Magini Nonkululeko A., Smith-Lawrence Pamela, Stevens Wendy, Dor Graeme, Tshiabuila Derek, Wolter Nicole, Preiser Wolfgang, Treurnicht Florette K., Venter Marietjie, Davids Michaela, Chiloane Georginah, Mendes Adriano, McIntyre Caitlyn, O’Toole Aine, Ruis Christopher, Peacock Thomas P., Roemer Cornelius, Williamson Carolyn, Pybus Oliver G., Bhiman Jinal, Glass Allison, Martin Darren P., Rambaut Andrew, Gaseitsiwe Simani, Gottberg Anne von, de Oliveira TulioORCID,
Abstract
AbstractSouth Africa’s fourth COVID-19 wave was driven predominantly by three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern. We have now identified two new lineages, BA.4 and BA.5. The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del, L452R, F486V and the wild type amino acid at Q493. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure with the TaqPath™ COVID-19 qPCR assay. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa from the first week of April 2022 onwards. Using a multinomial logistic regression model, we estimate growth advantages for BA.4 and BA.5 of 0.08 (95% CI: 0.07 - 0.09) and 0.12 (95% CI: 0.09 - 0.15) per day respectively over BA.2 in South Africa.
Publisher
Cold Spring Harbor Laboratory
Cited by
71 articles.
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