Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Authors: Tegally Houriiyah , Moir Monika , Everatt Josie , Giovanetti Marta , Scheepers Cathrine , Wilkinson Eduan , Subramoney Kathleen , Makatini Zinhle , 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 , Mbulawa Mpaphi B. , Msomi Nokukhanya ,   NGS-SA consortium, Bester Armand Phillip , Claassen Mathilda , Doolabh Deelan , Mudau Innocent , Mbhele Nokuzola , Engelbrecht Susan , Goedhals Dominique , Hardie Diana , Hsiao Nei-Yuan , Iranzadeh Arash , Ismail Arshad , Joseph Rageema , Maharaj Arisha , Mahlangu Boitshoko , Mahlakwane Kamela , Davis Ashlyn , Marais Gert , Mlisana Koleka , Mnguni Anele , Mohale Thabo , Motsatsi Gerald , Mwangi Peter , Ntuli Noxolo , Nyaga Martin , Olubayo Luicer , Radibe Botshelo , Ramphal Yajna , Ramphal Upasana , Strasheim Wilhelmina , Tebeila Naume , van Wyk Stephanie , Wilson Shannon , Lucaci Alexander G. , Weaver Steven , Maharaj Akhil , Pillay Yusasha , Davids Michaela , Mendes Adriano , Mayaphi Simnikiwe , 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 , Chiloane Georginah , McIntyre Caitlyn , O’Toole Aine , Ruis Christopher , Peacock Thomas P. , Roemer Cornelius , Kosakovsky Pond Sergei L. , Williamson Carolyn , Pybus Oliver G. , Bhiman Jinal N. , Glass Allison , Martin Darren P. , Jackson Ben , Rambaut Andrew , Laguda-Akingba Oluwakemi , Gaseitsiwe Simani , von Gottberg Anne , de Oliveira Tulio 
Published: June 2022

AbstractThree 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.