Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
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; Maponga, Tongai; Maruapula, Dorcas; Choga, Wonderful; Matshaba, Mogomotsi; Mbulawa, Mpaphi B.; Msomi, Nokukhanya; NGS-SA consortium; 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; Pond, Sergei L. Kosakovsky; 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; 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
Date:
2022-09
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.
Description:
DATA AVAILABILITY : All of the SARS-CoV-2 genomes generated and presented in this article are publicly accessible through the GISAID platform (https://www.gisaid.org/). The GISAID accession identifiers of the sequences analyzed in this study are provided as part of Supplementary Table 1. Other raw data for this study are provided as a supplementary dataset at https://github.com/krisp-kwazulu-natal/SARSCoV2_South_Africa_Omicron_BA4_BA5. The reference SARS-CoV-2 genome (MN908947.3) was downloaded from the National Center for Biotechnology Information database (https://www.ncbi.nlm.nih.gov/).
CODE AVAILABILITY : All custom scripts to reproduce the analyses and figures presented in this article are available at https://github.com/krisp-kwazulu-natal/ SARSCoV2_South_Africa_Omicron_BA4_BA5.