TY - JOUR
AU - Tegally, Houriiyah
AU - Moir, Monika
AU - Everatt, Josie
AU - Giovanetti, Marta
AU - Scheepers, Cathrine
AU - Wilkinson, Eduan
AU - Subramoney, Kathleen
AU - Makatini, Zinhle
AU - Moyo, Sikhulile
AU - Amoako, Daniel G.
AU - Baxter, Cheryl
AU - Althaus, Christian L.
AU - Anyaneji, Ugochukwu J.
AU - Kekana, Dikeledi
AU - Viana, Raquel
AU - Giandhari, Jennifer
AU - Lessells, Richard J.
AU - Maponga, Tongai
AU - Maruapula, Dorcas
AU - Choga, Wonderful T.
AU - Matshaba, Mogomotsi
AU - Mbulawa, Mpaphi B.
AU - Msomi, Nokukhanya
AU - NGS-SA Consortium
AU - Naidoo, Yeshnee
AU - Pillay, Sureshnee
AU - Sanko, Tomasz Janusz
AU - San, James E.
AU - Scott, Lesley
AU - Singh, Lavanya
AU - Magini, Nonkululeko A.
AU - Smith-Lawrence, Pamela
AU - Stevens, Wendy
AU - Dor, Graeme
AU - Tshiabuila, Derek
AU - Wolter, Nicole
AU - Preiser, Wolfgang
AU - Treurnicht, Florette
AU - Venter, Marietje
AU - Chiloane, Georginah
AU - McIntyre, Caitlyn
AU - O'Toole, Áine Niamh
AU - Ruis, Christopher
AU - Peacock, Thomas P.
AU - Roemer, Cornelius
AU - Kosakovsky Pond, Sergei L.
AU - Williamson, Carolyn
AU - Pybus, Oliver G.
AU - Bhiman, Jinal N.
AU - Glass, Allison
AU - Martin, Darren P.
AU - Jackson, Ben
AU - Rambaut, Andrew
AU - Laguda-Akingba, Oluwakemi
AU - Gaseitsiwe, Simani
AU - von Gottberg, Anne
AU - De Oliveira, Tulio
PY - 2022
DA - June
TI - Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
JO - Nature Medicine
DO - https://doi.org/10.1038/s41591-022-01911-2
AB - 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.
PB - Springer Nature
UR - https://www.research.ed.ac.uk/en/publications/e4469a25-526c-472c-9954-c9a596e94bea
KW - Coronavirus (COVID-19)
ER