Article
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Registro en:
TEGALLY, Houriiyah et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nature Medicine, v. 28, p. 1785-1790, p. 1 - 18, Sept. 2022.
1546-170X
10.1038/s41591-022-01911-2
Autor
Tegally, Houriiyah
Moir, Monika
Monika, 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
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
Jackson, Ben
Rambaut, Andrew
Laguda-Akingba, Oluwakemi
Gaseitsiwe, Simani
von Gottberg, Anne
Oliveira, Tulio de
Resumen
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.