Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

dc.creatorTegally, Houriiyah
dc.creatorMoir, Monika
dc.creatorMonika, Josie
dc.creatorGiovanetti, Marta
dc.creatorScheepers, Cathrine
dc.creatorWilkinson, Eduan
dc.creatorSubramoney, Kathleen
dc.creatorMakatini, Zinhle
dc.creatorMoyo, Sikhulile
dc.creatorAmoako, Daniel G.
dc.creatorBaxter, Cheryl
dc.creatorAlthaus, Christian L.
dc.creatorAnyaneji, Ugochukwu J.
dc.creatorKekana, Dikeledi
dc.creatorViana, Raquel
dc.creatorGiandhari, Jennifer
dc.creatorLessells, Richard J.
dc.creatorMaponga, Tongai
dc.creatorMaruapula, Dorcas
dc.creatorChoga, Wonderful
dc.creatorMatshaba, Mogomotsi
dc.creatorMbulawa, Mpaphi B.
dc.creatorMsomi, Nokukhanya
dc.creatorNaidoo, Yeshnee
dc.creatorPillay, Sureshnee
dc.creatorSanko, Tomasz Janusz
dc.creatorSan, James E.
dc.creatorScott, Lesley
dc.creatorSingh, Lavanya
dc.creatorMagini, Nonkululeko A.
dc.creatorSmith-Lawrence, Pamela
dc.creatorStevens, Wendy
dc.creatorDor, Graeme
dc.creatorTshiabuila, Derek
dc.creatorWolter, Nicole
dc.creatorPreiser, Wolfgang
dc.creatorTreurnicht, Florette K.
dc.creatorVenter, Marietjie
dc.creatorChiloane, Georginah
dc.creatorMcIntyre, Caitlyn
dc.creatorO’Toole, Aine
dc.creatorRuis, Christopher
dc.creatorPeacock, Thomas P.
dc.creatorRoemer, Cornelius
dc.creatorPond, Sergei L. Kosakovsky
dc.creatorWilliamson, Carolyn
dc.creatorPybus, Oliver G.
dc.creatorBhiman, Jinal N.
dc.creatorGlass, Allison
dc.creatorJackson, Ben
dc.creatorRambaut, Andrew
dc.creatorLaguda-Akingba, Oluwakemi
dc.creatorGaseitsiwe, Simani
dc.creatorvon Gottberg, Anne
dc.creatorOliveira, Tulio de
dc.date2022-12-28T11:21:24Z
dc.date2022-12-28T11:21:24Z
dc.date2022
dc.date.accessioned2023-09-26T20:21:21Z
dc.date.available2023-09-26T20:21:21Z
dc.identifierTEGALLY, 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.
dc.identifier1546-170X
dc.identifierhttps://www.arca.fiocruz.br/handle/icict/56219
dc.identifier10.1038/s41591-022-01911-2
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/8854990
dc.descriptionThree 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.
dc.formatapplication/pdf
dc.languageeng
dc.publisherNature
dc.rightsopen access
dc.subjectSARS-CoV-2
dc.subjectSurgimento de linhagens
dc.subjectOmicron BA.4
dc.subjectBA.5
dc.subjectÁfrica do Sul
dc.subjectSARS-CoV-2
dc.subjectOmicron lineages BA.4
dc.subjectOmicron lineages BA.5
dc.subjectSouth Africa
dc.subjectEmergence
dc.titleEmergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
dc.typeArticle


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