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; ... (2022). Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nature medicine, 28(9), pp. 1785-1790. Nature Publishing Group 10.1038/s41591-022-01911-2
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Three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern predominantly drove South Africa's fourth 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 comparable to BA.2 except for the addition of 69-70del (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 only differ 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 estimate growth advantages for BA.4 and BA.5 of 0.08 (95% 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.
Item Type: |
Journal Article (Original Article) |
|---|---|
Division/Institute: |
04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Social and Preventive Medicine (ISPM) |
UniBE Contributor: |
Althaus, Christian |
Subjects: |
300 Social sciences, sociology & anthropology > 360 Social problems & social services 600 Technology > 610 Medicine & health |
ISSN: |
1078-8956 |
Publisher: |
Nature Publishing Group |
Language: |
English |
Submitter: |
Pubmed Import |
Date Deposited: |
28 Jun 2022 09:35 |
Last Modified: |
29 Dec 2022 00:25 |
Publisher DOI: |
10.1038/s41591-022-01911-2 |
PubMed ID: |
35760080 |
BORIS DOI: |
10.48350/170962 |
URI: |
https://boris.unibe.ch/id/eprint/170962 |
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