1b), and early dispersal of BA.5 from Gauteng to KwaZulu-Natal, with more limited onward spread to other provinces (Fig. Phylogeographic analysis suggests early dispersal of BA.4 from Limpopo to Gauteng, with later spread to other provinces (Fig. 1a), coinciding with the emergence of the other lineages-for example, BA.2 in early November 2021 (HPD: 9 October 2021 to 29 November 2021). The most recent common ancestor of BA.4 and BA.5 is estimated to have originated in mid-November 2021 (HPD: 29 September 2021 to 6 December 2021) (Fig.
BA.4 and BA.5 are estimated to have originated in mid-December 2021 (95% highest posterior density (HPD): 25 November 2021 to 1 January 2022) and early January 2022 (HPD: 10 December 2021 to 6 February 2022), respectively (Fig. Bayesian phylogenetic methods revealed that BA.4 and BA.5 are distinct from the other Omicron lineages (molecular clock signal: correlation coefficient = 0.6, R 2 = 0.4 Extended Data Fig. We recently identified two new Omicron lineages that have been designated BA.4 and BA.5 by the Pango Network and pango-designation version 1.3, a system of naming and classifying SARS-CoV-2 lineages (Fig. This pattern was not consistent worldwide, however, and, in some countries, BA.2 was responsible for a greater share of cases, hospitalizations and deaths during the Omicron wave 2, 3, 4. Despite being associated with a modest prolongation of the fourth wave, the displacement of BA.1 by BA.2 in South Africa was not associated with a substantial resurgence in cases, hospital admissions or deaths. However, as that wave receded in mid-January 2022, BA.2 became the dominant South African lineage. BA.1 caused most of the infections in South Africa’s fourth epidemic wave. Initially, Omicron was comprised of three sister lineages: BA.1, BA.2 and BA.3. Within days of being discovered in South Africa and Botswana, on 26 November 2021, the Omicron variant of SARS-CoV-2 was designated as a variant of concern by the World Health Organization 1. 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. 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. 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.
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. The two lineages differ only outside of the spike region. 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. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. 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. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
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