Speaker
Description
Botswana, like the rest of the world, has been significantly impacted by SARS-CoV-2. In November 2022, we detected a monophyletic cluster of genomes comprising a sub-lineage of the Omicron variant of concern (VOC) designated as B.1.1.529.5.3.1.1.1.1.1.1.74.1 (alias FN.1; clade 22E). Genomes were from both epidemiologically linked and unlinked samples collected in three close locations in the district of Greater Gaborone. In this study, we evaluate the worldwide prevalence of the FN.1 lineage, analyse its mutation profile, and conduct a phylogeographic analysis to reveal its global dispersal dynamics. Among approximately 16 million publicly available SARS-CoV-2 sequences generated by September 30, 2023, only 87 were FN.1 lineage including 22 from Botswana, six from South Africa, and 59 from the United Kingdom. The estimated time to most recent common ancestor (tMRCA) of the 87 FN.1 sequences was November 2022 (95% highest-posterior-density (HPD): 25 October 2022 to 1 January 2023), with the earliest sampled of the 22 Botswana sequences being December 7, 2022. Spatiotemporal reconstruction of FN.1 dispersal dynamics indicated Botswana as the most probable place of origin. The FN.1 lineage is derived from the BQ.1.1, and carries three additional mutations in spike protein (NTDS:K182E; RDBS:T478R), nsp13 (nsp13ORF1ab:N268S), and one in the membrane protein (M:D3N). Among the 99 lineages circulating in Botswana, FN.1 was closely linked to BQ.1.1.74 based on phylogenetic inferences-based on maximum likelihood. Other lineage that likely to have emerged in Botswana based on sampling and submission dates is BQ.1.1.64 (September 7, 2022). In conclusion, although BQ.1 and BQ.1.1 were first reported in Nigeria (July 2022), here we report the pre-existence of BQ.1.1.74 as early as May 23, 2022, prior to its precursors. Given the early detection of numerous novel variants from Botswana and neighbouring countries, our study underscores the necessity of ongoing surveillance to track the emergence of potential VOCs.
