Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya

The recombinant FY.4 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant was first reported in Kenya in March 2023 and was the dominant circulating variant between April and July 2023. The variant was characterized by two important mutations: Y451H in the receptor-binding domain of the spike protein and P42L in open reading frame 3a. Using phylogenetics and phylodynamic approaches, we investigated the emergence and spread of FY.4 in Kenya and the rest of the world. Our findings suggest FY.4 circulated early in Kenya before its export to North America and Europe. Early circulation of FY.4 in Kenya was predominantly observed in the coastal part of the country, and the estimated time to the most recent common ancestor suggests FY.4 circulated as early as December 2022. The collected genomic and epidemiological data show that the FY.4 variant led to a large local outbreak in Kenya and resulted in localized outbreaks in Europe, North America, and Asia-Pacific. These findings underscore the importance of sustained genomic surveillance, especially in under-sampled regions, in deepening our understanding of the evolution and spread of SARS-CoV-2 variants.