Foot and mouth disease (FMD) is a contagious viral disease of cloven-hooved animals which is very significant economically in Kenya. Over 100 outbreaks occur annually, despite regular vaccinations. This is allegedly due to unavailability of vaccines of good quality and potency, and/or failure of vaccine matching with the circulating field strains. This study was aimed at establishing the match between field and vaccine strain. We sequenced the VP1 genomic region of the virus isolates collected in 2019 and 2020 and compared them to VP1 sequences of the vaccine and Gene bank. Phylogenetic analysis of the VP1 nucleotide sequences revealed that type A strains belonged to the genotype VII (G-VII) within the AFRICA topo type and had a 99.5%-99.8% nucleotide similarity with the vaccine strain. SAT 1 isolates showed 99.7% - 99.9% nucleotide identity with the vaccine strain and fell in Africa topo type I (North West Zimbabwe) with one sub lineage. There were no SAT 2 sequences generated for comparison. High similarity index of 99%-100% was noted between all the isolates and the reference vaccine strains in the country. Therefore, regular vaccinations, control of animal movements with regular monitoring of the circulating serotypes and topo types in Kenya are recommended.

Keywords: Vaccine, outbreaks, virus, strains, mismatch, Kenya.