Molecular characterization and vaccine matching of foot-and-mouth disease virus in Khyber Pakhtunkhwa, Pakistan

BACKGROUND: Foot-and-mouth disease (FMD) remains a major constraint to livestock productivity in Pakistan, particularly in Khyber Pakhtunkhwa (KP), where recurrent outbreaks cause substantial economic losses. Despite routine biannual vaccination, the continued circulation of FMD virus (FMDV) serotype A predominantly the A-Iran-05 lineage raises concerns regarding antigenic mismatch between field strains and vaccine formulations. METHODS: Results A total of 244 epithelial tissue samples were collected from clinically infected cattle and buffaloes across four districts of KP. Of these, 226 samples were confirmed positive for FMDV serotype A by RT-PCR, and 215 VP1 gene sequences were successfully obtained. Phylogenetic analysis revealed that all isolates clustered within the A-Iran-05 lineage and were genetically distinct from the vaccine strain A22/Iraq/64. Antigenic relationship analysis demonstrated low r₁-values (< 0.39), indicating poor antigenic matching and suggesting reduced vaccine effectiveness. Epidemiological analysis identified age (2-4 years) as a significant risk factor for infection, while no significant associations were observed with sex, species, vaccine brand, or clinical severity. CONCLUSIONS: The dominance of antigenically divergent FMDV serotype A strains in KP highlights the limitations of current vaccine formulations. Continuous molecular surveillance and the development of region-specific vaccines are essential to improve FMD control strategies in endemic regions of Pakistan.