Molecular characterization and epidemiological insights into serotypes of foot-and-mouth disease virus in Pakistan

Foot-and-mouth disease virus (FMDV) causes a highly infectious transboundary disease in cloven-hoofed animals. However, there is limited information on comparative genomic and evolutionary analysis of FMDV strains reported in Pakistan. In the current study, we investigated a few disease outbreaks in Pakistan and determined the complete genome sequences of three isolates belonging to different serotypes: O, A, and Asia-1. Comparative genomic analysis showed a close relationship between the FMDV strains from this study and those reported in neighboring Asian countries. Phylogenetic analysis based on the complete genome and VP1 gene sequences revealed that serotype O clustered within the Pak-98 lineage, serotype A within genotype I, and serotype Asia-1 within group 5, grouping with strains from Pakistan, India, and China. Potential negatively selected sites were identified in the region encoding the structural proteins VP4, VP3, VP2, and VP1, with the most episodic diversifying section observed in the VP1 and VP3 regions. Substantial variation was observed in polymorphic and monomorphic sites, with the highest diversity observed in the VP1 protein of serotype O viruses. No evidence of recombination events was found in the FMDV strains from this study. Our findings indicate the cocirculation of multiple serotypes and sublineages of FMDV in Pakistan, underscoring the potential for the emergence of new variants. This study adds to the existing knowledge on the genetic variation and evolutionary dynamics of FMDV serotypes in Pakistan, providing valuable insights for the development of effective vaccines and improved disease control strategies.