This work conducts a comprehensive evolutionary analysis of the Ind-2001 and Pan Asia II lineages, with a specific emphasis on their geographical distribution, lineage classification, and sub-lineage distribution within the region. Furthermore, it aims to expand our understanding of the conserved region of the VP1 protein.

During past few years, the Ind-2001 lineage of the Middle East-South Asia topotype (ME-SA) of the foot-and-mouth disease (FMD) virus has been implicated in FMD outbreaks in Pakistan. Aims: This work conducts a comprehensive evolutionary analysis of the Ind-2001 and Pan Asia II lineages, with a specific emphasis on their geographical distribution, lineage classification, and sub-lineage distribution within the region. Furthermore, it aims to expand our understanding of the conserved region of the VP1 protein.

Observed mutations suggest potential challenges to current vaccination efficacy against FMD. This emphasizes enhanced FMD surveillance and demonstrates that tracking the emergence of the O/ME-SA/Ind-2001e lineage is important for determining FMD control strategies in Asia.

Total samples (n=50) were subjected to antigen detection ELISA and RT-PCR for serotype determination. Confirmed serotype-O isolates (n=17) underwent sequencing for lineage comparison, mutation impact assessment on the VP1 protein GH loop, 3D structure prediction, and further comparative analysis.

Isolates collected from 2017 to 2020 were identified as serotypes O/ME-SA/Pan Asia II ANT10 and O/ME-SA/Pak14. Notably, isolates collected from 2020 to 2022 belonged to a novel FMDV serotype O/ME-SA/Ind-2001e lineage. Phylogenetic analyses indicated that these strains were distinct from dominant contemporaneous strains which may challenge Pakistan's FMD control measures. These isolates exhibited variance in the VP1 epitope, specifically in amino acid residues 135-155, known to influence neutralizing antibody generation.