Emergence of new sublineages of serotype O foot-and-mouth disease viruses circulating in Pakistan during 2012-2021.

Foot-and-mouth disease (FMD) is endemic in Pakistan and serotypes O, A and Asia-1 of FMD virus (FMDV) are responsible for the outbreaks in the country. The dominant serotype is type O represented by the O/ME-SA/PanAsia-2 lineage, which has diverged into different sublineages. Characterizing circulating viruses helps to trace the origin of outbreaks and provides evidence to select appropriate vaccines. The present study characterized viruses belonging to the O/ME-SA/PanAsia-2 lineage collected from bovines during 2012-2021. Phylogenetic analyses using the VP1 coding sequences revealed that these viruses grouped into five sublineages, of which two have been described previously, i.e. O/ME-SA/PanAsia-2 and O/ME-SA/PanAsia-2, while the three new sublineages are designated here as O/ME-SA/PanAsia-2, O/ME-SA/PanAsia-2 and O/ME-SA/PanAsia-2. Antigenic profiling of selected viruses belonging to the PanAsia-2 and PanAsia-2 sublineages was carried out using antisera raised against three reference vaccine strains: O Manisa, O/TUR 5/2009 and O 3039. The data highlighted that some of the viruses, belonging to these sublineages, were not efficiently neutralized by the reference antisera. This may be due to the individual or combined effects of multiple amino acid changes in these field isolates at known antigenic sites. This study reveals that serotype O FMDVs are continuously evolving in Pakistan and that continuous surveillance to characterize viruses causing field outbreaks is important to identify the emergence of new FMDV sublineages that may be poorly controlled using existing FMD vaccines.