Whole-genome sequencing of foot-and-mouth disease virus serotype O/PanAsia-۲/QOM-۱۵ and comparison of its VP۱-encoding region with two vaccine strains

Despite widespread vaccination against foot-and-mouth disease, many outbreaks still occur in endemic areas. We attempted to determine the genetic and antigenic properties of the O/PanAsia-۲/QOM-۱۵ foot-and-mouth disease virus new vaccine strain. Thus, whole-genome sequencing was used to identify vulnerable pinpoint sites across the genome. The VP۱ sequence (۱D gene) of the O/PanAsia-۲/QOM-۱۵ viral genome was then compared to the VP۱ sequences of two previously used vaccine strains, O/PanAsia (JQ۳۲۱۸۳۷) and O/PanAsia-۲ (JN۶۷۶۱۴۶). The antigenic relationship of these three viruses was calculated by the two dimensional-virus neutralization test. At the nucleotide level, ۴۷ single variants were identified, of which ۱۹.۰۰% were in the ۵' untranslated region (UTR), ۷۹.۰۰% in the polyprotein region, and ۲.۰۰% in the ۳' UTR region. Approximately half of the single nucleotide polymorphisms that have occurred in ۱D gene resulted in amino acid (AA) substitutions in the VP۱ structure. The single nucleotide polymorphisms also caused AA substitutions in other structural proteins, including VP۲ and VP۳, and some non-structural proteins (Lpro, ۲C, and ۳A). The O/PanAsia-۲/QOM-۱۵ shared higher sequence similarity with O/PanAsia-۲ (۹۱.۰۰%) compared to O/PanAsia (۸۷.۳۰%). Evaluating r-value showed that the antigenic relationship of O/PanAsia-۲/QOM-۱۵ with O/PanAsia-۲ (۲۹.۰۰%) was greater than that of the O/PanAsia (۲۴.۰۰%); however, all three viruses were immunologically distinct. After ۱۰ years, the alteration of virus antigenicity and the lack of detectable adaptive pressure on VP۱ sequence suggest that studying genetic dynamics beyond the VP۱ region is necessary to evaluate FMDV pathogenicity and vaccine failure.