Whole-genome sequencing of foot-and-mouth disease virus serotype O/PanAsia-2/QOM-15 and comparison of its VP1-encoding region with two vaccine strains

Mehrnoosh Gadir; Seyed Mahmoud Azimi; Naser Harzandi; Behzad Hemati; Neda Eskandarzade

doi:10.30466/vrf.2023.1978294.3704

Whole-genome sequencing of foot-and-mouth disease virus serotype O/PanAsia-2/QOM-15 and comparison of its VP1-encoding region with two vaccine strains

Vet Res Forum. 2023;14(11):615-623. doi: 10.30466/vrf.2023.1978294.3704. Epub 2023 Nov 15.

Authors

Mehrnoosh Gadir¹, Seyed Mahmoud Azimi², Naser Harzandi¹, Behzad Hemati¹, Neda Eskandarzade³

Affiliations

¹ Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran.
² Foot and Mouth Disease Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
³ Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran.

Abstract

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-2/QOM-15 foot-and-mouth disease virus new vaccine strain. Thus, whole-genome sequencing was used to identify vulnerable pinpoint sites across the genome. The VP1 sequence (1D gene) of the O/PanAsia-2/QOM-15 viral genome was then compared to the VP1 sequences of two previously used vaccine strains, O/PanAsia (JQ321837) and O/PanAsia-2 (JN676146). The antigenic relationship of these three viruses was calculated by the two dimensional-virus neutralization test. At the nucleotide level, 47 single variants were identified, of which 19.00% were in the 5' untranslated region (UTR), 79.00% in the polyprotein region, and 2.00% in the 3' UTR region. Approximately half of the single nucleotide polymorphisms that have occurred in 1D gene resulted in amino acid (AA) substitutions in the VP1 structure. The single nucleotide polymorphisms also caused AA substitutions in other structural proteins, including VP2 and VP3, and some non-structural proteins (L^pro, 2C, and 3A). The O/PanAsia-2/QOM-15 shared higher sequence similarity with O/PanAsia-2 (91.00%) compared to O/PanAsia (87.30%). Evaluating r-value showed that the antigenic relationship of O/PanAsia-2/QOM-15 with O/PanAsia-2 (29.00%) was greater than that of the O/PanAsia (24.00%); however, all three viruses were immunologically distinct. After 10 years, the alteration of virus antigenicity and the lack of detectable adaptive pressure on VP1 sequence suggest that studying genetic dynamics beyond the VP1 region is necessary to evaluate FMDV pathogenicity and vaccine failure.

Keywords: FMDV serotype O; RNA-Seq; SNP discovery; VP1; Whole-genome sequencing.