Abstract
Background and Aim: Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting a wide variety of domestic and wild cloven-hoofed animals, caused by an Aphthovirus, a member of the family Picornaviridae. Between 2015 and 2018, approximately 272 outbreaks of foot-and-mouth disease occurred in seven provinces across Saudi Arabia, affecting domestic and wild animals. This is a retrospective study designed to determine the topotypes/lineages that caused FMD outbreaks in the Kingdom of Saudi Arabia (KSA) during this period and to compare their genetic diversities with the vaccine strains.
Materials and Methods: A 603 clinical specimens were tested with quantitative RT-PCR and sandwich antigen ELISA. The level of agreement between the two assays was calculated using the Kappa statistics. About 17 samples were subjected to cultivation in the BHK21 cell culture. A partial sequencing of Viral protein1 (VP1) of 10 isolates was conducted with the Illumina Miseq platform.
Results: About 272 (45.1%) samples were tested positive with quantitative RT-PCR, and 199(33%) samples were tested positive with sandwich ELISA, of which 133(66.8%) were serotype O and 66(33.2%) were serotype A. the agreement between assays is substantial as calculated by the kappa statistic (kappa = 0.750, 95% CI = 0.00-0.005; p < 0). Fourteen out of seventeen samples were isolated on the BHK21 cell line. Phylogenetic Analysis grouped sequences of the VP1 gene that were generated from 10 FMDV isolates into previously observed topotypes in KSA. Serotypes (O) isolates clustered with sublineage (O/ME-SA/PanAsia-2/ANT-10) serotype (A) isolates clustered in a lineage (A/ASIA/ G-VII). Aligning the amino acid sequences at the G-H loop region with vaccine strains revealed crucial mutations at positions: (S134C, D139S, T140R/H, V141A, N143S, and A158T) for serotype O and S134N, T143A, T147Q/C, G148E, A151T, and I154V for serotype A.
Conclusion:
. This five-year study highlights the re-emergence of foot-and-mouth disease virus strains O/ME-SA/PanAsia-2 and A/ASIA/G-VII. The study encourages continuous updates and usage of multiple diagnostic methods (PCR, ELISA, and virus isolation). In particular, virus isolation is essential for improving the performance of the S-ELISA test. Further research is recommended to study the complete genome of circulating foot-and-mouth virus strains to select effective vaccines.

Key words: Foot and mouth disease, Kingdom of Saudi Arabia, lineage A/ASIA/G-VII, lineage O/ME-SA/PanAsia-2.