Molecular identification and phylogenetic analysis of emerging foot-and-mouth disease virus type O, topotype ME-SA, in the southwestern region of Pakistan
TL;DR
FMDV serotype O (ME-SA) is confirmed as the dominant strain causing endemic outbreaks in Quetta, Pakistan, and strengthening active surveillance and molecular monitoring systems is crucial for early detection, effective vaccination planning, and regulation of cross-border livestock movement with Afghanistan, Iran, and other regions of Pakistan.
Abstract
ABSTRACT: Foot-and-mouth disease virus (FMDV) is among the most contagious and economically significant viral pathogens of livestock worldwide. In Quetta, Balochistan, recurrent FMDV outbreaks continue to affect cattle and buffalo populations, yet genomic data on circulating strains remain scarce. This study investigated the molecular characteristics and phylogenetic relationships of FMDV serotypes and topotypes detected during 2021 surveillance in Quetta, Pakistan. Twenty epithelial tissue samples, previously confirmed as FMDV-positive through sandwich ELISA, were analyzed for viral RNA using real-time reverse transcription polymerase chain reaction (RT-PCR). Positive samples underwent VP1 gene sequencing, followed by phylogenetic analysis. FMDV RNA was detected in 80% (16/20; 95% CI: 56%-94%) of samples. Among infected animals, 87.5% were female, 69% were cattle, and most (63%) were aged 1-4 years. The highest number of cases (25%) originated from the Jan Muhammad Road area. Phylogenetic analysis revealed all isolates belonged to FMDV serotype O, topotype Middle East-South Asia (ME-SA). These findings confirm FMDV serotype O (ME-SA) as the dominant strain causing endemic outbreaks in Quetta. Strengthening active surveillance and molecular monitoring systems is crucial for early detection, effective vaccination planning, and regulation of cross-border livestock movement with Afghanistan, Iran, and other regions of Pakistan.