VP1 region-based molecular characterization of foot-and-mouth disease virus serotype O from clinical cases in Haryana, India.

BACKGROUND: Foot-and-mouth disease (FMD) is a highly transmissible viral infection affecting cloven-hoofed animals, significantly impacting livestock productivity and trade in India. The causative agent, FMD virus (FMDV), exhibits considerable genetic and antigenic diversity, with serotype O being most prevalent. Haryana, a northern Indian state with a large susceptible livestock population, has reported sporadic FMD cases despite ongoing vaccination efforts. This study aims to detect, type, and characterize FMDV from suspected animals in Haryana during 2024, with a focus on genetic variations in the VP1 region compared to the vaccine strain and contemporary isolates. RESULTS: Clinical samples from suspected cases were analyzed using RT-multiplex PCR, confirming the presence of FMDV O in five buffaloes from two districts. The partial P1 region was amplified and sequenced from five samples using 1C/2B gene-specific primers. Phylogenetic analysis classified all five samples (GenBank Accession Nos. PV068827-PV068830 & PV288326) within the Middle East-South Asia (ME-SA) topotype based on 1D gene sequences (639 nt). Four samples (PV068827-PV068830) exhibited 12.3-12.8% nucleotide divergence from the Indian vaccine strain FMDV O/IND/R2/1975 and clustered under the O/ME-SA/SA-2018 lineage, while one sample (PV288326), showing 14.3% divergence, belonged to the O/ME-SA/Ind2001e lineage. Amino acid analysis revealed 10-11 variations, including four common mutations. Antigenic sites remained conserved, except for an I144V substitution, which is common in all Indian serotype O isolates reported earlier. CONCLUSION: These findings underscore the need for targeted interventions, such as enhanced biosecurity at livestock fairs and markets, restrictions on animal movement from endemic to disease-free zones, wildlife surveillance, and the inclusion of the role of less-monitored species, like small ruminants and wildlife in virus maintenance. Future studies should include antigenic relationship (r-value) tests to assess vaccine efficacy against circulating strains.