Foot-and-mouth disease virus variability and recombination on dairy farms in Pakistan

Field studies on foot-and-mouth disease virus (FMDV) have historically concentrated on viral sequences obtained from clinical cases. However, FMDV often causes several forms of subclinical infections in ruminants, which are further complicated by heterologous FMDV coinfections and reinfections. The focus of this current study was genomic analysis of FMDV isolates obtained from domestic water buffalo (Bubalus bubalis) with no visible signs of disease - subclinical infections. Over a 12-month period, buffalo from dairy farms in Islamabad, Pakistan, were repeatedly sampled. We used full-genome next-generation sequencing to analyze FMDVs isolated from 68 oropharyngeal fluid (OPF) samples, representing 44 animals across 18 farms. The analysis revealed the circulation of three distinct serotypes - O, A, and Asia-1. Examination of persistent viruses showed variable within-host evolution, with 0-25 substitutions observed between sampling points. Notably, several animals were infected by recombinant viruses derived from antigenically distinct parental strains. This included at least five different recombinants recovered from one animal, as confirmed through plaque purification of OPF samples. In several instances, recombination events were determined to have occurred within the course of the study period. These results highlight the complexity of naturally occurring subclinical FMDV infections and emphasize the role of recombination in enhancing viral diversity in endemic regions.