Fecal virome characterization of dairy cows with winter dysentery reveals bovine torovirus, enterovirus F, a novel and recombinant enterovirus I, and a putative novel protoparvovirus

Background Winter dysentery (WD) is an acute diarrheal disease of adult cattle with a significant impact on milk production. Although bovine coronavirus (BCoV) is usually considered the primary etiological agent, other viruses may contribute to the disease. In this study, we investigated a WD outbreak in a bovine dairy herd in Uruguay through shotgun metagenomic sequencing and molecular virology techniques. Results Fecal samples from three affected cows were negative for common enteric pathogens, including BCoV, but two samples tested positive for bovine torovirus (BToV) by RT-qPCR. Virome analysis of pooled samples identified over 3,300 viral operational taxonomic units (vOTUs), predominantly bacteriophages, but also eukaryotic viruses from 11 families. Notably, we detected the complete genome of BToV (101/UY), closely related to a previously reported Uruguayan strain. Additionally, two enteroviruses were identified, including one divergent strain (MFB-556) that likely resulted from interspecies recombination between Enterovirus idromi and Enterovirus fitauri . A divergent protoparvovirus sequence, CPBI/UYU/2024, was also identified and confirmed by PCR and Sanger sequencing; phylogenetic and sequence identity analyses suggest it represents a putative new species within the genus Protoparvovirus . Conclusion These findings underscore the value of viral metagenomics for uncovering potential co-infections and novel viruses in diarrheic cattle with WD.