Viral infections can have a significant impact on the health of bovine livestock, with consequences that extend to economic productivity, human health, and the health of other animals. Identifying the viruses present in fecal samples, one of the main routes of pathogen transmission, contributes to the development of prevention, control, and surveillance plans. Viral metagenomics approaches provide a broader picture and have great potential in detecting unknown viruses or suggesting previously undescribed agents. Therefore, in this study, viral communities in fecal samples from bovines in one of the livestock epicenters in Colombia (Ubaté Province) were characterized using third-generation sequencing (Oxford Nanopore Technologies). We described the virome of fecal samples from cattle using a non-probabilistic convenience sampling of 42 samples collected from three municipalities in the Ubaté Province, Cundinamarca. We employed a metagenomic sequencing approach with Oxford Nanopore technologies, along with diversity and phylogenetic analyses. The virome showed a homogeneous and stable viral composition across municipalities, predominantly consisting of members of the Picornaviridae family. At the species level, the most abundant viruses were Enterovirus E (EVE) and Bovine Astrovirus (BoAstV). We report for the first time in Colombia the presence of economically important viruses with significant frequencies: EVE (59%), Bovine Kobuvirus (KVB) (52%), and BoAstV (19%), as well as confirmation of CRESS Virus in fecal samples from animals. The virome of bovine feces in the Ubaté Province is characterized by the predominance of potentially pathogenic viruses that have been reported with considerable prevalence and quantities. Several of these viruses are reported for the first time in Colombia. This study demonstrates the usefulness of implementing metagenomic sequencing techniques in epidemiological surveillance. It lays the foundation for future research on the effects of these agents on bovine health and their prevalence in the country, contributing to the control and prevention of infectious diseases.
