Large-scale characterization of the bovine virome reveals viral diversity and community patterns in Northwest China

Cattle play a critical role in global agriculture and food security while serving as hosts for diverse viruses with potential implications for animal and public health. To comprehensively characterize the bovine virome and its community patterns, we conducted a large-scale characterization of the beef cattle-associated virome in Northwest China using viral metagenomic sequencing. A total of 2,353 specimens, including nasal swabs, anal swabs, and serum, were collected from 794 cattle across 28 sites in Shaanxi, Gansu, and Ningxia, with nasal and anal swab specimens used for the metagenomic analyses. High-throughput sequencing identified viruses belonging to 14 phyla, 32 classes, 39 orders, 71 families, and 397 genera, revealing substantial viral diversity. Descriptive comparisons of the pooled libraries revealed differences in virome composition across geographic regions, farming systems, and sampling seasons, with the summer pool showing greater viral richness and contig abundance than the winter pool. Phylogenetic analyses revealed genetic relationships between several viral sequences detected in this study and viral lineages previously reported from humans and other animal hosts, raising hypotheses regarding broader host associations and potential cross-species transmission that require further investigation. Targeted PCR/RT-PCR screening and cell-culture-based virus characterization provided complementary validation of representative metagenomic findings and revealed frequent co-detection of multiple viral targets among the sampled cattle. Collectively, this study provides a large-scale characterization of the beef cattle-associated virome in Northwest China, expands current knowledge of viral diversity associated with beef cattle populations, and establishes a valuable resource for future virome surveillance, studies of viral evolution, and disease prevention.