Early-life bovine respiratory virome analysis reveals phage-driven adaptation and cross-host evolutionary signatures

Past outbreaks of zoonotic viral infections highlight the importance of understanding respiratory virome ecology. As major food-producing animals with frequent human contact, cattle represent a critical host at the human-animal interface; however, the early-life establishment of their respiratory virome and its evolutionary connections to viruses from other hosts remain underexplored. Here, we longitudinally profile the upper respiratory tract (URT) virome of beef calves from birth to weaning using an optimized viral enrichment procedure and metagenomic workflow. Viral communities exhibited increased richness and turnover, reflecting ecological structuring during early life. Temperate phages dominate the URT phage community and share virulence- and mobility-associated genes with bacterial hosts, likely contributing to host adaptation and colonization persistence. Vertebrate-associated viruses emerge after the first week of life. Targeted reassembly from bovine URT viromes recovers near-complete betacoronavirus-like (CoV-D180) and adenovirus-like (AdV-D56) genomes positioned phylogenetically between bovine and human viral lineages. Competitive mapping of bovine-derived CoV-D180 and AdV-D56 to human respiratory metatranscriptomic datasets reveals genome-specific, regionally structured coverage patterns distinct from reference viruses, supporting shared sequence features in conserved genomic regions across host-associated viral lineages. Collectively, these findings reveal early-life assembly dynamics of the bovine respiratory virome and highlight cross-host signatures in a One Health framework.