Abstract
The Qinghai-Tibet Plateau (QTP), known for its rich biodiversity and unique ecological niche, harbors numerous endemic species and serves as a reservoir for both established human pathogens and numerous poorly characterized pathogens. Despite certain advances, virological research on small mammals in this region is still limited. In this study, we investigated the diversity and evolution of viral communities in plateau voles, plateau pikas, and their associated environmental samples collected near pastoral settlements on the QTP. Our findings revealed 291,165 species-level viral operational taxonomic units, highlighting a diverse array of bacteriophages. In addition, we further characterized 774 novel eukaryotic viral genomes, primarily classified into 22 established viral families. Among them, 95.5% shared less than 80% amino acid sequence identity with known viruses, some of which may represent new genera or species. Furthermore, some eukaryotic viruses display distinct tissue distribution patterns in these small mammals. Notably, we identified 32 mammalian viruses capable of cross-species transmission, among which 22 are considered potential spillover risks, and most of them were detected for the first time in plateau pikas and plateau voles. Overall, this study expands the viral spectrum of small mammals on the QTP and broadens the host range of previously identified viruses, emphasizing the need for further research into their potential public health implications.