Virome diversity and zoonotic risks of rodents along ecological gradients in the Northern Tianshan Mountains, China

BACKGROUND: Rodents are primary reservoirs for zoonotic viruses, posing significant public health threats. However, our understanding of how habitat heterogeneity influences viral community composition and the spillover potential remains inadequate. RESULTS: Here, a comprehensive meta-transcriptomic analysis of rodent-associated viruses was conducted across four distinct ecological habitats in the northern foothills of the Tianshan Mountains, China. Multiple novel viral sequences belonging to families with known zoonotic potential were identified, including Nairo-, Arena-, Flavi-, Picorna-, and Paramyxoviridae. Phylogenetic analyses revealed significant genomic diversity and potential for cross-species transmission, particularly in viruses exhibiting broad tissue tropism. Notably, viruses from the family Nairoviridae were markedly enriched in rodent spleen and kidney tissues from mountain pastures and scenic zones. This enrichment likely reflects the high abundance and diversity of tick vectors in these habitats, which may facilitate viral persistence in rodent reservoirs and increase the risk of zoonotic spillover. In contrast, rodents in farm and community zones exhibited more diverse viral communities across multiple tissues, including the kidneys and intestines, suggesting that these high-density human-animal interfaces provide optimal conditions for multi-host viral circulation. Variations in viral distribution were observed across tissues and geographic locations among rodents from different habitats, indicating that viral patterns are closely influenced by host species, environmental factors, and vector organisms. Habitat differences accounted for 38.8% of the variation in viral community composition, highlighting both ecological diversity and the pivotal role of habitat in viral dynamics. CONCLUSIONS: These findings underscore the complex interplay between habitat type, host ecology, and viral evolution in shaping zoonotic spillover risks. This research offers crucial insights into the emergence of rodent-borne viral diseases and the development of targeted surveillance strategies in high-risk regions. Video Abstract.