Multi-host circulation and evolutionary dynamics of hantaviruses in small mammals in Southwestern China

China represents a major hemorrhagic fever with renal syndrome (HFRS)-endemic region, where small mammals, particularly rodents, constitute the principal reservoir hosts. This study characterized HV diversity, RNA detection rate, host range, evolutionary history, and tissue distribution in 1 717 wild small mammals collected from Yunnan Province, China. HVs were detected in 47 animals, corresponding to an overall RNA detection rate of 2.74% (47/1 717, 95% CI: 1.97%–3.51%). At least five HV species or lineages were identified across 10 small mammal species, including Orthohantavirus luxiense (LUXV), Orthohantavirus fugongense (FUGV), Orthohantavirus seoulense (SEOV), Orthohantavirus caobangense (CBNV), and Thottimvirus sp. Host‑virus coevolutionary analysis suggested extensive interspecies transmission, with particularly strong support for phylogenetically inferred host‑switching events involving SEOV and FUGV. Preliminary analysis of tissue viral loads revealed that LUXV was widely distributed across various tissues and that significant differences in viral levels existed among tissues (χ² = 27.500, P < 0.001). Collectively, these findings elucidate the genetic diversity and evolutionary dynamics of HVs in small mammals in Yunnan.