Characteristics of RNA viruses in rodents across different ecological regions of Yunnan and analysis of their evolutionary patterns and replication potential

Abstract Background Rodents are reservoirs of zoonotic viruses that significantly threaten public health. This study investigated the RNA virome of 624 rodents collected across six ecological zones in Yunnan Province, China, using meta-transcriptomic analyses to explore viral diversity, regional distribution, and evolutionary characteristics. Results Higher virome diversity was observed in the north-eastern and central Yunnan Plateaus, and lower diversity was observed in the north-western cold-temperate region. Phylogenetic analyses identified a unique Seoul virus lineage that represents an ancestral strain, while highlighting cross-species transmission events. Arenaviridae and Coronaviridae exhibited enrichment in specific regions, and tissue-specific viral preferences were observed, such as rotavirus in the gut tissues and Seoul virus in the lung tissues. Four zoonotic viral strains were isolated and demonstrated efficient replication in rodent cells, with limited adaptability in human cell lines. Conclusions These findings underscore the importance of ecological factors in shaping viral evolution and highlight the need for continuous surveillance.