Virome characterization of field-collected rodents in suburban Beijing reveals a spectrum of emerging pathogens

Abstract Background Rodents serve as natural reservoirs and transmission hosts for numerous zoonotic viruses, which can cause a range of animal and human diseases, posing significant public health concerns. Analyzing the viral diversity harbored by rodents is crucial for early warnings of emerging infectious diseases. Results By conducting meta-transcriptomic sequencing on spleen samples obtained from 432 wild rodents across three habitats, we characterized the high-depth RNA virome of wild rodents representing 9 species of two prominent mammalian families (Cricetidae and Muridae) in suburban Beijing. The composition of virome varied significantly at the virus family level among the nine rodent species and three types of natural habitats. A total of 142 viral species associated with vertebrates (n = 133) and invertebrates (n = 9) were identified from 26 families, including 75 novel viruses and 67 known viruses, thereby substantially expanding our knowledge about the diversity of rodent virome. Among these, twenty-five viruses were classified as high-risk, including 8 zoonotic viruses and 17 spillover-risk viruses. Additionally, nine previously unreported viruses were discovered for the first time in China. Furthermore, thirty-three viruses exhibited species transmission potential and some had evolutionary significance. Conclusions These findings enhance our understanding of rodent virome in Suburban Beijing and suggest that there is vast array of undiscovered viruses within these rodent species in China. Understanding the composition of rodent virome might provide insights into the potential risk of zoonotic spillover to humans.