Characterization of rodent viromes and epidemiology of key viruses in China

Rodents exhibit a high taxonomic diversity in China. To understand the diversity of rodent viromes in China and the factors influencing it, we investigate the prevalence of key viruses carried by rodents and discuss measures to prevent and control viral diseases of rodent origin. We obtained sequencing data of Chinese rodent viromes from online databases, and used Fastp for quality control, Bowtie2 to remove host and ribosomal RNA reads, MEGAHIT for assembly, DIAMOND and BLAST for viral species annotation, Pysamstats to splice consensus sequences, and IQ-TREE for phylogenetic analysis. We integrated 426 sequenced libraries across 9 families, 23 genera, and 42 species of rodents, totaling 2 817 individuals. Our analyses recovered 358 viruses belonging to 31 RNA virus families and 9 DNA virus families. We found that viral composition and abundance varied with host species, regional origin, and sampling organ. Among all detected viruses, 38 viruses from 16 viral families were known to be infectious to humans. Most of these human-associated viruses were detected in Muridae, with which humans have close contact. Phylogenetic analyses of Hantaviridae and Coronaviridae revealed that many viruses are distributed across various host species in multiple regions, suggesting potential cross-species and cross-region transmission. This study systematically characterized the virome of Chinese rodents based on virome sequencing data. Our analysis of key viruses indicates the necessity of monitoring viruses carried by Muridae, which offers new insights into the potential emergence of infectious diseases within rodent populations.