Evaluating the zoonotic potential of RNA viromes of rodents provides new insight into rodent-borne zoonotic pathogens in Guangdong, China

Emerging and re-emerging infectious diseases have been on the rise, with a significant proportion being zoonotic. Rodents, as the natural reservoirs of numerous diverse zoonotic viruses, pose a substantial threat to human health. To investigate the diversity of known and unknown viruses harbored by rodents in Guangdong (southern province of China), we conducted a comprehensive analysis of viral genomes through metagenomic sequencing of organs from 194 rodents. Our analysis yielded 2163 viral contigs that were assigned to 25 families known to infect a wide range of hosts, including vertebrates, invertebrates, amoebas, and plants. The viral compositions vary considerably among different organs, but not in rodent species. We also assessed and prioritized zoonotic potential of those detected viruses. Ninety-two viral species that are either known to infect vertebrates and invertebrates or only vertebrates were identified, among which 21 are considered high-risk to humans. The high-risk viruses included members of the Hantavirus, Picobirnaviruses, Astroviruses and Pestivirus. The phylogenetic trees of four zoonotic viruses revealed features of novel viral genomes that seem to fit evolutionarily into a zone of viruses that potentially pose a risk of transmission to humans. Recognizing that zoonotic diseases are a One Health issue, we approached the problem of identifying the zoonotic risk from rodent-transmitted disease in the Guangdong province by performing next-generation sequencing to look for potentially zoonotic viruses in these animals.