Highly Divergent Virome in Wild Rodents of Xinjiang, China: Implication for Rodent Origin of Porcine Reproductive and Respiratory Syndrome Virus 1

Rodents serve as key reservoirs for zoonotic viruses. The Yili River Valley, one of the most biodiverse regions in Xinjiang, functions as a critical corridor linking China with Central and Western Asia and Europe. However, the virome of this ecologically significant area remains largely unexplored. Using meta-transcriptomic sequencing, we characterized the viromes of wild rodents collected from the Yili River Valley from 2020 to 2023 and assessed viral distribution across different host species and tissues (liver, lung, spleen, intestine). A total of 19 vertebrate-associated viral families were identified, including those with high zoonotic potential and/or evolutionary significance, such as Arteriviridae, Coronaviridae, Flaviviridae, Hantaviridae, Hepeviridae, Hepadnaviridae, and Picornaviridae. Notably, over 80% of the detected viruses were putative novel species, highlighting the vast and largely unexplored viral diversity in rodents from this region. Viral composition varied significantly by host wspecies and tissue type. Critically, we identified novel rodent-derived arteriviruses (RtArteVs) in M. obscurus, with a high similarity (~86%) with porcine reproductive and respiratory syndrome virus 1 (PRRSV1), indicating the rodent origin of PRRSV1. Additionally, recombination analysis indicates that PRRSV1 likely originated from recombination events among ancestral RtArteVs. This study enhances our understanding of virome composition of rodents in a biodiversity hotspot in Yili, Xinjiang, revealing a substantial yet largely uncharted viral diversity. These findings emphasize the need for continuous surveillance of viruses that may have potential risks of viral spillover to humans and domestic animals, including Arteriviridae, Flaviviridae, Hantaviridae, Hepeviridae, and Hepadnaviridae.