Highly divergent virome in wild rodents of Xinjiang, China: Implications for rodent origin of porcine reproductive and respiratory syndrome virus 1

Rodents play a pivotal role in the maintenance and transmission of zoonotic viruses. The Yili River Valley, one of the most biodiverse regions in Xinjiang, functions as a critical biogeographic corridor linking China with Central and Western Asia, and historically with Europe via the ancient Silk Road. Despite its significance, the viral landscape of this region remains largely unexplored. To elucidate the virological landscape of this understudied region, meta-transcriptomic sequencing was conducted on wild rodent samples collected between 2020 and 2023, encompassing multiple host species and tissue types (liver, lung, spleen, and intestine). Analysis identified 18 vertebrate-associated viral families, including several of known zoonotic or evolutionary relevance, such as Arteriviridae, Coronaviridae, Flaviviridae, Hantaviridae, Hepeviridae, Hepadnaviridae, and Picornaviridae. Remarkably, over 80% of the detected viruses represented putative novel species, highlighting the vast and previously undocumented viral diversity harbored by rodents in this region. Viral community composition exhibited clear host- and tissue-specific patterns. Critically, novel rodent-derived arteriviruses (RtArteVs) in Microtus obscurus were identified, exhibiting approximately 86% nucleotide identity with porcine reproductive and respiratory syndrome virus 1 (PRRSV1). Additionally, phylogenetic and recombination analyses support the hypothesis that PRRSV1 emerged through ancestral recombination among divergent RtArteVs, implicating rodents as the likely origin of this economically significant swine pathogen. These findings expand current understanding of rodent viromes in an important biodiversity hotspot, revealing a substantial yet largely uncharted viral diversity. Furthermore, this study underscores the critical need for continued surveillance of viral groups with potential for viral spillover to humans and domestic animals, including Arteriviridae, Flaviviridae, Hantaviridae, Hepeviridae, and Hepadnaviridae.