Abstract:

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.

Key words: Rodents, Macroviromes, Storage hosts, Human-associated viruses

摘要：

中国啮齿动物种类繁多，且携带多种重点病毒。为了解中国啮齿动物病毒组多样性及影响因素，探究啮齿动物携带的重点病毒的流行情况，防控啮齿动物源病毒性疾病。本研究整合了数据库中中国啮齿动物病毒组测序数据并进行生物信息学分析，使用Fastp质控，Bowtie2去除宿主和核糖体RNA reads，MEGAHIT进行组装，DIAMOND和Blast进行病毒物种注释，Pysamstats拼接共识序列，IQ‑TREE进行系统发育分析。本研究在9科23属42种共计2 817只啮齿动物的426个测序文库中鉴定出属于31个RNA病毒科和9个DNA病毒科的358种病毒。分析显示宿主物种、地区分布和采样部位对病毒组组成和丰度均存在影响。在啮齿动物携带的病毒中，有来自16个科的38种人类相关病毒。其中鼠科携带的人类相关病毒数量最多，与人类接触也更为密切。对汉坦病毒科和冠状病毒科的系统发育分析显示多种病毒在不同地区和宿主中流行，提示这些病毒可能存在跨物种和地区传播现象。本研究基于病毒组测序数据系统描述了中国啮齿动物病毒组特征及影响因素，对重点病毒的分析显示应重点监测鼠科动物携带病毒的情况，为啮齿动物中潜在的新发传染病监测提供新线索。

关键词: 啮齿动物, 病毒组, 储存宿主, 人类相关病毒