Viral diversity in wild and urban rodents of Yunnan Province, China

Rodents represent over 40% of known mammal species and are found in various terrestrial habitats. They are significant reservoirs for zoonotic viruses, including harmful pathogens such as arenaviruses and hantaviruses, yet knowledge of their hosts and distributions is limited. Therefore, characterizing the virome profile in these animals is invaluable for outbreak preparedness, especially in potential hotspots of mammal diversity. This study included 681 organs from 124 rodents and one Chinese tree shrew collected from Yunnan Province, China, during 2020-2021. Metagenomic analysis revealed unique features of mammalian viruses in rodent organs across habitats with varying human disturbances. R. tanezumi in locations with high anthropogenic disturbance exhibited the highest mammal viral diversity, with spleen and lung samples showing the highest diversities for these viruses at the organ level. Mammal viral diversity for both commensal and non-commensal rats was identified to positively correlate with landscape disturbance. Some virus families were associated with particular organs or host species, suggesting tropism for these pathogens. Notably, known and novel viral species that are likely to infect humans were identified. R. tanezumi was identified as a reservoir and carrier for various zoonotic viruses, including porcine bocavirus, hantavirus, cardiovirus, and lyssavirus. These findings highlight the influence of rodent community composition and anthropogenic activities on diverse virome profiles, with R. tanezumi as an important reservoir for zoonotic viruses.啮齿类动物占已知哺乳动物物种总数的40%以上，广泛分布于各类陆地生境中。它们是重要的人畜共患病毒（zoonotic viruses）储存宿主，可携带沙粒病毒（arenaviruses）、汉坦病毒（hantaviruses）等有害病原体，但目前学界对其宿主类群与分布范围的认知仍较为有限。因此，解析这类动物的病毒组（virome）特征，对于疫情防控准备工作具有极高价值，在哺乳动物多样性潜在热点区域尤为如此。本研究纳入了2020-2021年于中国云南省采集的124只啮齿动物与1只中国树鼩（Chinese tree shrew）的共计681份器官组织。宏基因组分析（metagenomic analysis）结果显示，不同人类干扰程度的生境下，啮齿动物器官中的哺乳动物病毒呈现出独特的特征。在人类活动干扰较强的区域采集的R. tanezumi所携带的哺乳动物病毒多样性最高，其中脾脏与肺脏样本的病毒多样性在器官层面位居前列。研究发现，无论是伴生鼠类（commensal rats）还是非伴生鼠类（non-commensal rats），其携带的哺乳动物病毒多样性均与生境干扰程度呈显著正相关。部分病毒科与特定器官或宿主类群存在关联，提示这类病原体具有组织或宿主嗜性（tropism）。值得注意的是，本研究还鉴定出了多种可能感染人类的已知与新型病毒物种。研究证实R. tanezumi是多种人畜共患病毒的储存宿主与传播载体，包括猪博卡病毒（porcine bocavirus）、汉坦病毒、心病毒（cardiovirus）以及狂犬病毒属（lyssavirus）病毒。本研究结果凸显了啮齿动物群落组成与人类活动对多样病毒组特征的影响，并证实R. tanezumi是一类重要的人畜共患病毒储存宿主。