Virome diversity in small mammals from south China: Insights into virus evolution, transmission, and ecology

Yiwei Shi; Letian Fang; Cixiu Li; Peng Li; Jiluo Liu; Yifan Chen; Yue Zhao; Zishuai Li; Shuqi Liu; Yibo Ding; Xinyu Zhou; Dongming Jiang; Jiaying Shen; Zihan Zhang; Junheng Lyu; Rui Pu; Xiaojie Tan; Jianhua Yin; Weifeng Shi; Guangwen Cao

doi:10.1016/j.virs.2025.06.004

August 2025

Citation: Yiwei Shi, Letian Fang, Cixiu Li, Peng Li, Jiluo Liu, Yifan Chen, Yue Zhao, Zishuai Li, Shuqi Liu, Yibo Ding, Xinyu Zhou, Dongming Jiang, Jiaying Shen, Zihan Zhang, Junheng Lyu, Rui Pu, Xiaojie Tan, Jianhua Yin, Weifeng Shi, Guangwen Cao. Virome diversity in small mammals from south China: Insights into virus evolution, transmission, and ecology .VIROLOGICA SINICA, 2025, 40(4) : 520-534. http://dx.doi.org/10.1016/j.virs.2025.06.004

Virome diversity in small mammals from south China: Insights into virus evolution, transmission, and ecology

Yiwei Shi ^a,b,c ,
Letian Fang ^a,b,c ,
Cixiu Li ^d,e,f ,
Peng Li ^a,b,c ,
Jiluo Liu ^a,b,c ,
Yifan Chen ^a,b,c ,
Yue Zhao ^a,b,c ,
Zishuai Li ^a,b,c ,
Shuqi Liu ^d,e,f ,
Yibo Ding ^a,b,c ,
Xinyu Zhou ^a,b,c ,
Dongming Jiang ^a,b,c ,
Jiaying Shen ^a,b,c ,
Zihan Zhang ^a,b,c ,
Junheng Lyu ^a,b,c ,
Rui Pu ^a,b,c ,
Xiaojie Tan ^a,b,c ,
Jianhua Yin ^a,b,c ,
Weifeng Shi ^{g,h
,,} ,
Guangwen Cao ^{a,b,c
,,}

a. Department of Epidemiology, Naval Medical University, Shanghai, 200433, China;
b. Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai, 200433, China;
c. Shanghai Key Laboratory of Medical Bioprotection, Naval Medical University, Shanghai, 200433, China;
d. Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;
e. School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;
f. School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China;
g. Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China;
h. Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China

Corresponding author: Weifeng Shi, shiwf@ioz.ac.cn
Guangwen Cao, gcao@smmu.edu.cn
Received Date: 04 April 2025
Accepted Date: 24 June 2025
Available online: 27 June 2025

Abstract

Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions. We conducted meta-transcriptomic sequencing of 226 mammals (bats, rodents, hedgehogs, and shrews) representing 20 species collected across eight cities in south China between 2018 and 2024. Samples included internal organs, oropharyngeal and anal swabs, and feces. We identified 63 vertebrate-associated viruses, including 34 novel viruses. Phylogenetic analysis revealed six viruses with potential infection risks to humans or domestic animals due to their close phylogenetic relationships with known pathogens. Cross-species transmission was observed in 14.3% (9/63) of viruses, shared by at least two host species, with bats, particularly Rhinolophus and Hipposideros, serving as key hubs for viral circulation and zoonotic spillover. Virome composition varied substantially among mammalian species and geographic regions (adonis test, R² = 0.50, P = 0.001). Generalized linear models quantified the roles of host taxonomy, ecotypes, and meteorological factors in shaping viral diversity, demonstrating host taxonomy (at the order level) as a predominant role (25.70% deviance explained), followed by ecotypes (10.27% deviance explained). Phylogenetic analysis conducted using our betacoronavirus sequences, as well as betacoronavirus sequences derived from 2.0 × 10⁴ bats sampled in China between July 2013 and March 2024, revealed that no betacoronaviruses exhibited closer phylogenetic relationships to SARS-CoV-2 than the known strains (e.g., RaTG13). These findings provide critical insights into virus evolution, transmission, and ecological determinants, which are essential for the prevention of emerging infectious diseases.
- Wildlife virome
- , Meta-transcriptomics
- , Virus evolution
- , Virus ecology
- , Zoonotic disease

Electronic Supplementary Material

10.1016j.virs.2025.06.004-ESM.docx
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