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Literature detail

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

Yiwei Shi1,2,3 Letian Fang1,2,3 Cixiu Li4,5,6 Peng Li1,2,3 Jiluo Liu1,2,3 Yifan Chen1,2,3 Yue Zhao1,2,3 Zishuai Li1,2,3 Shuqi Liu4,5,6 Yibo Ding1,2,3 Xinyu Zhou1,2,3 Dongming Jiang1,2,3 Jiaying Shen1,2,3 Zihan Zhang1,2,3 Junheng Lyu1,2,3 Rui Pu1,2,3 Xiaojie Tan1,2,3 Jianhua Yin1,2,3 Weifeng Shi7,8 Guangwen Cao1,2,9
Affiliations 9 institutions
  1. Department of Epidemiology, Naval Medical University, Shanghai, 200433, China
  2. Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai, 200433, China
  3. Shanghai Key Laboratory of Medical Bioprotection, Naval Medical University, Shanghai, 200433, China.
  4. Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China
  5. School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China
  6. School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Ji'nan, 250117, China.
  7. Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
  8. Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. Electronic address: [email protected].
  9. Shanghai Key Laboratory of Medical Bioprotection, Naval Medical University, Shanghai, 200433, China. Electronic address: [email protected].
PMID 40582414 2025 Virol Sin eng ppublish
PubMed DOI Browse context

Article

Publication summary

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, R<sup>2</sup> ​= ​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 ​× ​10<sup>4</sup> 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.

Meta-transcriptomics Virus ecology Virus evolution Wildlife virome Zoonotic disease Mammals Virome Virus Diseases Viruses Animals China Chiroptera Evolution, Molecular Feces Hedgehogs Humans Phylogeny Rodentia

Structured evidence records

Evidence records

10 total
Zoonotic Surveillance 4 records
Zoonotic Surveillance Extraction confidence 1.00
Key finding

Meta-transcriptomic monitoring of bats, rodents, hedgehogs, and shrews from south China revealed 63 vertebrate viruses, including novel viruses, highlighting their role as reservoirs relevant to zoonotic spillover.

Virus
Not specified
Host
Chiroptera
Location
China south China, China
Supporting text

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.

Method
meta-transcriptomic sequencing
Sample type
internal organs; oropharyngeal swabs; anal swabs; feces
Geographic raw
south China
Country inferred
China
Zoonotic Surveillance Extraction confidence 1.00
Key finding

Rodents from south China were part of a meta-transcriptomic survey that uncovered diverse vertebrate-associated viruses, including novel ones, indicating potential for cross-species transmission.

Virus
Not specified
Host
Rodentia
Location
China south China, China
Supporting text

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.

Method
meta-transcriptomic sequencing
Sample type
internal organs; oropharyngeal swabs; anal swabs; feces
Geographic raw
south China
Country inferred
China
Zoonotic Surveillance Extraction confidence 1.00
Key finding

Hedgehogs from south China were included in a broad virome monitoring effort that revealed novel vertebrate viruses relevant to understanding zoonotic reservoirs.

Virus
Not specified
Location
China south China, China
Supporting text

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.

Method
meta-transcriptomic sequencing
Sample type
internal organs; oropharyngeal swabs; anal swabs; feces
Geographic raw
south China
Country inferred
China
Zoonotic Surveillance Extraction confidence 1.00
Key finding

Shrews from south China were part of the meta-transcriptomic surveillance that characterized viral diversity and identified several novel vertebrate-associated viruses.

Virus
Not specified
Host
Soricidae
Location
China south China, China
Supporting text

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.

Method
meta-transcriptomic sequencing
Sample type
internal organs; oropharyngeal swabs; anal swabs; feces
Geographic raw
south China
Country inferred
China
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.95
Key finding

Phylogenetic analysis of betacoronavirus sequences from bats in China showed that none were more closely related to SARS-CoV-2 than the known strain RaTG13.

Host
Chiroptera
Location
Not specified
Supporting text

Phylogenetic analysis conducted using our betacoronavirus sequences, as well as betacoronavirus sequences derived from 2.0 × 10^4 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).

Analysis methods
phylogenetic analysis
Genomic Evolution Extraction confidence 0.90
Key finding

Phylogenetic analysis of newly identified viruses from small mammals in south China showed six viruses closely related to known pathogens, indicating potential infection risks to humans or domestic animals.

Virus
Not specified
Host
Mammalia
Location
Not specified
Supporting text

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.

Analysis methods
phylogenetic analysis
Reservoir Ecology 2 records
Reservoir Ecology Extraction confidence 0.90
Key finding

Bats, especially Rhinolophus and Hipposideros, function as major reservoirs supporting viral circulation and potential zoonotic spillover among small mammals in south China.

Virus
Not specified
Location
China south China, China
Supporting text

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.

Method
meta-transcriptomic sequencing
Sample type
internal organs; oropharyngeal swabs; anal swabs; feces
Geographic raw
south China
Country inferred
China
Reservoir Ecology Extraction confidence 0.90
Key finding

Viral diversity across small mammals in south China was primarily determined by host taxonomy, ecotype, and meteorological factors.

Virus
Not specified
Host
Mammalia
Location
China south China, China
Supporting text

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).

Method
meta-transcriptomic sequencing; adonis test; generalized linear models
Sample type
internal organs; oropharyngeal swabs; anal swabs; feces
Geographic raw
south China
Country inferred
China
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 0.98
Key finding

Several viruses were detected in multiple non-human small mammal species, showing interspecies viral transmission, with bats acting as central reservoirs.

Virus
Not specified
Location
China south China, China
Supporting text

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.

Method
meta-transcriptomic sequencing; phylogenetic analysis
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Spillover Event 1 records
Spillover Event Extraction confidence 0.88
Key finding

Bats, especially Rhinolophus and Hipposideros, were identified as major hubs for viral circulation and zoonotic spillover in south China.

Virus
Not specified
Location
China south China, China
Supporting text

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.

Method
meta-transcriptomic sequencing; phylogenetic analysis
Study design
field surveillance
Transmission direction
animal-to-human
Geographic raw
south China
Country inferred
China