OmniVira

Literature detail

Virome characterization of game animals in China reveals a spectrum of emerging pathogens.

Wan-Ting He1 Xin Hou2 Jin Zhao1 Jiumeng Sun1 Haijian He3 Wei Si4 Jing Wang2 Zhiwen Jiang1 Ziqing Yan1 Gang Xing4 Meng Lu1 Marc A Suchard5 Xiang Ji6 Wenjie Gong7 Biao He7 Jun Li8 Philippe Lemey9 Deyin Guo2 Changchun Tu7 Edward C Holmes10 Mang Shi11 Shuo Su12
Affiliations 12 institutions
  1. Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.
  2. The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
  3. Agricultural College, Jinhua Polytechnic, Jinhua 320017, China.
  4. MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China.
  5. Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
  6. Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA.
  7. Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China.
  8. Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China.
  9. Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium.
  10. Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, the University of Sydney, Sydney, NSW 2006, Australia. Electronic address: [email protected].
  11. The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China. Electronic address: [email protected].
  12. Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: [email protected].
PMID 35298912 2022 Cell eng ppublish
PubMed DOI Browse context

Article

Publication summary

Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, sampled across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.

coronavirus disease emergence emerging pathogens evolution game animals host switch virome Disease Reservoirs Virome Animals Animals, Wild China Communicable Diseases, Emerging Mammals Phylogeny Zoonoses

Structured evidence records

Evidence records

12 total
Cross Species Transmission 6 records
Cross Species Transmission Extraction confidence 0.95
Key finding

Bat-associated coronavirus was transmitted from bats to civets.

Location
China China
Supporting text

We inferred the transmission of bat-associated coronavirus from bats to civets.

Method
meta-transcriptomic analysis
Study design
meta-transcriptomic analysis
Transmission direction
animal-to-animal
Geographic raw
China
Country inferred
China
Cross Species Transmission Extraction confidence 0.95
Key finding

Coronaviruses were transmitted from bats to hedgehogs.

Location
China China
Supporting text

We inferred ... cross-species jumps of coronaviruses from bats to hedgehogs.

Method
meta-transcriptomic analysis
Study design
meta-transcriptomic analysis
Transmission direction
animal-to-animal
Geographic raw
China
Country inferred
China
Cross Species Transmission Extraction confidence 0.95
Key finding

Coronaviruses were transmitted from birds to porcupines.

Host
Aves
Location
China China
Supporting text

We inferred ... cross-species jumps of coronaviruses ... from birds to porcupines.

Method
meta-transcriptomic analysis
Study design
meta-transcriptomic analysis
Transmission direction
animal-to-animal
Geographic raw
China
Country inferred
China
Cross Species Transmission Extraction confidence 0.95
Key finding

Coronaviruses were transmitted from dogs to raccoon dogs.

Location
China China
Supporting text

We inferred ... cross-species jumps of coronaviruses ... from dogs to raccoon dogs.

Method
meta-transcriptomic analysis
Study design
meta-transcriptomic analysis
Transmission direction
animal-to-animal
Geographic raw
China
Country inferred
China
Cross Species Transmission Extraction confidence 0.95
Key finding

Avian Influenza A virus H9N2, originally from birds, was detected in civets and Asian badgers, indicating cross-species transmission from birds.

Virus
IAV H9N2
Location
China China
Supporting text

We identified avian Influenza A virus H9N2 in civets and Asian badgers.

Method
meta-transcriptomic analysis
Study design
meta-transcriptomic analysis
Transmission direction
animal-to-animal
Geographic raw
China
Country inferred
China
Cross Species Transmission Extraction confidence 0.95
Key finding

Avian Influenza A virus H9N2 was detected in Asian badgers, suggesting avian-to-mammal transmission accompanied by respiratory symptoms.

Virus
IAV H9N2
Location
China China
Supporting text

We identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms.

Method
meta-transcriptomic analysis
Study design
meta-transcriptomic analysis
Transmission direction
animal-to-animal
Geographic raw
China
Country inferred
China
Spillover Event 4 records
Spillover Event Extraction confidence 0.90
Key finding

Avian Influenza A(H9N2) virus spilled over from birds to civets and Asian badgers in China.

Virus
IAV H9N2
Location
China China
Supporting text

We identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms.

Method
meta-transcriptomic analysis
Study design
field surveillance
Transmission direction
animal-to-human
Geographic raw
China
Country inferred
China
Spillover Event Extraction confidence 0.90
Key finding

Avian Influenza A(H9N2) virus spilled over from birds to Asian badgers in China.

Virus
IAV H9N2
Location
China China
Supporting text

We identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms.

Method
meta-transcriptomic analysis
Study design
field surveillance
Transmission direction
animal-to-human
Geographic raw
China
Country inferred
China
Spillover Event Extraction confidence 0.90
Key finding

A bat-associated coronavirus was transmitted from bats to civets, indicating an animal-to-animal spillover event in China.

Location
China China
Supporting text

We inferred the transmission of bat-associated coronavirus from bats to civets.

Method
meta-transcriptomic analysis
Study design
field surveillance
Transmission direction
animal-to-human
Geographic raw
China
Country inferred
China
Spillover Event Extraction confidence 0.90
Key finding

The study detected likely human-to-wildlife virus spillback events in China.

Virus
Not specified
Location
China China
Supporting text

We identified cases of likely human-to-wildlife virus transmission.

Method
meta-transcriptomic analysis
Study design
field surveillance
Transmission direction
human-to-animal
Geographic raw
China
Country inferred
China
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.80
Key finding

Phylogenetic and sequence analysis of game animal viromes in China revealed bat-associated coronaviruses spilling over into civets and other species, signifying genomic evolution underlying cross-species jumps.

Location
Not specified
Supporting text

We performed a meta-transcriptomic analysis of 1,941 game animals... We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs.

Genes or proteins
whole genome
Analysis methods
meta-transcriptomic analysis; phylogenetic inference
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Meta-transcriptomic surveillance of 1,941 game animals across China revealed diverse mammalian viruses, several of which are potentially zoonotic.

Virus
Not specified
Host
Not specified
Location
China China
Supporting text

We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, sampled across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time.

Method
meta-transcriptomic analysis
Geographic raw
China
Country inferred
China