OmniVira

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].
PMID35298912 DOI10.1016/j.cell.2022.02.014 Year2022 Journal Cell Languageeng Statusppublish

Abstract

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.

Supporting text Virus Host Location
coronavirus 195 disease emergence 6 emerging pathogens 3 evolution 62 game animals 1 host switch 2 virome 44 Disease Reservoirs 149 Virome 33 Animals 1948 Animals, Wild 187 China 229 Communicable Diseases, Emerging 33 Mammals 92 Phylogeny 805 Zoonoses 397

Evidence records

8 total
Zoonotic Surveillance
3 records · 1 evidence types
Evidence type Viral Detection
3 records
OVE5767 Viral Detection
Key finding

Meta-transcriptomic analysis of game animals sampled across China identified 102 mammalian-infecting viruses, including 65 described for the first time.

Virus
102 mammalian-infecting viruses
Host
Not specified
Location
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
CHN
Genomic Evolution
5 records · 1 evidence types
Evidence type Phylogenetic Evolution
5 records
OVE5775 Phylogenetic Evolution
Key finding

The study detected cases of likely human-to-wildlife virus transmission, indicating human-to-animal spillback events in Chinese game animals.

Virus
virus
Host
human Homo sapiens Natural host
Location
China
Supporting text

as well as cases of likely human-to-wildlife virus transmission.

Analysis methods
meta-transcriptomic sequencing