OmniVira

Literature detail

Virus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals.

Xinyuan Cui1 Kewei Fan2 Xianghui Liang1 Wenjie Gong3,4 Wu Chen5 Biao He4 Xiaoyuan Chen1 Hai Wang1 Xiao Wang1 Ping Zhang1 Xingbang Lu1 Rujian Chen1 Kaixiong Lin6 Jiameng Liu1 Junqiong Zhai5 Ding Xiang Liu7,8 Fen Shan5 Yuqi Li2 Rui Ai Chen8 Huifang Meng1 Xiaobing Li1,2 Shijiang Mi3,4 Jianfeng Jiang3,4 Niu Zhou5 Zujin Chen5 Jie-Jian Zou9 Deyan Ge10 Qisen Yang10 Kai He11 Tengteng Chen6 Ya-Jiang Wu5 Haoran Lu12 David M Irwin13,14 Xuejuan Shen1 Yuanjia Hu1 Xiaoman Lu1 Chan Ding15,16 Yi Guan17,18 Changchun Tu19,20 Yongyi Shen21,22
Affiliations 22 institutions
  1. State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
  2. Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, College of Life Sciences, Longyan University, Longyan, 364012, China.
  3. State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
  4. Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
  5. Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China.
  6. Fujian Meihuashan Institute of South China Tiger Breeding, Longyan, 364201, China.
  7. Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
  8. Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, 526000, Guangdong, China.
  9. Guangdong Provincial Wildlife Monitoring and Rescue Center, Guangzhou, 510000, China.
  10. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
  11. Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, 510006, China.
  12. School of Mathematics, Sun Yat-sen University, Guangzhou, 510275, China.
  13. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S1A8, Canada.
  14. Banting and Best Diabetes Centre, University of Toronto, Toronto, M5S1A8, Canada.
  15. Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, 201106, China. [email protected].
  16. Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China. [email protected].
  17. Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College (SUMC), Shantou, 515041, China. [email protected].
  18. Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China. [email protected].
  19. Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China. [email protected].
  20. Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China. [email protected].
  21. State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China. [email protected].
  22. Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, Guangzhou, 510642, China. [email protected].
PMID 37120646 2023 Nat Commun eng epublish
PubMed DOI Browse context

Article

Publication summary

Wildlife is reservoir of emerging viruses. Here we identified 27 families of mammalian viruses from 1981 wild animals and 194 zoo animals collected from south China between 2015 and 2022, isolated and characterized the pathogenicity of eight viruses. Bats harbor high diversity of coronaviruses, picornaviruses and astroviruses, and a potentially novel genus of Bornaviridae. In addition to the reported SARSr-CoV-2 and HKU4-CoV-like viruses, picornavirus and respiroviruses also likely circulate between bats and pangolins. Pikas harbor a new clade of Embecovirus and a new genus of arenaviruses. Further, the potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified, complicating wildlife protection and the prevention and control of these diseases in domestic animals. This study provides a nuanced view of the frequency of host-jumping events, as well as assessments of zoonotic risk.

Chiroptera COVID-19 Viruses Animals Animals, Domestic Animals, Wild Animals, Zoo Mammals Pangolins Phylogeny Zoonoses

Structured evidence records

Evidence records

19 total
Cross Species Transmission 8 records
Cross Species Transmission Extraction confidence 0.95
Key finding

Picornavirus and respiroviruses were found to circulate between bats and pangolins, indicating cross-species transmission among wildlife species.

Location
China south China, China
Supporting text

Picornavirus and respiroviruses also likely circulate between bats and pangolins.

Method
virus isolation; sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Cross Species Transmission Extraction confidence 0.95
Key finding

Picornavirus and respiroviruses were found to circulate between bats and pangolins, indicating cross-species transmission among wildlife species.

Location
China south China, China
Supporting text

Picornavirus and respiroviruses also likely circulate between bats and pangolins.

Method
virus isolation; sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Cross Species Transmission Extraction confidence 0.90
Key finding

Paramyxovirus was identified as potentially transmitted between wildlife and domestic animals.

Host
Metazoa
Location
China south China, China
Supporting text

The potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified.

Method
virus isolation; sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Cross Species Transmission Extraction confidence 0.90
Key finding

Astrovirus was identified as potentially transmitted between wildlife and domestic animals.

Virus
Astroviridae
Host
Metazoa
Location
China south China, China
Supporting text

The potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified.

Method
virus isolation; sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Cross Species Transmission Extraction confidence 0.90
Key finding

Pseudorabies virus was identified as potentially transmitted between wildlife and domestic animals.

Virus
PRV
Host
Metazoa
Location
China south China, China
Supporting text

The potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified.

Method
virus isolation; sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Cross Species Transmission Extraction confidence 0.90
Key finding

Porcine circovirus 2 was identified as potentially transmitted between wildlife and domestic animals.

Virus
PCV
Host
Metazoa
Location
China south China, China
Supporting text

The potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified.

Method
virus isolation; sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Cross Species Transmission Extraction confidence 0.90
Key finding

Porcine circovirus 3 was identified as potentially transmitted between wildlife and domestic animals.

Virus
PCV3
Host
Metazoa
Location
China south China, China
Supporting text

The potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified.

Method
virus isolation; sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Cross Species Transmission Extraction confidence 0.90
Key finding

Parvovirus was identified as potentially transmitted between wildlife and domestic animals.

Host
Metazoa
Location
China south China, China
Supporting text

The potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified.

Method
virus isolation; sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Geographic raw
south China
Country inferred
China
Reservoir Ecology 5 records
Reservoir Ecology Extraction confidence 0.85
Key finding

Wildlife and zoo animals from south China were found to be reservoirs harboring diverse mammalian viruses.

Virus
Not specified
Location
China south China, China
Supporting text

Wildlife is reservoir of emerging viruses. Here we identified 27 families of mammalian viruses from 1981 wild animals and 194 zoo animals collected from south China between 2015 and 2022.

Method
field sampling; virus isolation and characterization
Geographic raw
south China
Country inferred
China
Reservoir Ecology Extraction confidence 0.85
Key finding

Bats in south China were identified as reservoirs hosting diverse coronaviruses, picornaviruses, astroviruses, and a novel Bornaviridae lineage.

Host
Chiroptera
Location
China south China, China
Supporting text

Bats harbor high diversity of coronaviruses, picornaviruses and astroviruses, and a potentially novel genus of Bornaviridae.

Method
virus isolation and characterization
Geographic raw
south China
Country inferred
China
Reservoir Ecology Extraction confidence 0.85
Key finding

The study identified circulation and potential cross-species transmission of multiple RNA and DNA viruses between wildlife and domestic animals, indicating shared reservoir ecology.

Host
Metazoa
Location
China south China, China
Supporting text

Further, the potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified.

Method
virus detection
Geographic raw
south China
Country inferred
China
Reservoir Ecology Extraction confidence 0.80
Key finding

Pikas were found to maintain a new clade of Embecovirus and a new genus of arenaviruses, indicating an ecological reservoir role.

Location
China south China, China
Supporting text

Pikas harbor a new clade of Embecovirus and a new genus of arenaviruses.

Method
virus characterization
Geographic raw
south China
Country inferred
China
Reservoir Ecology Extraction confidence 0.80
Key finding

Picornavirus and respiroviruses show circulation between bats and pangolins, suggesting overlapping reservoir or ecological interface.

Location
China south China, China
Supporting text

Picornavirus and respiroviruses also likely circulate between bats and pangolins.

Method
virus detection
Geographic raw
south China
Country inferred
China
Zoonotic Surveillance 4 records
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Field surveillance in south China identified a wide range of viruses in wild and zoo animals between 2015 and 2022, demonstrating active monitoring of potential zoonotic viruses.

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

Here we identified 27 families of mammalian viruses from 1981 wild animals and 194 zoo animals collected from south China between 2015 and 2022, isolated and characterized the pathogenicity of eight viruses.

Method
viral identification; virus isolation
Geographic raw
south China
Country inferred
China
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Surveillance of bats in south China revealed high diversity of several viral families including coronaviruses, picornaviruses, astroviruses, and a novel bornavirus genus.

Host
Chiroptera
Location
China south China, China
Supporting text

Bats harbor high diversity of coronaviruses, picornaviruses and astroviruses, and a potentially novel genus of Bornaviridae.

Method
viral diversity analysis
Geographic raw
south China
Country inferred
China
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Surveillance indicated circulation of picornavirus and respiroviruses between bats and pangolins, suggesting monitoring at an animal interface for potential zoonotic viruses.

Location
China south China, China
Supporting text

Picornavirus and respiroviruses also likely circulate between bats and pangolins.

Method
virus identification
Geographic raw
south China
Country inferred
China
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Surveillance detected potential cross-species transmission of multiple RNA and DNA viruses between wildlife and domestic animals in south China.

Host
Not specified
Location
China south China, China
Supporting text

Further, the potential cross-species transmission of RNA viruses (paramyxovirus and astrovirus) and DNA viruses (pseudorabies virus, porcine circovirus 2, porcine circovirus 3 and parvovirus) between wildlife and domestic animals was identified.

Method
virus identification
Geographic raw
south China
Country inferred
China
Genomic Evolution 2 records
Genomic Evolution Extraction confidence 0.80
Key finding

Genomic and phylogenetic analyses identified a new clade of Embecovirus and a new genus of arenaviruses in pikas.

Virus
Embecovirus
Location
Not specified
Supporting text

Pikas harbor a new clade of Embecovirus and a new genus of arenaviruses.

Analysis methods
phylogenetic analysis
Genomic Evolution Extraction confidence 0.80
Key finding

Sequence and phylogenetic analyses showed that bats harbor diverse coronaviruses, picornaviruses, astroviruses, and a novel bornavirus genus.

Virus
Bornaviridae
Host
Chiroptera
Location
Not specified
Supporting text

Bats harbor high diversity of coronaviruses, picornaviruses and astroviruses, and a potentially novel genus of Bornaviridae.

Analysis methods
phylogenetic analysis