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Literature detail

Farmed fur animals harbour viruses with zoonotic spillover potential.

Jin Zhao1 Wenbo Wan1 Kang Yu1,2 Philippe Lemey3 John H-O Pettersson4,5,6 Yuhai Bi7 Meng Lu1 Xinxin Li8 Zhuohang Chen1 Mengdi Zheng8 Ge Yan2 JianJun Dai2 Yuxing Li1 Ayidana Haerheng1 Na He1 Changchun Tu9 Marc A Suchard10 Edward C Holmes11,12 Wan-Ting He13 Shuo Su14
Affiliations 14 institutions
  1. Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
  2. State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
  3. Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.
  4. Clinical Microbiology, Department of Medical Sciences, University of Uppsala, Uppsala, Sweden.
  5. Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital, Uppsala, Sweden.
  6. Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
  7. CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
  8. Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
  9. Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
  10. 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, USA.
  11. School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
  12. Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China.
  13. State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China. [email protected].
  14. Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China. [email protected].
PMID 39232170 2024 Nature eng ppublish
PubMed DOI Browse context

Article

Publication summary

Animals such as raccoon dogs, mink and muskrats are farmed for fur and are sometimes used as food or medicinal products<sup>1,2</sup>, yet they are also potential reservoirs of emerging pathogens<sup>3</sup>. Here we performed single-sample metatranscriptomic sequencing of internal tissues from 461 individual fur animals that were found dead due to disease. We characterized 125 virus species, including 36 that were novel and 39 at potentially high risk of cross-species transmission, including zoonotic spillover. Notably, we identified seven species of coronaviruses, expanding their known host range, and documented the cross-species transmission of a novel canine respiratory coronavirus to raccoon dogs and of bat HKU5-like coronaviruses to mink, present at a high abundance in lung tissues. Three subtypes of influenza A virus-H1N2, H5N6 and H6N2-were detected in the lungs of guinea pig, mink and muskrat, respectively. Multiple known zoonotic viruses, such as Japanese encephalitis virus and mammalian orthoreovirus<sup>4,5</sup>, were detected in guinea pigs. Raccoon dogs and mink carried the highest number of potentially high-risk viruses, while viruses from the Coronaviridae, Paramyxoviridae and Sedoreoviridae families commonly infected multiple hosts. These data also reveal potential virus transmission between farmed animals and wild animals, and from humans to farmed animals, indicating that fur farming represents an important transmission hub for viral zoonoses.

Animal Fur Animals, Domestic Animals, Wild Disease Reservoirs Host Specificity Viral Zoonoses Animals Arvicolinae Chiroptera Coronavirus Dogs Encephalitis Virus, Japanese Guinea Pigs Humans Influenza A virus Lung Mink Orthoreovirus

Structured evidence records

Evidence records

8 total
Genomic Evolution 3 records
Genomic Evolution Extraction confidence 0.92
Key finding

Metatranscriptomic and phylogenetic analyses identified a novel canine respiratory coronavirus transmitted to raccoon dogs and bat HKU5-like coronaviruses infecting mink, revealing genomic evidence of host expansion within Coronaviridae.

Location
Not specified
Supporting text

We performed single-sample metatranscriptomic sequencing of internal tissues from 461 individual fur animals that were found dead due to disease. We characterized 125 virus species, including 36 that were novel and 39 at potentially high risk of cross-species transmission. Notably, we identified seven species of coronaviruses, expanding their known host range, and documented the cross-species transmission of a novel canine respiratory coronavirus to raccoon dogs and of bat HKU5-like coronaviruses to mink.

Analysis methods
metatranscriptomic sequencing; phylogenetic analysis
Genomic Evolution Extraction confidence 0.86
Key finding

Genomic sequencing detected influenza A virus subtypes H1N2, H5N6, and H6N2 in fur-farmed guinea pigs, mink, and muskrats, respectively, providing genomic evidence for host-associated viral diversity.

Virus
IAV
Location
Not specified
Supporting text

Three subtypes of influenza A virus-H1N2, H5N6 and H6N2-were detected in the lungs of guinea pig, mink and muskrat, respectively.

Analysis methods
genomic sequencing
Genomic Evolution Extraction confidence 0.84
Key finding

Metatranscriptomic sequencing recovered genomes of Japanese encephalitis virus and mammalian orthoreovirus from guinea pigs, supporting genomic detection of these zoonotic viruses in a novel host context.

Virus
JEV
Location
Not specified
Supporting text

Multiple known zoonotic viruses, such as Japanese encephalitis virus and mammalian orthoreovirus, were detected in guinea pigs.

Analysis methods
metatranscriptomic sequencing
Cross Species Transmission 2 records
Cross Species Transmission Extraction confidence 0.98
Key finding

A novel canine respiratory coronavirus was transmitted from dogs to raccoon dogs.

Location
Not specified
Supporting text

We documented the cross-species transmission of a novel canine respiratory coronavirus to raccoon dogs.

Method
metatranscriptomic sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Cross Species Transmission Extraction confidence 0.98
Key finding

Bat HKU5-like coronaviruses were transmitted from bats to mink.

Virus
BatCoV-HKU5
Location
Not specified
Supporting text

We documented the cross-species transmission of ... bat HKU5-like coronaviruses to mink, present at a high abundance in lung tissues.

Method
metatranscriptomic sequencing
Study design
field surveillance
Transmission direction
animal-to-animal
Reservoir Ecology 1 records
Reservoir Ecology Extraction confidence 0.85
Key finding

Fur farming creates an ecological interface that facilitates virus persistence and transmission among farmed, wild, and human populations, acting as a reservoir for zoonotic viruses.

Virus
Not specified
Host
Not specified
Location
Not specified
Supporting text

These data also reveal potential virus transmission between farmed animals and wild animals, and from humans to farmed animals, indicating that fur farming represents an important transmission hub for viral zoonoses.

Method
metatranscriptomic sequencing
Sample type
internal tissues; lung tissues
Spillover Event 1 records
Spillover Event Extraction confidence 0.90
Key finding

Evidence of potential human-to-animal viral spillback in farmed fur animals was observed.

Virus
Not specified
Location
Not specified
Supporting text

These data also reveal potential virus transmission between farmed animals and wild animals, and from humans to farmed animals, indicating that fur farming represents an important transmission hub for viral zoonoses.

Method
metatranscriptomic sequencing
Study design
metatranscriptomic sequencing
Transmission direction
human-to-animal
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Metatranscriptomic monitoring of 461 diseased farmed fur animals revealed numerous known and novel viruses with zoonotic potential.

Virus
Not specified
Host
Metazoa
Location
Not specified
Supporting text

Here we performed single-sample metatranscriptomic sequencing of internal tissues from 461 individual fur animals that were found dead due to disease. We characterized 125 virus species, including 36 that were novel and 39 at potentially high risk of cross-species transmission, including zoonotic spillover.

Method
metatranscriptomic sequencing
Sample type
internal tissues