OmniVira

Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance.

Yuqi Shi1 Yuxing Li1 Haipeng Li1 Ayidana Haerheng1 Vanessa R Marcelino2,3 Meng Lu1 Philippe Lemey4 Jia Tang1 Yuhai Bi5 John H-O Pettersson2,6,7 Jon Bohlin8,9 Joon Klaps4 Zuowei Wu10 Wenbo Wan1 Bowen Sun1 Mei Kang1 Edward C Holmes11,12 Na He1 Shuo Su13
Affiliations 13 institutions
  1. Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
  2. Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
  3. Melbourne Integrative Genomics, School of Biosciences, University of Melbourne, Melbourne, VIC, Australia.
  4. Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.
  5. CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
  6. Zoonosis Science Center, Clinical Microbiology, Department of Medical Sciences, University of Uppsala, Uppsala, Sweden
  7. Department of Microbiology, Swedish Veterinary Agency, Uppsala, Sweden.
  8. Norwegian Institute of Public Health, Domain for Infection Control, Section for Modeling and Bioinformatics, Oslo, Norway
  9. Center for Fertility and Health, Norwegian Institute of Public Health, P.O. Box 222 Skøyen, Oslo, Norway.
  10. Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA , USA.
  11. School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
  12. Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China.
  13. Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China. Electronic address: [email protected].
PMID40865528 DOI10.1016/j.cell.2025.08.016 Year2025 Journal Cell Languageeng Statusppublish

Abstract

Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears and Getah virus in rabbits, while the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat. We identified potential bacterial pathogen transmission between farmed and wild mammals and bacterial strains with high genetic similarity to those found in humans. We observed 157 clinically prioritized antibiotic resistance genes (ARGs) in mammalian microbiomes with greater than 99% identity to ARGs from human microbiomes, often co-occurring with mobile genetic elements. Overall, this work highlights cross-species risks at the human-animal interface.

Supporting text Virus Host Location
antibiotic resistance 1 avian influenza virus 59 cross-species transmission 75 Getah virus 5 microbial surveillance 1 mobile genetic element 1 unexported bacterial diversity 1 Drug Resistance, Microbial 2 Mammals 92 Public Health Surveillance 6 Animals 1948 Animals, Domestic 35 Animals, Wild 187 Bacteria 3 Feces 113 Humans 1440 Metagenomics 37 Microbiota 3 Phylogeny 805 Viruses 49

Evidence records

4 total
Zoonotic Surveillance
4 records · 1 evidence types
Evidence type Viral Detection
4 records
OVE9745 Viral Detection
Key finding

The 2.3.4.4b clade of H5N1 avian influenza virus was detected in a wild leopard cat.

Virus
Influenza A virus H5N1
Host
leopard cat Prionailurus bengalensis Natural host
Location
Not specified
Supporting text

the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat

Method
metagenomic sequencing | metatranscriptomic sequencing
Sample type
fecal samples | tissue samples
OVE9743 Viral Detection
Key finding

Canine coronavirus was detected in Asiatic black bears.

Virus
Canine Coronavirus
Host
Asiatic black bear Ursus thibetanus Natural host
Location
Not specified
Supporting text

Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears

Method
metagenomic sequencing | metatranscriptomic sequencing
Sample type
fecal samples | tissue samples
OVE9744 Viral Detection
Key finding

Getah virus was detected in rabbits.

Virus
getah virus
Host
rabbit Oryctolagus cuniculus Natural host
Location
Not specified
Supporting text

Farmed and wild mammals shared 13.3% of virus species, including ... Getah virus in rabbits

Method
metagenomic sequencing | metatranscriptomic sequencing
Sample type
fecal samples | tissue samples
OVE9746 Viral Detection
Key finding

Farmed and wild mammals shared 13.3% of virus species, indicating cross-species viral transmission between these animal groups.

Virus
virus species
Host
mammals Mammalia Natural host
Location
Not specified
Supporting text

Farmed and wild mammals shared 13.3% of virus species, indicating cross-species viral transmission between animal groups.

Method
metagenomic sequencing | metatranscriptomic sequencing | comparative analysis of shared viral species