Affiliations 

  • 1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
  • 2 Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA
  • 3 Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
  • 4 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800 Kongens Lyngby, Denmark
  • 5 Departments of Bioengineering and Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA
  • 6 National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
  • 7 Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark
Emerg Microbes Infect, 2016 Aug 17;5(8):e90.
PMID: 27530749 DOI: 10.1038/emi.2016.90

Abstract

Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.