title: High diversity of picornaviruses in rats from different continents revealed by deep sequencing.
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.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: Thomas Arn
authors.initials: TA
authors.lastname: Hansen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: Sarah
authors.initials: S
authors.lastname: Mollerup
authors.affiliation: Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA.
authors.forename: Nam-Phuong
authors.initials: NP
authors.lastname: Nguyen
authors.affiliation: Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia.
authors.forename: Nicole E
authors.initials: NE
authors.lastname: White
authors.affiliation: Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia.
authors.forename: Megan
authors.initials: M
authors.lastname: Coghlan
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: David E
authors.initials: DE
authors.lastname: Alquezar-Planas
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800 Kongens Lyngby, Denmark.
authors.forename: Tejal
authors.initials: T
authors.lastname: Joshi
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: Randi Holm
authors.initials: RH
authors.lastname: Jensen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.|Virus Research and Development, Statens Serum Institut, DK-2300 Copenhagen, Denmark.
authors.forename: Helena
authors.initials: H
authors.lastname: Fridholm
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: Kristín Rós
authors.initials: KR
authors.lastname: Kjartansdóttir
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: Tobias
authors.initials: T
authors.lastname: Mourier
authors.affiliation: Departments of Bioengineering and Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA.
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark.
authors.forename: Graham J
authors.initials: GJ
authors.lastname: Belsham
authors.affiliation: Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia.
authors.forename: Michael
authors.initials: M
authors.lastname: Bunce
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark.
authors.forename: Lars Peter
authors.initials: LP
authors.lastname: Nielsen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: Lasse
authors.initials: L
authors.lastname: Vinner
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
authors.forename: Anders Johannes
authors.initials: AJ
authors.lastname: Hansen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D003718:Denmark / Q000453:epidemiology; D004197:Disease Reservoirs; D005243:Feces / Q000821:virology*; D000069196:Gastrointestinal Microbiome; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D006723:Hong Kong / Q000453:epidemiology; D006801:Humans; D008296:Malaysia / Q000453:epidemiology; D056186:Metagenomics; D010802:Phylogeny; D010849:Picornaviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010850:Picornaviridae Infections / Q000453:epidemiology* / Q000635:transmission; D012367:RNA, Viral; D051381:Rats / Q000821:virology*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics; D015047:Zoonoses
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins