title: Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.
abstract: Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Anita C
authors.initials: AC
authors.lastname: Schürch
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Debby
authors.initials: D
authors.lastname: Schipper
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Maarten A
authors.initials: MA
authors.lastname: Bijl
authors.affiliation: Alaska Department of Fish and Game, Kotzebue, Alaska, United States of America.
authors.forename: Jim
authors.initials: J
authors.lastname: Dau
authors.affiliation: Alaska Department of Fish and Game, Division of Wildlife Conservation, Fairbanks, Alaska, United States of America.
authors.forename: Kimberlee B
authors.initials: KB
authors.lastname: Beckmen
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Claudia M E
authors.initials: CM
authors.lastname: Schapendonk
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: V Stalin
authors.initials: VS
authors.lastname: Raj
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands; Viroclinics Biosciences, Rotterdam, The Netherlands.
authors.forename: Albert D M E
authors.initials: AD
authors.lastname: Osterhaus
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Bart L
authors.initials: BL
authors.lastname: Haagmans
authors.affiliation: Research Group for Arctic Infection Biology, Department of Arctic and Marine Biology, UiT - the Arctic University of Norway, Tromsø, Norway; Genøk - Centre for Biosafety, Tromsø, Norway.
authors.forename: Morten
authors.initials: M
authors.lastname: Tryland
authors.affiliation: Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands; Viroclinics Biosciences, Rotterdam, The Netherlands.
authors.forename: Saskia L
authors.initials: SL
authors.lastname: Smits
mesh_terms: D000413:Alaska; D000818:Animals; D000957:Antigens, Viral, Tumor / Q000235:genetics; D036022:Capsid Proteins / Q000235:genetics; D003332:Coronaviridae / Q000235:genetics; D005260:Female; D005814:Genes, Viral; D008297:Male; D054892:Metagenome; D008969:Molecular Sequence Data; D028381:Nidovirales / Q000235:genetics; D027383:Papillomaviridae / Q000235:genetics; D010321:Parvoviridae / Q000235:genetics; D010802:Phylogeny; D027382:Polyomaviridae / Q000235:genetics; D012053:Reindeer / Q000821:virology*; D017422:Sequence Analysis, DNA; D017361:Viral Nonstructural Proteins / Q000235:genetics; D014777:Virus Diseases / Q000662:veterinary* / Q000821:virology
chemical_list: D000957:Antigens, Viral, Tumor; D036022:Capsid Proteins; D017361:Viral Nonstructural Proteins