title: Identification and complete genome analysis of a novel bovine picornavirus in Japan.
abstract: We identified novel viruses in feces from cattle with diarrhea collected in 2009 in Hokkaido Prefecture, Japan, by using a metagenomics approach and determined the (near) complete sequences of the virus. Sequence analyses revealed that they had a standard picornavirus genome organization, i.e. 5' untranslated region (UTR) - L- P1 (VP4- VP3- VP2- VP1) - P2 (2A- 2B- 2C) - P3 (3A- 3B- 3C-3D) - 3'UTR- poly(A). They are closely related to other unclassified Chinese picornaviruses; bat picornaviruses group 1-3, feline picornavirus, and canine picornavirus, sharing 45.4-51.4% (P1), 38.0-44.9% (P2), and 49.6-53.3% (P3) amino acid identities, respectively. The phylogenetic analyses and detailed genome characterization showed that they, together with the unclassified Chinese picornaviruses, grouped as a cluster for the P1, 2C, 3CD and VP1 coding regions. These viruses had conserved features (e.g. predicted protein cleavage sites, presence of a leader protein, 2A, 2C, 3C, and 3D functional domains), suggesting they have a common ancestor. Reverse-transcription-PCR assays, using specific primers designed from the 5'UTR sequence of these viruses, showed that 23.0% (20/87) of fecal samples from cattle with diarrhea were positive, indicating the prevalence of these picornavirus in the Japanese cattle population in Hokkaido Prefecture. However, further studies are needed to investigate the pathogenic potential and etiological role of these viruses in cattle.
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan. Electronic address: m-nagai@cc.tuat.ac.jp.
authors.forename: Makoto
authors.initials: M
authors.lastname: Nagai
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Omatsu
authors.affiliation: Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Aoki
authors.affiliation: Veterinary Science, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kaku
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: Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan.
authors.forename: Kei
authors.initials: K
authors.lastname: Haga
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Naoi
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Sano
authors.affiliation: Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan.
authors.forename: Moeko
authors.initials: M
authors.lastname: Umetsu
authors.affiliation: Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan.
authors.forename: Mai
authors.initials: M
authors.lastname: Shiokawa
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Shinobu
authors.initials: S
authors.lastname: Tsuchiaka
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Furuya
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Sachiko
authors.initials: S
authors.lastname: Okazaki
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Yukie
authors.initials: Y
authors.lastname: Katayama
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Mami
authors.initials: M
authors.lastname: Oba
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Junsuke
authors.initials: J
authors.lastname: Shirai
authors.affiliation: Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan.
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Katayama
authors.affiliation: Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Mizutani
mesh_terms: D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000453:epidemiology / Q000821:virology*; D016000:Cluster Analysis; D003967:Diarrhea / Q000453:epidemiology / Q000662:veterinary / Q000821:virology; D005243:Feces / Q000821:virology; D023061:Gene Order; D005814:Genes, Viral; D016679:Genome, Viral; D007564:Japan / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D010849:Picornaviridae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010850:Picornaviridae Infections / Q000662:veterinary* / Q000821:virology; D015995:Prevalence; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D012367:RNA, Viral
keywords: Bovine; Feces; Japan; Metagenomics; Novel picornavirus