title: Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination.
abstract: Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs. Based on a phylogenetic analysis and pairwise sequence comparison, 10, 5, 15, and 6 sequences were classified as PoAstV2, PoAstV3, PoAstV4, and PoAstV5, respectively. Co-infection with two or three strains was found in individual fecal samples from eight pigs. The phylogenetic trees of ORF1a, ORF1b, and ORF2 of PoAstV2 and PoAstV4 showed differences in their topologies. The PoAstV3 and PoAstV5 strains shared high sequence identities within each genotype in all ORFs; however, one PoAstV3 strain and one PoAstV5 strain showed considerable sequence divergence from the other PoAstV3 and PoAstV5 strains, respectively, in ORF2. Recombination analysis using whole genomes revealed evidence of multiple possible intra-genotype recombination events in PoAstV2 and PoAstV4, suggesting that recombination might have contributed to the genetic diversity and played an important role in the evolution of Japanese PoAstVs.
authors.affiliation: Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan.
authors.forename: Mika
authors.initials: M
authors.lastname: Ito
authors.affiliation: Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan.
authors.forename: Moegi
authors.initials: M
authors.lastname: Kuroda
authors.affiliation: Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan.
authors.forename: Tsuneyuki
authors.initials: T
authors.lastname: Masuda
authors.affiliation: Kenhoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan.
authors.forename: Masataka
authors.initials: M
authors.lastname: Akagami
authors.affiliation: Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, 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: 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.
authors.forename: Mai
authors.initials: M
authors.lastname: Kishimoto
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: 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: 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: 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: Department of Health and Medical Sciences, Ishikawa Prefectural Nursing University, Kahoku, Ishikawa, 929-1210, Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Ichimaru
authors.affiliation: Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan.
authors.forename: Itsuro
authors.initials: I
authors.lastname: Mukono
authors.affiliation: Kenhoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan.
authors.forename: Yoshinao
authors.initials: Y
authors.lastname: Ouchi
authors.affiliation: Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yamasato
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: Junsuke
authors.initials: J
authors.lastname: Shirai
authors.affiliation: Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, 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
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 Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan. Electronic address: m-nagai@ishikawa-pu.ac.jp.
authors.forename: Makoto
authors.initials: M
authors.lastname: Nagai
mesh_terms: D000818:Animals; D019350:Astroviridae Infections / Q000662:veterinary* / Q000821:virology; D005075:Biological Evolution; D003967:Diarrhea / Q000662:veterinary* / Q000821:virology; D005243:Feces / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007564:Japan; D001257:Mamastrovirus / Q000145:classification / Q000235:genetics*; D016366:Open Reading Frames; D010802:Phylogeny; D011995:Recombination, Genetic; D013552:Swine; D013553:Swine Diseases / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D014764:Viral Proteins
keywords: Astrovirus; Genotyping; Japan; Porcine feces; Recombination event