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Virus Genes. 2017 Aug;53(4):593-602. doi: 10.1007/s11262-017-1464-9. Epub 2017 May 8.

Complete genome analysis of porcine kobuviruses from the feces of pigs in Japan.

Author information

1
Kenpoku Livestock Hygiene Service Center, Mito, Ibaraki, 310-0002, Japan.
2
Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, 920-3101, Japan.
3
Tochigi Prefectural South District Animal Hygiene Service Center, Tochigi, Tochigi, 328-0002, Japan.
4
Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, 683-0017, Japan.
5
Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo, 108-8641, Japan.
6
Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo, 208-0011, Japan.
7
Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
8
Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo, 180-8602, Japan.
9
Department of Health and Medical Sciences, Ishikawa Prefectural Nursing University, Kahoku, Ishikawa, 929-1210, Japan.
10
Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan. m-nagai@ishikawa-pu.ac.jp.
11
Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan. m-nagai@ishikawa-pu.ac.jp.

Abstract

Porcine kobuviruses (PoKoVs) are ubiquitously distributed in pig populations worldwide and are thought to be enteric viruses in swine. Although PoKoVs have been detected in pigs in Japan, no complete genome data for Japanese PoKoVs are available. In the present study, 24 nearly complete or complete sequences of the PoKoV genome obtained from 10 diarrheic feces and 14 non-diarrheic feces of Japanese pigs were analyzed using a metagenomics approach. Japanese PoKoVs shared 85.2-100% identity with the complete coding nucleotide (nt) sequences and the closest relationship of 85.1-98.3% with PoKoVs from other countries. Twenty of 24 Japanese PoKoVs carried a deletion of 90 nt in the 2B coding region. Phylogenetic tree analyses revealed that PoKoVs were not grouped according to their geographical region of origin and the phylogenetic trees of the L, P1, P2, and P3 genetic regions showed topologies different from each other. Similarity plot analysis using strains from a single farm revealed partially different similarity patterns among strains from identical farm origins, suggesting that recombination events had occurred. These results indicate that various PoKoV strains are prevalent and not restricted geographically on pig farms worldwide and the coexistence of multiple strains leads to recombination events of PoKoVs and contributes to the genetic diversity and evolution of PoKoVs.

KEYWORDS:

Genetic analysis; Japan; Kobuvirus; Porcine feces; Recombination event

PMID:
28484931
DOI:
10.1007/s11262-017-1464-9
[Indexed for MEDLINE]

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