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Genomic characterization of a US porcine kobuvirus strain

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Abstract

Porcine kobuvirus has been detected from pig fecal samples in the USA, but there is still no information on the full-length genomes. In this study, we characterized the first complete genomic sequence of a US porcine kobuvirus strain OH/RV50/2011. The viral genome is 8123 nucleotides (nt) long, including a 576-nt 5′-untranslated region (UTR), a 7380-nt polyprotein encoding sequence, and a 167-nt 3′-UTR. A complete genome sequence alignment suggested that two types of porcine kobuviruses were found based on whether a 30-aa deletion existed in the 2B encoding region. Furthermore, several conserved motifs that can be used for the design of universal kobuvirus or porcine kobuvirus-specific primers were verified in non-structural protein genes. Phylogenetic analysis based on the complete genome sequence showed that RV50 was grouped with other porcine kobuviruses and more closely related to Chinese strains. Secondary structure analysis of the 5′-UTR showed that RV50 has three stem-loop domains in the first 108 nt and has a potential hepacivirus-/pestivirus-like type IV group-B-like internal ribosomal entry site, like the porcine kobuvirus prototype strain S-1. Codon usage analysis showed that the most preferred usage tends to be C or U at the end of a codon in a porcine kobuvirus genome. These results will be useful in understanding the evolution of porcine kobuviruses .

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References

  • Amimo JO, Vlasova AN, Saif LJ (2013a) Detection and genetic diversity of porcine group A rotaviruses in historic (2004) and recent (2011 and 2012) swine fecal samples in Ohio: predominance of G9P[13] genotype in nursing piglets. J Clin Microbiol 51(4):1142–1151

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Amimo JO, Vlasova A, Saif L (2013b) Prevalence and genetic heterogeneity of porcine group C rotaviruses in nursing and weaned piglets in Ohio, USA and identification of a potential new VP4 genotype. Vet Microbiol 164:27–38

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Amimo JO, Okoth E, Junga JO, Ogara WO, Njahira MN, Wang Q, Vlasova AN, Saif LJ, Djikeng A (2014) Molecular detection and genetic characterization of kobuviruses and astroviruses in asymptomatic local pigs in East Africa. Arch Virol 159:1313–1319

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Asnani M, Kumar P, Hellen CU (2015) Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae. Virology 478:61–74

    Article  CAS  PubMed  Google Scholar 

  • Barry AF, Ribeiro J, Alfieri AF, van der Poel WH, Alfieri AA (2011) First detection of kobuvirus in farm animals in Brazil and the Netherlands. Infect Genet Evol 11:1811–1814

    Article  PubMed  Google Scholar 

  • Carmona-Vicente N, Buesa J, Brown P, Merga J, Darby A, Stavisky J, Sadler L, Gaskell R, Dawson S, Radford A (2013) Phylogeny and prevalence of kobuviruses in dogs and cats in the UK. Vet Microbiol 164:246–252

    Article  CAS  PubMed  Google Scholar 

  • Chung J-Y, Kim S-H, Kim Y-H, Lee M-H, Lee K-K, Oem J-K (2013) Detection and genetic characterization of feline kobuviruses. Virus Gen 47:559–562

    Article  CAS  Google Scholar 

  • De Rijk P, De Wachter R (1997) RnaViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res 25:4679–4684

    Article  PubMed Central  PubMed  Google Scholar 

  • Di Martino B, Di Profio F, Melegari I, Robetto S, Di Felice E, Orusa R, Marsilio F (2014) Molecular evidence of kobuviruses in free-ranging red foxes (Vulpes vulpes). Arch Virol 159:1803–1806

    Article  PubMed  Google Scholar 

  • Di Profio F, Ceci C, Di Felice E, Marsilio F, Di Martino B (2013) Molecular detection of porcine kobuviruses in Italian swine. Res Vet Sci 95:782–785

    Article  PubMed  Google Scholar 

  • Dufkova L, Scigalkova I, Moutelikova R, Malenovska H, Prodelalova J (2013) Genetic diversity of porcine sapoviruses, kobuviruses, and astroviruses in asymptomatic pigs: an emerging new sapovirus GIII genotype. Arch Virol 158:549–558

    Article  CAS  PubMed  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Ingvarsson PK (2008) Molecular evolution of synonymous codon usage in Populus. BMC Evol Biol 8:307

    Article  PubMed Central  PubMed  Google Scholar 

  • Kernbauer E, Ding Y, Cadwell K (2014) An enteric virus can replace the beneficial function of commensal bacteria. Nature 516:94–98

    PubMed Central  CAS  PubMed  Google Scholar 

  • Khamrin P, Maneekarn N, Kongkaew A, Kongkaew S, Okitsu S, Ushijima H (2009) Porcine kobuvirus in piglets, Thailand. Emerg Infect Dis 12:2075–2076

    Article  Google Scholar 

  • Khamrin P, Maneekarn N, Hidaka S, Kishikawa S, Ushijima K, Okitsu S, Ushijima H (2010) Molecular detection of kobuvirus sequences in stool samples collected from healthy pigs in Japan. Infect Genet Evol 10:950–954

    Article  CAS  PubMed  Google Scholar 

  • Lee M-H, Jeoung H-Y, Lim J-A, Song J-Y, Song D-S, An D-J (2012) Kobuvirus in South Korean black goats. Virus Gen 45:186–189

    Article  CAS  Google Scholar 

  • Li L, Victoria JG, Wang C, Jones M, Fellers GM, Kunz TH, Delwart E (2010) Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol 84:6955–6965

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Li L, Pesavento PA, Shan T, Leutenegger CM, Wang C, Delwart E (2011) Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses. J Gen Virol 92:2534–2541

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • McInerney JO (1998) Replicational and transcriptional selection on codon usage in borrelia burgdorferi. Proc Nat Acad Sci 95:10698–10703

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Oh D-Y, Silva P, Hauroeder B, Diedrich S, Cardoso D, Schreier E (2006) Molecular characterization of the first aichi viruses isolated in Europe and in South America. Arch Virol 151:1199–1206

    Article  CAS  PubMed  Google Scholar 

  • Pankovics P, Boros Á, Kiss T, Reuter G (2015) Identification and complete genome analysis of kobuvirus in faecal samples of European roller (Coracias garrulus): for the first time in a bird. Arch Virol 160:345–351

    Article  CAS  PubMed  Google Scholar 

  • Park S-J, Kim H-K, Moon H-J, Song D-S, Rho S-M, Han J-Y, Nguyen V-G, Park B-K (2010) Molecular detection of porcine kobuviruses in pigs in Korea and their association with diarrhea. Arch Virol 155:1803–1811

    Article  CAS  PubMed  Google Scholar 

  • Phan TG, Kapusinszky B, Wang C, Rose RK, Lipton HL, Delwart EL (2011) The fecal viral flora of wild rodents. PLoS Pathog 7:e1002218

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Reuter G, Egyed L (2009) Bovine kobuvirus in Europe. Emerg Infect Dis 15:822

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Reuter G, Boldizsár Á, Kiss I, Pankovics P (2008) Candidate new species of kobuvirus in porcine hosts. Emerg Infect Dis 14:1968

    Article  PubMed Central  PubMed  Google Scholar 

  • Reuter G, Boldizsár Á, Pankovics P (2009) Complete nucleotide and amino acid sequences and genetic organization of porcine kobuvirus, a member of a new species in the genus kobuvirus, family picornaviridae. Arch Virol 154:101–108

    Article  CAS  PubMed  Google Scholar 

  • Reuter G, Boros Á, Pankovics P, Egyed L (2010a) Kobuvirus in domestic sheep. Hungary. Emerg Infect Dis 16:869

    Article  PubMed  Google Scholar 

  • Reuter G, Kecskeméti S, Pankovics P (2010b) Evolution of porcine kobuvirus infection. Hungary. Emerg Infect Dis 16:696

    Article  PubMed  Google Scholar 

  • RoyChoudhury S, Mukherjee D (2010) A detailed comparative analysis on the overall codon usage pattern in herpesviruses. Virus Res 148:31–43

    Article  CAS  PubMed  Google Scholar 

  • Scotto-Lavino E, Du G, Frohman MA (2006) 5′ end cDNA amplification using classic RACE. Nat Protoc 1:2555–2562

    Article  CAS  PubMed  Google Scholar 

  • Sisay Z, Wang Q, Oka T, Saif L (2013) Prevalence and molecular characterization of porcine enteric caliciviruses and first detection of porcine kobuviruses in US swine. Arch Virol 158:1583–1588

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Smits SL, Raj VS, Oduber MD, Schapendonk CM, Bodewes R, Provacia L, Stittelaar KJ, Osterhaus AD, Haagmans BL (2013) Metagenomic analysis of the ferret fecal viral flora. PLoS ONE 8:e71595

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sweeney TR, Dhote V, Yu Y, Hellen CU (2012) A distinct class of internal ribosomal entry site in members of the kobuvirus and proposed salivirus and paraturdivirus genera of the picornaviridae. J Virol 86:1468–1486

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Verma H, Mor SK, Abdel-Glil MY, Goyal SM (2013) Identification and molecular characterization of porcine kobuvirus in US swine. Virus Gen 46:551–553

    Article  CAS  Google Scholar 

  • Yamashita T, Kobayashi S, Sakac K, Nakata S, Chiba S, Ishihara Y, Isomura S (1991) Isolation of cytopathic small round viruses with BS-Cl cells from patients with gastroenteritis. J Infec Dis 164:954–957

    Article  CAS  Google Scholar 

  • Yamashita T, Sakae K, Tsuzuki H, Suzuki Y, Ishikawa N, Takeda N, Miyamura T, Yamazaki S (1998) Complete nucleotide sequence and genetic organization of aichi virus, a distinct member of the picornaviridaeassociated with acute gastroenteritis in humans. J Virol 72:8408–8412

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yamashita T, Ito M, Kabashima Y, Tsuzuki H, Fujiura A, Sakae K (2003) Isolation and characterization of a new species of kobuvirus associated with cattle. J Gen Virol 84:3069–3077

    Article  CAS  PubMed  Google Scholar 

  • Yu J-m, Jin M, Zhang Q, Li H-y, Li D-d, Xu Z-q, Li J-s, Cui S-x, Yang S-h, Liu N (2009) Candidate porcine kobuvirus. China. Emerg Infect Dis 15:823

    Article  CAS  PubMed  Google Scholar 

  • Yu Y, Sweeney TR, Kafasla P, Jackson RJ, Pestova TV, Hellen CU (2011) The mechanism of translation initiation on Aichivirus RNA mediated by a novel type of picornavirus IRES. EMBO J 30:4423–4436

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Nucleotide sequencing was performed at the Molecular and Cellular Imaging Center, the Ohio Agricultural Research and Development Center (OARDC), The Ohio State University. We thank Drs. Chang-Won Lee and Anastasia Vlasova for their critical review, and Susan Sommer-Wagner for her grammatical editing of this manuscript. We thank State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, for scholarship support toward X. Liu. Salaries and research support were provided by state and federal funds appropriated to the Ohio Agricultural Research and Development Center (OARDC), The Ohio State University.

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Authors and Affiliations

  1. Food Animal Health Research Program, Ohio Agricultural Research and Development Center, College of Food, Agricultural and Environmental Sciences, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA

    Xinsheng Liu, Tomoichiro Oka & Qiuhong Wang

  2. State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot-and-Mouth Disease Reference Laboratory of China, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People’s Republic of China

    Xinsheng Liu

  3. Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan

    Tomoichiro Oka

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  1. Xinsheng Liu
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  2. Tomoichiro Oka
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Correspondence to Qiuhong Wang.

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Communicated by Shuang-Jiang Liu.

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Liu, X., Oka, T. & Wang, Q. Genomic characterization of a US porcine kobuvirus strain. Arch Microbiol 197, 1033–1040 (2015). https://doi.org/10.1007/s00203-015-1139-7

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  • DOI: https://doi.org/10.1007/s00203-015-1139-7

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