title: Molecular and phylogenetic analysis of the porcine kobuvirus VP1 region using infected pigs from Sichuan Province, China.
abstract: BACKGROUND
  Porcine kobuvirus (PKoV) is a member of the Kobuvirus genus within the Picornaviridae family. PKoV is distributed worldwide with high prevalence in clinically healthy pigs and those with diarrhea.
  
  
  METHODS
  Fecal and intestinal samples (n = 163) from pig farms in Sichuan Province, China were obtained to determine the presence of PKoV using reverse transcription polymerase chain reaction assays. Specific primers were used for the amplification of the gene encoding the PKoV VP1 protein sequence. Sequence and phylogenetic analyses were conducted to clarify evolutionary relationships with other PKoV strains.
  
  
  RESULTS
  Approximately 53% (87/163) of pigs tested positive for PKoV. PKoV was widespread in asymptomatic pigs and those with diarrhea. A high prevalence of PKoV was observed in pigs younger than 4 weeks and in pigs with diarrhea. Phylogenetic analysis of 36 PKoV VP1 protein sequences showed that Sichuan PKoV strains formed four distinct clusters. Two pigs with diarrhea were found to be co-infected with multiple PKoV strains. Sequence and phylogenetic analyses revealed diversity within the same host and between different hosts. Significant recombination breakpoints were observed between the CHN/SC/31-A1 and CHN/SC/31-A3 strains in the VP1 region, which were isolated from the same sample.
  
  
  CONCLUSIONS
  PKoV was endemic in Sichuan Province regardless of whether pigs were healthy or suffering from diarrhea. Based on our statistical analyses, we suggest that PKoV was the likely causative agent of high-mortality diarrhea in China from 2010. For the first time, we provide evidence for the co-existence of multiple PKoV strains in one pig, and possible recombination events in the VP1 region. Our findings provide further insights into the molecular properties of PKoV, along with its epidemiology.
authors.affiliation: Animal Biotechnology Center, College of Veterinary Medicine of Sichuan Agricultural University, 46# Xinkang Road, Yucheng District, Ya'an 625014Sichuan province, P,R, China. abtcxzw@126.com.
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.forename: Ling
authors.initials: L
authors.lastname: Zhu
authors.forename: Yuan-cheng
authors.initials: YC
authors.lastname: Zhou
authors.forename: Zhi-wen
authors.initials: ZW
authors.lastname: Xu
authors.forename: Wan-zhu
authors.initials: WZ
authors.lastname: Guo
authors.forename: Wen-yu
authors.initials: WY
authors.lastname: Yang
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D016000:Cluster Analysis; D060085:Coinfection / Q000662:veterinary / Q000821:virology; D019353:Endemic Diseases; D005243:Feces / Q000821:virology; D007422:Intestines / Q000821:virology; D052699:Kobuvirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000821:virology*; D015678:Viral Structural Proteins / Q000235:genetics*
chemical_list: D012367:RNA, Viral; D015678:Viral Structural Proteins
references.citation: Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13757-62
references.pmid: 11717435
references.citation: Bioinformatics. 2000 Jun;16(6):562-3
references.pmid: 10980155
references.citation: Virus Genes. 2012 Aug;45(1):186-9
references.pmid: 22528642
references.citation: Arch Virol. 2011 May;156(5):747-51
references.pmid: 21274731
references.citation: Emerg Infect Dis. 2010 May;16(5):869-70
references.pmid: 20409388
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Arch Virol. 2010 Nov;155(11):1803-11
references.pmid: 20820823
references.citation: Arch Virol. 2013 Nov;158(11):2379-83
references.pmid: 23736978
references.citation: Arch Virol. 2013 Jan;158(1):281-2
references.pmid: 22926717
references.citation: J Infect Dis. 1991 Nov;164(5):954-7
references.pmid: 1658159
references.citation: Emerg Infect Dis. 2008 Jun;14(6):985-6
references.pmid: 18507924
references.citation: Bioinformatics. 2000 Jul;16(7):573-82
references.pmid: 11038328
references.citation: Emerg Infect Dis. 2010 Apr;16(4):696-8
references.pmid: 20350391
references.citation: Emerg Infect Dis. 2009 May;15(5):823-5
references.pmid: 19402982
references.citation: AIDS Res Hum Retroviruses. 2005 Jan;21(1):98-102
references.pmid: 15665649
references.citation: J Virol. 1998 Oct;72(10):8408-12
references.pmid: 9733894
references.citation: Virol J. 2011 Aug 05;8:390
references.pmid: 21819561
references.citation: Arch Virol. 2013 Mar;158(3):549-58
references.pmid: 23124843
references.citation: J Virol. 2010 Jul;84(14):6955-65
references.pmid: 20463061
references.citation: Emerg Infect Dis. 2009 Dec;15(12):2075-6
references.pmid: 19961712
references.citation: Virus Genes. 2013 Jun;46(3):551-3
references.pmid: 23334473
references.citation: Rev Med Virol. 2011 Jan;21(1):32-41
references.pmid: 21294214
references.citation: Vet Microbiol. 2013 Jun 28;164(3-4):246-52
references.pmid: 23490561
references.citation: J Clin Microbiol. 2008 Dec;46(12):4011-7
references.pmid: 18842942
references.citation: Virology. 1999 Dec 20;265(2):218-25
references.pmid: 10600594
references.citation: J Clin Microbiol. 2008 Apr;46(4):1252-8
references.pmid: 18256215
references.citation: Arch Virol. 2009;154(1):101-8
references.pmid: 19096904
references.citation: J Clin Microbiol. 2000 Aug;38(8):2955-61
references.pmid: 10921958
references.citation: J Virol. 1999 Jan;73(1):152-60
references.pmid: 9847317
references.citation: Virus Genes. 2012 Apr;44(2):253-7
references.pmid: 22109708
references.citation: Emerg Infect Dis. 2009 May;15(5):822-3
references.pmid: 19402981
references.citation: J Virol. 2012 Nov;86(21):11947
references.pmid: 23043177
references.citation: Rev Med Virol. 2010 Sep;20(5):327-37
references.pmid: 20632373
references.citation: Virus Genes. 2011 Apr;42(2):208-11
references.pmid: 21161358
references.citation: Emerg Infect Dis. 2008 Dec;14(12):1968-70
references.pmid: 19046542
references.citation: Infect Genet Evol. 2010 Oct;10(7):950-4
references.pmid: 20547246
references.citation: Infect Genet Evol. 2011 Oct;11(7):1811-4
references.pmid: 21763785
references.citation: J Clin Microbiol. 2008 Apr;46(4):1349-55
references.pmid: 18287312
references.citation: J Clin Microbiol. 2007 Jul;45(7):2287-8
references.pmid: 17522267
references.citation: Arch Virol. 2006 Jun;151(6):1199-206
references.pmid: 16421634
references.citation: J Gen Virol. 2011 Sep;92(Pt 9):2047-2059
references.pmid: 21632566
references.citation: J Virol. 2011 Nov;85(21):11520-5
references.pmid: 21880761
references.citation: Virus Genes. 2011 Dec;43(3):350-2
references.pmid: 21789634
references.citation: PLoS Pathog. 2011 Sep;7(9):e1002218
references.pmid: 21909269
references.citation: J Med Virol. 2008 Jul;80(7):1222-7
references.pmid: 18461624
references.citation: J Mol Evol. 1992 Feb;34(2):126-9
references.pmid: 1556748
references.citation: J Gen Virol. 2003 Nov;84(Pt 11):3069-3077
references.pmid: 14573811
references.citation: Infect Genet Evol. 2011 Jul;11(5):1178-82
references.pmid: 21382521