4株猪流行性腹泻病毒S1基因生物信息学分析

doi:10.16431/j.cnki.1671-7236.2016.11.032

Abstract

Abstract:

To analyse the genetic variation of porcine epidemic diarrhea virus（PEDV),one pair of primers was designed and RT-PCR was used to amplify the S1 gene epitope sequences of 4 PEDV field strains.Phylogenetic analysis showed that 4 strains were closely related to each other and belonged to the second group,and the Hunan and Henan isolates had a close relationship with JXGZ2013,GDZQ2012,GDZQ2014 strains,with the nucleotide homologies at 98.3% to 98.7%;Shanghai strain had a closed relationship with BJ-2011 strain and LZW isolates,with the higher homology at about 98.7%;Fujian isolates had a close relationship with strain of American in 2013,Japanese and Taiwan variation of China with the nucleotide homology at 99.0% to 99.5%;These results showed that a rapid variation and evolution of PEDV strains occurred in recent years,and linear B-cell epitope analysis showed that the threshold values at site 265 to 278 amino acid of 4 filed strains were higher than that of vaccine strains.The epitope differences indicated a possible of infectious that cause of patterns of epidemiology of PEDV.

Key words: porcine epidemic diarrhea virus; genetic variation; B-cell epitope

CLC Number:

S852.65

ZHU Hai-xia. Bioinformatics Analysis on S1 Gene of Four Porcine Epidemic Diarrhea Virus Strains[J]. , 2016, 43(11): 3024-3030.

References

[1] 施标,董世娟,朱于敏,等.中国猪流行性腹泻病毒分子流行病学研究进展[J].中国农业科学,2013,46(20):4362-4369.
[2] Penanert M B,de Bouck P.A new coronavirus-like particle associated with diarrhea in swine[J].Arch Virol,1978,58(3):243-247.
[3] Xuan H,Xing D,Wang D,et al.Study on the culture of porcine epidemic diarrhea virus adapted to fetal porcine primary cell monolayer[J].Chin J Vet Sci,1984,4(3):202-208.
[4] Chen Q,Li G,Stasko J,et al.Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States[J].J Clin Microbiol,2014,52(1):234-243.
[5] Chen J,Liu X,Shi D,et al.Detection and molecular diversity of spike gene of porcine epidemic diarrhea virus in China[J].Virus,2013,5:2601-2613.
[6] Tian P F,Jin Y L,Xing G,et al.Evidence of recombinant strains of porcine epidemic diarrhea virus,United States,2013[J].Emerg Infect Dis,2014,20(10):1735-1738.
[7] 陈慧娟,吴志明,闫若潜,等.2012年河南省猪流行性腹泻病毒分离株S1基因遗传变异分析[J].中国畜牧兽医,2014,41(3):14-18.
[8] 刘艳成,卢婷,刘丹丹,等.2010-2014年猪流行性腹泻病毒S基因遗传进化分析[J].动物医学进展,2015,36(8):28-34.
[9] Sun R,Leng Z,Zhai S,et al.Genetic variability and phylogeny of current Chinese porcine epidemic diarrhea virus strain based on spike,ORF3,and membrane genes[J].The Scientific World Journal,2014,22(1):1-8.
[10] Chen J F,Liu X Z,Shi D,et al.Complete gene sequence of porcine epidemic diarrhea virus variant[J].J Virol,2012,86(6):3408.
[11] 蔡清秀,陈晓春,吴华伟,等.4株猪流行性腹泻病毒S蛋白序列特征和遗传进化分析[J].中国兽药杂志,2015,49(7):1-7.
[12] 郑逢梅,霍金耀,赵军,等.2010-2012年华中地区猪流行性腹泻病毒分子特征和遗传进化分析[J].病毒学报,2013,29(2):197-205.
[13] Chang S H,Bae J L,Kang T J,et al.Identification of the epitope region capable of inducing neutralizing antibodies against the porcine epidemic diarrhea virus[J].Mol Cells,2002,14(2):295-299.
[14] Sun D,Feng L,Shi H,et al.Identification of two novel B cell epitopes on porcine epidemic diarrhea virus spike protein[J].Vet Microbiol,2008,131(1-2):73-81.
[15] Vlasova A N,Marthaler D,Wang Q,et al.Distinct characteristics and complex evolution of PEDV strains,North America,May 2013-February 2014[J].Emerge Infect Dis,2014,20(10):1620-1628.
[16] 程小娜,张志,樊雅婷,等.猪流行性腹泻病毒流行毒株S基因的遗传变异和B细胞线性抗原表位分析[J].动物医学进展,2015,36(8):45-50.

Bioinformatics Analysis on S1 Gene of Four Porcine Epidemic Diarrhea Virus Strains

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