猪非典型瘟病毒GX01-2018株全基因组分子特征的分析
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摘要
猪非典型瘟病毒(APPV)被证实是新生仔猪先天性震颤的致病因子。为了解广西APPV流行毒株的分子遗传特征,采用RT-PCR分段扩增APPV阳性病料,经克隆、测序、拼接,获得1株APPV的全基因序列,遂被命名为GX01-2018株。结果显示,GX01-2018株基因组全长11 565 bp,包括一个编码3 635个氨基酸的阅读框(ORF)。同源性分析显示,GX01-2018株与国内代表毒株广西GX-CH_2016株、江西JX-JM01-2018A01株、广东China/GD-SD/2016株、广东GD株核苷酸序列的同源性分别为98.2%、92.9%、83.4%、90.8%。GX01-2018株与国外代表毒株美国000515株、德国Bavaria_S5/9株、奥地利AUT-2016_C株、荷兰NL1株核苷酸序列的同源性分别为87.8%、90.7%、90.5%、90.7%。上述国内外代表毒株间Npro、Erns、E2基因核苷酸序列的同源性分别为79.1%～97.2%、83.0%～98.4%、83.1%～96.8%。基于APPV全基因组以及E2、Npro、Erns基因核苷酸序列绘制遗传进化树,获得相似的进化树图。来自广西的GX01-2018株与欧洲型毒株位于一个分支,而同样来自广西的GX04/2017株与美洲型毒株位于另一个分支。表明APPV流行毒株具有遗传多样性,来自同一地区的流行毒株出现较大的遗传变异。
Atypical porcine pestivirus(APPV) was recently demonstrated to be the causative agent of congenital tremor(CT) in newborn piglets.To investigate the genomic characteristics of APPV from Guangxi Province,APPV fragments were amplified from APPV positive sample,coloned,sequenced and ligated,and the full-length genomic sequence of an APPV isolate named as GX01-2018 strain was acquired.In result,the complete genome of GX01-2018 strain was 11 565 bp,which included an open reading frame(ORF)encoding a polyprotein with 3 635 amino acids.Homology analysis revealed that homology identity of complete nucleotide sequence of GX01-2018 strain with GX-CH_2016 strain from Guangxi,JX-JM01-2018 A01 strain from Jiangxi,China/GD-SD/2016 strain from Guangdong,GD strain from Guangdong was 98.2%,92.9%,83.4% and 90.8%,respectively.GX01-2018 strain shared 87.8%,90.7%,90.5% and 90.7% homology identity with 000515 strain from USA,Bavaria_S5/9 strain from Germany,AUT-2016_C strain from Austria,NL1 strain from The Netherlands,respectively.The nucleotide sequence homology identity of E2,Npro,Ernsgenes among the above-mentioned strains was 79.1% —97.2%,83.0% —98.4% and 83.1% —96.8%,respectively.Phylogenetic analysis showed that the phylogenetic trees based on complete genome and E2,Nproand Ernsgene nucleotide sequences resulted in similar topology.GX01-2018 strain from Guangxi together with European strains belonged to one group,while GX04/2017 strain also from Guangxi together with American strains belonged to another group.The above-mentioned results indicated that APPV isolates showed genetic diversity and there existed large genetic variation among different strains from the same region.
Atypical porcine pestivirus(APPV) was recently demonstrated to be the causative agent of congenital tremor(CT) in newborn piglets.To investigate the genomic characteristics of APPV from Guangxi Province,APPV fragments were amplified from APPV positive sample,coloned,sequenced and ligated,and the full-length genomic sequence of an APPV isolate named as GX01-2018 strain was acquired.In result,the complete genome of GX01-2018 strain was 11 565 bp,which included an open reading frame(ORF)encoding a polyprotein with 3 635 amino acids.Homology analysis revealed that homology identity of complete nucleotide sequence of GX01-2018 strain with GX-CH_2016 strain from Guangxi,JX-JM01-2018 A01 strain from Jiangxi,China/GD-SD/2016 strain from Guangdong,GD strain from Guangdong was 98.2%,92.9%,83.4% and 90.8%,respectively.GX01-2018 strain shared 87.8%,90.7%,90.5% and 90.7% homology identity with 000515 strain from USA,Bavaria_S5/9 strain from Germany,AUT-2016_C strain from Austria,NL1 strain from The Netherlands,respectively.The nucleotide sequence homology identity of E2,Npro,Ernsgenes among the above-mentioned strains was 79.1% —97.2%,83.0% —98.4% and 83.1% —96.8%,respectively.Phylogenetic analysis showed that the phylogenetic trees based on complete genome and E2,Nproand Ernsgene nucleotide sequences resulted in similar topology.GX01-2018 strain from Guangxi together with European strains belonged to one group,while GX04/2017 strain also from Guangxi together with American strains belonged to another group.The above-mentioned results indicated that APPV isolates showed genetic diversity and there existed large genetic variation among different strains from the same region.
引文
[1] HAUSE B M,COLLIN E A,PEDDIREDDI L,et al.Discovery of a novel putative atypical porcine pestivirus in pigs in the USA[J].Journal of General Virology,2015,96(10):2994-2998.
[2] ARRUDA B L,ARRUDA P H,MAGSTADT D R,et al.Identification of a divergent lineage porcine pestivirus in nursing piglets with congenital tremors and reproduction of disease following experimental inoculation[J].PLoS One,2016,11(2):e0150104.
[3] DE GROOF A,DEIJS M,GUELEN L,et al.Atypical porcine pestivirus:A possible cause of congenital tremor type A-Ⅱin newborn piglets[J].Viruses,2016,8(10):e271.
[4] POSTEL A,HANSMANN F,BAECHLEIN C,et al.Presence of atypical porcine pestivirus(APPV)genomes in newborn piglets correlates with congenital tremor[J].Scientific Reports,2016(6):27735.
[5] SCHWARZ L,RIEDEL C,HOGLER S,et al.Congenital infection with atypical porcine pestivirus(APPV)is associated with disease and viral persistence[J].Veterinary Research,2017,48(1):1.
[6] MUNOZ-GONZALEZ S,CANTURRI A,PEREZ-SIMO M,et al.First report of the novel atypical porcine pestivirus in Spain and a retrospective study[J].Transboundary and Emerging Diseases,2017,64(6):1645-1649.
[7] MOSENA A C S,WEBER M N,DA CRUZ R A S,et al.Presence of atypical porcine pestivirus(APPV)in Brazilian pigs[J].Transboundary and Emerging Diseases,2018,65(1):22-26.
[8] GATTO I R H,HARMON K,BRADNER L,et al.Detection of atypical porcine pestivirus in Brazil in the central nervous system of suckling piglets with congenital tremor[J].Transboundary and Emerging Diseases,2018,65(2):375-380.
[9] DONES L,BIKSI I,ALBERT M,et al.Detection and phylogenetic characterization of atypical porcine pestivirus strains in Hungary[J].Transboundary and Emerging Diseases,2018,65(6):2039-2042.
[10] WILLIAMSON S.Congenital tremor associated with atypical porcine pestivirus[J].Veterinary Record,2017,180(2):42-43.
[11] BLOMSTROM A L,FOSSUM C,WALLGREN P,et al.Viral metagenomic analysis displays the co-infection situation in healthy and PMWS affected pigs[J].PLoS One,2016,11(12):e0166863.
[12] ZHANG K,WU K,LIU J,et al.Identification of atypical porcine pestivirus infection in swine herds in China[J].Transboundary and Emerging Diseases,2017,64(4):1020-1023.
[13] YUAN J,HAN Z,LI J,et al.Atypical porcine pestivirus as a novel type of pestivirus in pigs in China[J].Fronts in Microbiology,2017(8):862.
[14] ZHANG H,WEN W,HAO G,et al.Phylogenetic and genomic characterization of a novel atypical porcine pestivirus in China[J].Transboundary and Emerging Diseases,2018,65(1):e202-e204.
[15] SHEN H,LIU X,ZHANG P,et al.Identification and characterization of atypical porcine pestivirus genomes in newborn piglets with congenital tremor in China[J].Journal of Veterinary Science,2018,19(3):468-471.
[16] WU S,WANG Z,ZHANG W,et al.Complete genome sequence of an atypical porcine pestivirus isolated from Jiangxi Province,China[J].Genome Announcements,2018,6(24):e00439-18.
[17] PAN S,YAN Y,SHI K,et al.Molecular characterization of two novel atypical porcine pestivirus(APPV)strains in China[J]. Transboundary and Emerging Diseases,2019,66(1):35-42.
[18] BEER M,WEMIKE K,DR魧GER C,et al.High prevalence of highly variable atypical porcine pestiviruses found in Germany[J].Transboundary and Emerging Diseases,2017,64(5):e22-e26.
[19] POSTEL A,MEYER D,CAGATAY G N,et al.High abundance and genetic variability of atypical porcine pestivirus in pigs from Europe and Asia[J].Transboundary and Emerging Diseases,2017,23(12):2104-2107.
[20] POSTELl A,MEYER D,PETROY A,et al.Recent emergence of a novel porcine pestivirus:interference with classical swine fever diagnosis[J].Emerging Microbes&Infections,2017,6(4):e19.
[21] POSSATTI F,HEADLEY S A,LEME R A,et al.Viruses associated with congenital tremor and high lethality in piglets[J].Transboundary and Emerging Diseases,2018,65(2):331-337.
[22]张文波,吴松松,邓舜洲,等.一种新型仔猪先天性震颤及其病原的初步研究[J].中国畜牧兽医,2017,44(7):2147-2154.ZHANG Wen-bo,WU Song-song,DENG Shun-zhou,et al.Preliminary study on a novel atypical congenital tremor of piglets and its etiology[J].China Animal Husbandry&Veterinary Medicine,2017,44(7):2147-2154.(in Chinese)
[23]许古明,葛士坤,张凯照,等.猪非典型瘟病毒的基因组特征分析及荧光定量RT-PCR检测方法的建立[J].中国兽医科学,2017,47(11):1357-1362.XU Gu-ming,GE Shi-kun,ZHANG Kai-zhao,et al.Genomic characterization and development of real-time RT-PCR for the detection of atypical porcine pestivirus[J].Chinese Veterinary Science,2017,47(11):1357-1362.(in Chinese)
[24]贺东生,殷三鸿,石坚,等.广东猪群新发非典型瘟病毒病的诊断和病毒鉴定[J].猪业科学,2018,35(7):81-84.HE Dong-sheng,YIN San-hong,SHI Jian,et al.Diagnosis and identification of new emerging atypical porcine pestivirus in Guangdong Province[J].Swine Industry Science,2018,35(7):81-84.(in Chinese)
[25]周磊.中国非典型性瘟病毒的鉴定与演化分析[J].北方牧业,2018(13):16-17.ZHOU Lei. Identification and genomic characterization of atypical porcine pestivirus in China[J].Northern Animal Husbandry,2018(13):16-17.(in Chinese)
[26] COLOM-CADENA A,GANGES L,MU OZ-GONZALEZ S,et al.Atypical porcine pestivirus in wild boar(Sus scrofa),Spain[J].Veterinary Record,2018,183(18):569.
[27] CAGATAY G N,ANTOS A,MEYER D,et al.Frequent infection of wild boar with atypical porcine pestivirus(APPV)[J].Transboundary and Emerging Diseases,2018,65(4):1087-1093.
[28] GATTO I R H,ARRUDA P H,VISEK C A,et al.Detection of atypical porcine pestivirus in semen from commercial boar studs in the United States[J].Transboundary and Emerging Diseases,2018,65(2):e339-e343.
[2] ARRUDA B L,ARRUDA P H,MAGSTADT D R,et al.Identification of a divergent lineage porcine pestivirus in nursing piglets with congenital tremors and reproduction of disease following experimental inoculation[J].PLoS One,2016,11(2):e0150104.
[3] DE GROOF A,DEIJS M,GUELEN L,et al.Atypical porcine pestivirus:A possible cause of congenital tremor type A-Ⅱin newborn piglets[J].Viruses,2016,8(10):e271.
[4] POSTEL A,HANSMANN F,BAECHLEIN C,et al.Presence of atypical porcine pestivirus(APPV)genomes in newborn piglets correlates with congenital tremor[J].Scientific Reports,2016(6):27735.
[5] SCHWARZ L,RIEDEL C,HOGLER S,et al.Congenital infection with atypical porcine pestivirus(APPV)is associated with disease and viral persistence[J].Veterinary Research,2017,48(1):1.
[6] MUNOZ-GONZALEZ S,CANTURRI A,PEREZ-SIMO M,et al.First report of the novel atypical porcine pestivirus in Spain and a retrospective study[J].Transboundary and Emerging Diseases,2017,64(6):1645-1649.
[7] MOSENA A C S,WEBER M N,DA CRUZ R A S,et al.Presence of atypical porcine pestivirus(APPV)in Brazilian pigs[J].Transboundary and Emerging Diseases,2018,65(1):22-26.
[8] GATTO I R H,HARMON K,BRADNER L,et al.Detection of atypical porcine pestivirus in Brazil in the central nervous system of suckling piglets with congenital tremor[J].Transboundary and Emerging Diseases,2018,65(2):375-380.
[9] DONES L,BIKSI I,ALBERT M,et al.Detection and phylogenetic characterization of atypical porcine pestivirus strains in Hungary[J].Transboundary and Emerging Diseases,2018,65(6):2039-2042.
[10] WILLIAMSON S.Congenital tremor associated with atypical porcine pestivirus[J].Veterinary Record,2017,180(2):42-43.
[11] BLOMSTROM A L,FOSSUM C,WALLGREN P,et al.Viral metagenomic analysis displays the co-infection situation in healthy and PMWS affected pigs[J].PLoS One,2016,11(12):e0166863.
[12] ZHANG K,WU K,LIU J,et al.Identification of atypical porcine pestivirus infection in swine herds in China[J].Transboundary and Emerging Diseases,2017,64(4):1020-1023.
[13] YUAN J,HAN Z,LI J,et al.Atypical porcine pestivirus as a novel type of pestivirus in pigs in China[J].Fronts in Microbiology,2017(8):862.
[14] ZHANG H,WEN W,HAO G,et al.Phylogenetic and genomic characterization of a novel atypical porcine pestivirus in China[J].Transboundary and Emerging Diseases,2018,65(1):e202-e204.
[15] SHEN H,LIU X,ZHANG P,et al.Identification and characterization of atypical porcine pestivirus genomes in newborn piglets with congenital tremor in China[J].Journal of Veterinary Science,2018,19(3):468-471.
[16] WU S,WANG Z,ZHANG W,et al.Complete genome sequence of an atypical porcine pestivirus isolated from Jiangxi Province,China[J].Genome Announcements,2018,6(24):e00439-18.
[17] PAN S,YAN Y,SHI K,et al.Molecular characterization of two novel atypical porcine pestivirus(APPV)strains in China[J]. Transboundary and Emerging Diseases,2019,66(1):35-42.
[18] BEER M,WEMIKE K,DR魧GER C,et al.High prevalence of highly variable atypical porcine pestiviruses found in Germany[J].Transboundary and Emerging Diseases,2017,64(5):e22-e26.
[19] POSTEL A,MEYER D,CAGATAY G N,et al.High abundance and genetic variability of atypical porcine pestivirus in pigs from Europe and Asia[J].Transboundary and Emerging Diseases,2017,23(12):2104-2107.
[20] POSTELl A,MEYER D,PETROY A,et al.Recent emergence of a novel porcine pestivirus:interference with classical swine fever diagnosis[J].Emerging Microbes&Infections,2017,6(4):e19.
[21] POSSATTI F,HEADLEY S A,LEME R A,et al.Viruses associated with congenital tremor and high lethality in piglets[J].Transboundary and Emerging Diseases,2018,65(2):331-337.
[22]张文波,吴松松,邓舜洲,等.一种新型仔猪先天性震颤及其病原的初步研究[J].中国畜牧兽医,2017,44(7):2147-2154.ZHANG Wen-bo,WU Song-song,DENG Shun-zhou,et al.Preliminary study on a novel atypical congenital tremor of piglets and its etiology[J].China Animal Husbandry&Veterinary Medicine,2017,44(7):2147-2154.(in Chinese)
[23]许古明,葛士坤,张凯照,等.猪非典型瘟病毒的基因组特征分析及荧光定量RT-PCR检测方法的建立[J].中国兽医科学,2017,47(11):1357-1362.XU Gu-ming,GE Shi-kun,ZHANG Kai-zhao,et al.Genomic characterization and development of real-time RT-PCR for the detection of atypical porcine pestivirus[J].Chinese Veterinary Science,2017,47(11):1357-1362.(in Chinese)
[24]贺东生,殷三鸿,石坚,等.广东猪群新发非典型瘟病毒病的诊断和病毒鉴定[J].猪业科学,2018,35(7):81-84.HE Dong-sheng,YIN San-hong,SHI Jian,et al.Diagnosis and identification of new emerging atypical porcine pestivirus in Guangdong Province[J].Swine Industry Science,2018,35(7):81-84.(in Chinese)
[25]周磊.中国非典型性瘟病毒的鉴定与演化分析[J].北方牧业,2018(13):16-17.ZHOU Lei. Identification and genomic characterization of atypical porcine pestivirus in China[J].Northern Animal Husbandry,2018(13):16-17.(in Chinese)
[26] COLOM-CADENA A,GANGES L,MU OZ-GONZALEZ S,et al.Atypical porcine pestivirus in wild boar(Sus scrofa),Spain[J].Veterinary Record,2018,183(18):569.
[27] CAGATAY G N,ANTOS A,MEYER D,et al.Frequent infection of wild boar with atypical porcine pestivirus(APPV)[J].Transboundary and Emerging Diseases,2018,65(4):1087-1093.
[28] GATTO I R H,ARRUDA P H,VISEK C A,et al.Detection of atypical porcine pestivirus in semen from commercial boar studs in the United States[J].Transboundary and Emerging Diseases,2018,65(2):e339-e343.
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