Complete Genome Sequencing and Molecular Structure Prediction of C81 Attenuated Strain of 
CSFV

XU Zhuo-fei; QIAN Ping; LI Xiang-min; GUO Dong-chun; YAO Qing-xia; CHEN Huan-chun*

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August 2005

XU Zhuo-fei, QIAN Ping, LI Xiang-min, GUO Dong-chun, YAO Qing-xia and CHEN Huan-chun*. Complete Genome Sequencing and Molecular Structure Prediction of C81 Attenuated Strain of CSFV[J]. Virologica Sinica, 2005, 20(4): 413-419.

Citation: XU Zhuo-fei, QIAN Ping, LI Xiang-min, GUO Dong-chun, YAO Qing-xia, CHEN Huan-chun*. Complete Genome Sequencing and Molecular Structure Prediction of C81 Attenuated Strain of CSFV .VIROLOGICA SINICA, 2005, 20(4) : 413-419.

猪瘟弱毒C81株全基因组测序及分子结构预测

1.
华中农业大学动物医学院动物病毒室湖北武汉

摘要

参照已发表的猪瘟病毒弱毒株的序列,设计7对覆盖全长基因组的引物,通过RT-PCR从感染猪瘟病毒弱毒株的PK-15细胞中扩增得到7个cDNA片段,分别克隆到pMD18-T载体并测序,利用DNASIS软件获得猪瘟病毒C81株全基因组序列(GenBank:AY663656)。C81株基因组全长12310nt,只有一个大的开放阅读框,编码3898个氨基酸的聚蛋白。序列分析表明,C81株开放阅读框与其它各毒株核苷酸和氨基酸序列的同源性变化较大,分别为84.4%~99.6%和91.6%~99.4%。同时,我们绘制了26株CSFVORF的进化树,比较了CSFV5’非翻译区核苷酸序列并推测其二级结构,发现不同毒株之间存在较大的差异,另外对C81株聚蛋白的功能域和三维结构进行了预测。
- 猪瘟病毒
- , RT-PCR
- , 序列比对
- , 5’非翻译区
- , 同源建模

Complete Genome Sequencing and Molecular Structure Prediction of C81 Attenuated Strain of CSFV

Abstract

Seven pair of primers covering the whole genome of Classical swine fever virus(CSFV) attenuated strain were devised according to the published sequences . 7 cDNA fragments were amplified by RT-PCR from PK-15 cell infected by CSFV attenuated strain. The amplifid fragments were further sequenced after cloned into the pMD18-T vector. The whole genome sequence of C81-strain was assembled by DNASIS (GenBank: AY663656). The genome is 12310 nucleotides in length and contains one large open reading frame encoding a polyprotein of 3898 amino acids. Sequence comparison with other CSFV strains revealed major differences in the open reading frame,84.4%～99.6% identities at the nucleotide level and 91.6%～99.4% identities at the amino acid level.26 ORF phylogenetic trees of CSFV strain were also protracted. The nucleotide sequence and secondary structure of CSFV 5′-untranslated region (5′-UTR) were compared and deduced, and found the major difference exists among diverse virus strains. Furthermore, functional domains and 3-D structure of CSFV/ C81 polyprotein were predicted.
- Classical swine fever virus
- , RT-PCR
- , Sequence alignment
- , 5′-UTR
- , Homology modeling

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Complete Genome Sequencing and Molecular Structure Prediction of C81 Attenuated Strain of CSFV

Abstract: Seven pair of primers covering the whole genome of Classical swine fever virus(CSFV) attenuated strain were devised according to the published sequences . 7 cDNA fragments were amplified by RT-PCR from PK-15 cell infected by CSFV attenuated strain. The amplifid fragments were further sequenced after cloned into the pMD18-T vector. The whole genome sequence of C81-strain was assembled by DNASIS (GenBank: AY663656). The genome is 12310 nucleotides in length and contains one large open reading frame encoding a polyprotein of 3898 amino acids. Sequence comparison with other CSFV strains revealed major differences in the open reading frame,84.4%～99.6% identities at the nucleotide level and 91.6%～99.4% identities at the amino acid level.26 ORF phylogenetic trees of CSFV strain were also protracted. The nucleotide sequence and secondary structure of CSFV 5′-untranslated region (5′-UTR) were compared and deduced, and found the major difference exists among diverse virus strains. Furthermore, functional domains and 3-D structure of CSFV/ C81 polyprotein were predicted.