猪传染性胃肠炎病毒SC-Y株全基因组克隆及特性分析

Cloning and analysis of genome of transmissible gastroenteritis virus SC-Y strain

参考Genebank上收录的PUR46-MAD株(NC-002306)、TS株(DQ201447)和Purdue-115株(Z34093)核苷酸序列,设计并合成16对引物,应用RT-PCR技术成功地分16个片段扩增了猪传染性胃肠炎病毒(TGEV)SC-Y株全长基因组序列,将这16个基因片段克隆,并测定其核苷酸序列.应用生物软件BioEdit对各测序结果进行序列拼接,确认SC-Y株基因组全长cDNA28590bp(GenBank收录号DQ443743),共包含7个开放阅读框.基因组5端非编码区长315nt,3端非编码区长277nt.与MillerM60株、MillerM6株和TS株相比,SC-Y株S基因缺失6个碱基.通过构建结构蛋白基因(S、sM、M和N)系统进化树,结果表明,SC-Y株可能与美国Purdue株来源于共同的祖先病毒.密码子偏爱性分析结果认为猪传染性胃肠炎病毒对以T和A结尾的密码子表现轻微的偏爱性,病毒基因表达选择酵母等真核系统可能更为合适.

Sixteen pair of primers covering the whole genome of TGEV were devised according to the published sequences, 16 cDNA fragments were amplified by RT-PCR. The amplified fragments were further cloned and sequenced. The genome of SC-Y strain was assembled by BioEdit （GenBank： DQ443743）. The size of complete genome was 28590 nucleotides （including Poly A）, and was comprised of 7 ORFs, which was flanked by untranslated regions （UTRs）, 315 bases at the 5＇-end and 277 bases at the 3＇-end. there were 6 nt deletions in S genes compared with that of the other isolates, Miller M60, Miller M6 and TS. Phylogenetic analysis based on S, sM, M and N suggested that SC-Y may belong to same genogroup with purdue strain. TGEV SC-Y has slightly bias at the codons which are T and A at the end. Yeast system should be more suitable for TGEV＇gene expression.