新型鹅细小病毒四川株的全基因组扩增及遗传进化分析

Amplification and Phylogenetic Analysis of Novel Goose Parvovirus Sichuan Strain

【目的】了解四川地区新型鹅细小病毒(Novel goose parvovirus,NGPV)的分子生物学特征及遗传变异情况。【方法】根据Gen Bank中发表的新型鹅细小病毒的全基因组序列,设计5对兼并引物采用PCR方法分段扩增新型鹅细小病毒四川株的全基因组序列,并利用DNAstar等生物信息分析软件对获得的基因组序列进行分子特性与遗传演变分析。【结果】获得的新型鹅细小病毒四川株(命名为SC16)全长5 109 nt,5′端ITR长408 nt,3′端ITR长407 nt,NS基因长1 884 nt,VP基因长2 199 nt。序列比对和遗传进化分析显示,SC16株与山东分离株SDLC01(KT343253.1)及QH15(KT751090.1)的基因组核苷酸同源性高达99%,与两者的亲缘关系最近,基于NS及VP蛋白的氨基酸序列系统进化树分析结果与此一致。但SC16株的5′端ITR还是发生了一定的变异:与SDLC01及QH15相比,多了几个14 nt的插入片段。【结论】研究结果丰富了NGPV的分子生物学资料。

【Objective】The aim of this study was to learn the molecular biological characteristics and genetic variation of novel goose parvovirus(NGPV)in Sichuan area.【Methods】5 pairs of degenerate primers were designed to amplify the whole genome sequence of NGPV Sichuan strain using PCR method,according to the genome sequences of the NGPV deposited in Gen Bank.Then,the study usd DNAstar and other bioinformatics softwares to analyze the molecular characteristics and genetic evolution of the obtained sequences.【Results】The genomic sequence of Novel goose parvovirus from Sichuan(named SC16) was 5 109 nucleotides(nt) in length.The inverted terminal repeats(ITRs) at the 5′ and 3′ end of the genome were 408 nt and 407 nt respectively.The NS protein was encoded by 1 884 nt and the VP protein was encoded by 2 199 nt.Sequence alignment and phylogenetic analysis demonstrated that the nucleotide identities of SC16 genome and Shandong isolates SDLC01(KT343253.1) and QH15(KT751090.1) was up to 99%,showing a very close genetic relationship with them.The phylogenetic tree analyses of amino acids of NS and VP protein were consistent with this result.However,SC16 still had some genetic variations:compared with SDLC01 and QH15,SC16 had two or three 14-nt extra fragments at the 5′ end of the genome.【Conclusion】These findings will enrich the molecular biology information of NGPV.