广西鸭坦布苏病毒流行株GXQZ01-DTMUV-2020全基因组序列分子特征分析

Genome characteristics analysis of a novel duck Tembusu virus GXQZ01-DTMUV-2020 strain from Guangxi Province

为了解广西壮族自治区鸭坦布苏病毒(duck Tembusu virus,DTMUV)流行毒株分子遗传特征,经RT-PCR对全基因组序列分段扩增,并克隆、测序及拼接,获得DTMUV全基因组序列,命名为GXQZ01-DTMUV-2020株。结果显示,该毒株基因组全长为10991 bp,5′端UTR为94 bp,3′端UTR为619 bp,含有1个开放阅读框(ORF)为10278 bp,编码3425个氨基酸。相似性分析结果显示,GXQZ01-DTMUV-2020株与水禽源TMUV参考毒株的核苷酸相似性为85.7%~99.7%,氨基酸相似性为92.0%~100%;与NCBI上其他广西DTMUV流行株的核苷酸相似性为94.1%~98.5%,氨基酸相似性为97.7%~100%;与TMUV首个分离株MM_1775核苷酸相似性为85.8%~91.6%,氨基酸相似性为92.0%~98.5%。基于ORF、E及NS1基因绘制遗传进化树显示,GXQZ01-DTMUV-2020株与广西DTMUV流行株GX2012、GX2013E同属于2.1亚群,而广西的GX2011、GX2015株同国内其他DTMUV流行株属于2.2亚群,表明广西DTMUV流行株呈现不同的遗传进化趋势。重组分析结果显示,CHN-YC、AH2014、HB2016、HD2-2013株存在重组现象,而广西DTMUV毒株未检测到重组信号。利用BEAST软件对ORF、E及NS1基因遗传进化速率评估结果为1.146×10^(-3),1.467×10^(-3),1.319×10^(-3)替换/(位点·年),表明E基因进化最快。本研究丰富了DTMUV基因库信息,同时为广西地区DTMUV分子流行病学研究与防控技术制定提供基础数据。

To investigate the molecular characteristics of duck Tembusu virus(DTMUV)genome from Guangxi Province,the genomic segments of DTMUV were cloned from positive samples by RT-PCR,then were sequenced and ligated to obtain the nearly complete genome sequence of a DTMUV strain named GXQZ01-DTMUV-2020.The genome length for GXQZ01-DTMUV-2020 strain was 10991 bp,with 5’untranslated region(UTR)and 3’UTR was 94 bp and 619 bp,containing an opening reading fragment(ORF)(10278 bp),encoding 3425 amino acid.Homology analysis of GXQZ01-DTMUV-2020 strain revealed that nucleotide similarity to waterfowl-origin TMUV was85.7%-99.7%,and amino acid similarity was 92.0%-100%.That shared 94.1%-98.5% nucleotide similarity and 97.7%-100% amino acid similarity to DTMUV strains of Guangxi Province in NCBI,and with 85.8%-91.6% nucleotide similarity and 92.0%-98.5% amino acid similarity to first TMUV isolate MM1775.Phylogenetic analysis using ORF,envelope(E)and non-structure(NS1)gene for DTMUV strains indicated that GXQZ01-DTMUV-2020,GX2012 and GX2013 E clustered into subgroup 2.1,while subgroup 2.2 was formed by GX2011 and GX2015 of Guangxi Province with others DTMUV reference strains.This suggested that DTMUV strains of Guangxi mentioned in this study were genetic diversity.Recombination analysis of GXQZ01-DTMUV-2020 and reference strains showed recombination phenomenon was existed in CHN-YC,AH2014,HB2016 and HD2-2013 genomes,without sign of recombination was detected in DTMUV strains of Guangxi.Estimation of genetic evolution rate of ORF,E and NS1 segments of GXQZ01-DTMUV-2020 and reference strains by BEAST was 1.146×10^(-3),1.467×10^(-3)and 1.319×10^(-3)substitutions/(sites·year),respectively.The result indicated genetic evolution rate of E genes was the highest.These studies enrich the genetic information of DTMUV and provided basic data for molecular epidemic research and prevention and control strategies formulated of DTMUV in future.