柯萨奇病毒A组2型分离毒株序列及遗传进化分析
|
摘要
目的研究柯萨奇病毒A组2型(CVA2)分离株基因特征和遗传进化规律。方法利用分子信息学软件对GenBank核苷酸数据库收录CVA2分离株进行全长VP1区基因序列分析,构建系统进化树,测算分离毒株核苷酸和氨基酸同源性,计算核苷酸分子进化速率。采用Datamonkey在线软件预测正向选择位点,用Bioedit软件计算氨基酸置换熵值。结果共纳入CVA2分离株108株,主要为基因型D分离株;与原型株Fleetwood相比,各基因型分离株核苷酸和氨基酸同源性为79.3%～83.0%和94.6%～97.3%;基因型D分离株核苷酸进化速率为4×10~(-3)位点/年;选用SLAC模型发现1个正向选择位点,氨基酸置换熵值分析合计6个熵值大于0.6的位点。结论 CVA2分离株VP1区未出现明显的基因变异,与原型株亲缘性关系较远,需加强对CVA2分离毒株的实验室和分子流行特征监测。
Objective To analyze genetic characteristics and evolution patterns of Coxsackievirus A2(CVA2)isolated strains.Method The molecular informatics software was used to analyze the full length of VP1 gene sequences of CVA2 isolates collected from GenBank nucleotide database.The phylogenetic tree was constructed.The nucleotide and amino acid homology and the nucleotide molecular evolution rate were calculated.The positive selection sites were predicted by Datamonkey online software and Bioedit software was used to calculate the amino acid replacement entropy.Results A total of 108 isolated strains were included in this study.The majority of CVA2 isolates belonged to genotype D.Comparing with prototype strain of Fleetwood,the homology of nucleotide sequences and amino acid sequences of complete VP1 regions were 79.3%-83.0% and 94.6%-97.3%,respectively;the estimated rate of evolution of the CVA2 isolates was 4×10~(-3) site/year;the SLAC model analysis were used and 1 positive selection sites was identified;a total of 6 amino acid sites with entropy values>0.6 were obtained by the calculation of amino acid displacement entropy.Conclusion No obvious genetic variation were identified in the full-length VP1 region.The genetic relationship of isolated strains with prototype strain was far.Both laboratory and molecular epidemiological surveillance of CVA 2 isolated strains should be strengthed.
Objective To analyze genetic characteristics and evolution patterns of Coxsackievirus A2(CVA2)isolated strains.Method The molecular informatics software was used to analyze the full length of VP1 gene sequences of CVA2 isolates collected from GenBank nucleotide database.The phylogenetic tree was constructed.The nucleotide and amino acid homology and the nucleotide molecular evolution rate were calculated.The positive selection sites were predicted by Datamonkey online software and Bioedit software was used to calculate the amino acid replacement entropy.Results A total of 108 isolated strains were included in this study.The majority of CVA2 isolates belonged to genotype D.Comparing with prototype strain of Fleetwood,the homology of nucleotide sequences and amino acid sequences of complete VP1 regions were 79.3%-83.0% and 94.6%-97.3%,respectively;the estimated rate of evolution of the CVA2 isolates was 4×10~(-3) site/year;the SLAC model analysis were used and 1 positive selection sites was identified;a total of 6 amino acid sites with entropy values>0.6 were obtained by the calculation of amino acid displacement entropy.Conclusion No obvious genetic variation were identified in the full-length VP1 region.The genetic relationship of isolated strains with prototype strain was far.Both laboratory and molecular epidemiological surveillance of CVA 2 isolated strains should be strengthed.
引文
[1]杨赫.人类肠道病毒A组山东地方株的基因型分布及其所致疾病分子流行病学研究[D].济南:山东大学,2011.
[2]陈鹏,陶泽新,王海岩,等.柯萨奇病毒A组2、6、8、12型山东地方株型别鉴定及其基因特征分析[J].病毒学报,2012,28(5):522-526.
[3]Yang Q,Zhang Y,Yan D,et al.Two Genotypes of Coxsackievirus A2Associated with Hand,Foot,and Mouth Disease Circulating in China since 2008[J].Plos One,2016,11(12):e0169021.
[4]周兰兰,魏泉德,张丽荣,等.珠海市2013年手足口病患儿柯萨奇病毒A2型分离株基因特征分析[J].中国病毒病杂志,2015,5(2):109-113.
[5]檀晓娟.1998-2011年中国肠道病毒71型的分子流行病学研究[D].北京:中国疾病预防控制中心,2012.
[6]姚学君,单军,嵇红,等.江苏省2012-2014年柯萨奇病毒A组16型分子流行病学特征分析[J].中华疾病控制杂志,2016,20(5):481-485.
[7]文婕,王鹏飞,李秀芳,等.2015年昆明市柯萨奇病毒A16型VP1区基因特征分析[J].中华疾病控制杂志,2018,22(6):607-612.
[8]张晓玲,俞慧菊,宋志刚,等.上海市柯萨奇病毒A6型流行株基因进化与选择压力分析[J].国际病毒学杂志,2017,24(6):365-370.
[2]陈鹏,陶泽新,王海岩,等.柯萨奇病毒A组2、6、8、12型山东地方株型别鉴定及其基因特征分析[J].病毒学报,2012,28(5):522-526.
[3]Yang Q,Zhang Y,Yan D,et al.Two Genotypes of Coxsackievirus A2Associated with Hand,Foot,and Mouth Disease Circulating in China since 2008[J].Plos One,2016,11(12):e0169021.
[4]周兰兰,魏泉德,张丽荣,等.珠海市2013年手足口病患儿柯萨奇病毒A2型分离株基因特征分析[J].中国病毒病杂志,2015,5(2):109-113.
[5]檀晓娟.1998-2011年中国肠道病毒71型的分子流行病学研究[D].北京:中国疾病预防控制中心,2012.
[6]姚学君,单军,嵇红,等.江苏省2012-2014年柯萨奇病毒A组16型分子流行病学特征分析[J].中华疾病控制杂志,2016,20(5):481-485.
[7]文婕,王鹏飞,李秀芳,等.2015年昆明市柯萨奇病毒A16型VP1区基因特征分析[J].中华疾病控制杂志,2018,22(6):607-612.
[8]张晓玲,俞慧菊,宋志刚,等.上海市柯萨奇病毒A6型流行株基因进化与选择压力分析[J].国际病毒学杂志,2017,24(6):365-370.