| 潘玥,邵聪文,王晓辉,朱艳菊,陈俊英,陈伟,马绍辉,刘建生.人埃可病毒20型KM/EV20/2010分离株的全基因组序列分析[J].Chinese journal of Epidemiology,2015,36(5):501-505 |
| 人埃可病毒20型KM/EV20/2010分离株的全基因组序列分析 |
| Genomic characteristics of an echovirus 20 strain (KM/EV20/2010) isolated in Kunming, Yunnan, China |
| Received:December 17, 2014 |
| DOI：10.3760/cma.j.issn.0254-6450.2015.05.019 |
| KeyWord: 埃可病毒 全基因组 序列分析 |
| English Key Word: Echovirus Complete genome Sequence analysis |
| FundProject:国家自然科学基金(30471595) |
| Author Name | Affiliation | E-mail | | Pan Yue | Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China | | | Shao Congwen | Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China | | | Wang Xiaohui | Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China | | | Zhu Yanju | Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China | | | Chen Junying | Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China | | | Chen Wei | Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China | | | Ma Shaohui | Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China | | | Liu Jiansheng | Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming 650118, China | ljsh3300@163.com |
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| Abstract: |
| 目的 对人埃可病毒20型(ECHO20)KM/EV20/2010分离株全基因组进行序列测定, 并分析其分子变异和进化特点。方法 设计针对KM/EV20/2010引物, 提取病毒RNA, RT-PCR扩增和序列测定获得全基因序列。利用Mega 4.1、RDP3和SimPlot 3.5.1软件分析全基因序列。结果 KM/EV20/2010病毒株基因组全长7 395 bp个核苷酸(nt), 5'端和3'端分别为744 nt和96 nt的非编码区, 5'和3'非编码区间为一个6 549 nt长的开放阅读框, 编码一个含2 183个氨基酸的多聚蛋白, 编码区内未见核苷酸的插入或缺失。与GenBank中现有唯一1株ECHO20 JV-1原型株全基因组序列相比对, 核苷酸同源性为80.1%, 氨基酸同源性为96.7%;构建基于全长VP1基因序列的进化树图并进行基因分型分析, ECHO20可分为6个基因型, 中国分离株分属Ⅲ和Ⅳ基因型, 其中KM/EV20/2010属于基因型Ⅳ, 且6个基因型之间核苷酸的差异为9.4%～21.7%。基于全基因组序列的种系进化分析提示KM/EV20/2010分离株与ECHO20原型株JV-1遗传距离很远, 未与原型株JV-1聚簇分布, 而与ECHO30病毒株遗传距离较近。分析发现KM/EV20/2010序列在非结构区可能存在重组。结论 中国ECHO20可分为6个基因型, KM/EV20/2010分离株属于Ⅳ基因型。 |
| English Abstract: |
| Objective To identify the complete genome sequence of an echovirus 20 isolate (KM/EV20/2010) and understand its genetic variation and evolution characteristics. Methods Seven overlapping clones covering the whole viral genome (excluding the poly-A tail) were obtained by RT-PCR and sequenced, and their nucleotide and amino acid sequences were aligned with other echovirus 20 isolates. Phylogenetic and pairwise alignment analyses based on genome and complete VP1 regions were conducted with software Mega 4.1, RDP3 and SimPlot 3.5.1. Results The genome of the echovirus strain was 7 395 nucleotides in length, and contained a 744-nt non-translated region (NTR) at the 5' end and a 96-nt NTR at the 3'end. The entire open reading frame contained 6 549 nt, encoding a 2 183-aa polyprotein. In the coding region, there was no nucleotide deletion or insertion. Based on the complete genome sequence alignments, the echovirus strain showed 80.1% nucleotide and 96.7% amino acid homology to echovirus 20 prototype JV-1 strain. The phylogenetic trees constructed on the genome and complete VP1 regions all indicated that the echovirus strain was not in one cluster with echovirus 20 prototype JV-1 strain, while had a closer relationship with echovirus 30 prototype Bastianni. Genotyping results from phylogenetic analysis showed that echovirus 20 has six genotypes. The strain used in this study belonged to genotype Ⅳ. The nucleotide divergence was 9.4%-21.7% among the 6 genotypes. The possible putative recombination was detected in its non-coding sequence of the echovirus 20 strain used in this study. Conclusion Based on the bioinformatics analysis. The echovirus 20 strains isolated in China could be divided into six genotypes, and the echovirus 20 in this study belonged to genotype Ⅳ. |
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