肠道病毒共感染简易鉴定方法的建立及评价  

Establishment and evaluation of a simple method to identify mixed infection of enterovirus

作　　者：孙玉兰[1] 沈悦 黎新宇[1] 杨扬[1] 梁志超[1] 李仁清[1] Sun Yulan;Shen Yue;Li Xinyu;Yang Yang;Liang Zhichao;Li Renqing(Institute for Infectious Disease and Endemic Disease Control,Beijing Center for Disease Prevention andControl,Beijing Research Center for Preventive Medicine,Beijing 100013,China;School of Public Health,Capital Medical University,Beijing 100069,China)

机构地区：[1]北京市疾病预防控制中心,北京市预防医学研究中心传染病地方病控制所,100013 [2]首都医科大学公共卫生学院,北京100069

出　　处：《国际病毒学杂志》2021年第5期402-406,共5页International Journal of Virology

基　　金：首都卫生发展科研专项基金(2020-2-1012)。

摘　　要：目的在一代测序的基础上建立一种简易的肠道病病毒共感染鉴定方法。方法制备共感染的模拟样本,对其进行一代测序。使用Perl语言编写脚本对测序图谱进行分析,获得主峰和次峰序列。采用blastn与本地构建的肠道病毒数据库进行局部比对,同时采用stretcher进行全局比对,对主要和次要序列进行肠道病毒分型比较。结果编写了一个能够自动识别并分析一代测序色谱图结果中共感染状态并获得两个肠道病毒核苷酸序列的脚本。对于次要病毒DNA含量大于等于65ng的混合样本,只要次要病毒在混合样本中占比适中(如大于等于12.5%并小于等于25.0%)均能够顺利识别并准确分型。分型时,采用局部比对与采用全局比对的结果相当,但在1:1混合样本的分型时,局部比对的效果更好。结论本研究建立的肠道病毒共感染的简易鉴定方法可用于肠道病毒共感染的病毒识别与分型。Objective To establish a simple method based on the results of first-generation sequencing for identifying mixed infection of enterovirus.Methods Simulated mixed infection samples were constructed and sequenced by first-generation sequencing.The perl script was used to analyze the sequencing chromatograms to obtain the sequences of primary and secondary peaks.Local alignment search with blastn against local database of enteroviruses and global alignment with stretcher were carried out.The enterovirus genotyping results by the primary and secondary sequences were compared.Results The script was compiled for automatic analysis and identification of mixed infection status based on the chromatograms of the first generation sequencing and for obtaining the nucleotide sequences of the two viruses.For mixed samples with secondary virus DNA content of over or equal to 65ng,all genotypes were recognized and identified correctly if the proportions of secondary virus in the mixed sample were moderate(over or equal to 12.5%and below or equal to 25.0%).For genotyping,local alignment was similar to global alignment but the results of local alignment were better if the viruses were mixed at the ratio of 1:1.Conclusions The simple identification method for mixed infections of enterovirus established in this study can be used for rapid detection and typing of viruses causing hand,foot,and mouth disease.

关 键 词：肠道病毒 共感染 一代测序 测序图谱 

分 类 号：R725.1[医药卫生—儿科]