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了解北京市分离的埃可病毒5型（Echovirus 5, E5）全长基因组和进化特征，为揭示其分子特征提供本底资料。收集2010年3月至2019年10月至首都儿科研究所附属儿童医院就诊临床诊断为手足口病的患儿咽拭子样本，通过荧光定量PCR方法进行肠道病毒通用（pan-EV）及肠道病毒A组71型（Enterovirus A71, EV-A71）、柯萨奇病毒A组16型（Coxsackievirus A16, CVA16）、CVA6和CVA10检测；对pan-EV核酸阳性但EV-A71、CVA16、CVA6和CVA10筛查均阴性的样本，扩增VP1编码区序列进行分型；对确定为E5阳性的样本接种人横纹肌肉瘤细胞（Rhabdomyosarcoma, RD）进行病毒分离并测序病毒全长基因组序列；应用生物信息学方法进行分子分型和进化分析。本研究共计筛查7652份咽拭子标本，EV-A71、CVA16、CVA6和CVA10阳性检出率分别为4.67%、6.73%、16.96%和2.04%，其他血清型和未定型的EV为7.48%，其中E5核酸阳性样本2份，成功分离1株（s7335株）。该株全基因组序列与E5原型株（Noyce株）相比核苷酸相似性为80.20%。VP1编码区系统进化分析提示世界范围内E5存在A-E 5个基因型，其相互间的遗传距离为17.80%～24.60%，其中C基因型划分为C1和C2两个基因亚型。s7335株属于基因型E，与中国流行的E5同属于一个独立的进化分支。CVA9(GenBank号：OL519579)是其P3编码区潜在的重组供体。本研究报道了来自于北京市的一株E5分离株，其全基因组序列与原型株比较有较大变异，有可能存在重组；VP1编码区核苷酸序列持续变异和进化，在中国存在独立的传播链。这提示加强少见EV血清型监测具有重要的前瞻性价值。
Abstract：To characterize the full-length genome and evolutionary features of an Echovirus 5(E5) strain circulating in Beijing and to provide baseline data for understanding its molecular epidemiological characteristics.Throat swab samples were collected from pediatric patients clinically diagnosed with hand, foot, and mouth disease(HFMD) at the Children's Hospital affiliated with the Capital Institute of Pediatrics between March 2010 and October 2019. Samples were screened using quantitative RT-PCR for pan-enteroviruses(pan-EV), Enterovirus A71(EV-A71), Coxsackievirus A16(CVA16), CVA6, and CVA10. For samples that tested positive for pan-EV but negative for the four common serotypes, the VP1 coding region was amplified and sequenced for serotyping. E5-positive samples were subjected to virus isolation using human rhabdomyosarcoma(RD) cells, and the complete genome of the isolated strain was sequenced. Molecular typing and phylogenetic analysis were performed using bioinformatics tools. Among the 7,652 throat swab samples screened, the positivity rates for EV-A71, CVA16, CVA6, and CVA10 were 4.67%, 6.73%, 16.96%, and 2.04%, respectively. Other enterovirus serotypes and untyped strains accounted for 7.48%. Two samples were positive for E5, and one isolate(strain s7335) was successfully obtained. The full-length genome of strain s7335 shared 80.2% nucleotide identity with the E5 prototype Noyce strain. Phylogenetic analysis of the VP1 coding region revealed that E5 strains globally cluster into five genotypes(A-E), with inter-genotypic nucleotide divergence ranging from 17.80% to 24.60%. Genotype C could be further divided into subgenotypes C1 and C2. Strain s7335 belonged to genotype E and formed an independent evolutionary lineage along with other E5 strains circulating in China. Recombination analysis suggested that the P3 region may have originated from CVA9(GenBank accession no. OL519579). This study reports the complete genome sequence of an echovirus 5isolate from Beijing. Compared to the prototype strain, it exhibits substantial genetic divergence and potential recombination events. Continuous nucleotide variation in the VP1 region and the presence of an independent transmission chain in China underscore the need for enhanced surveillance of rare enterovirus serotypes.
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Basic Information:
DOI：10.13242/j.cnki.bingduxuebao.250044
China Classification Code:R373.24
Citation Information:
[1]韩振志,贾立平,朱汝南等.北京地区一株埃可病毒5型全基因组序列特征分析[J].病毒学报,2025,41(04):1007-1017.DOI:10.13242/j.cnki.bingduxuebao.250044.
Fund Information:
首都儿科研究所青年优才专项（项目号：YCYJ-2025-05）,题目：北京市儿童中多血清型肠道病毒B组的共同流行和进化机制研究; 首都卫生发展科研专项（项目号：首发-1G-1131）,题目：建立基于准种病原体种群进化分析的儿童新发传染病监测及预警模型; 北京市自然科学基金资助项目（项目号：L242052）,题目：脑炎/脑膜炎患者中肠道病毒病原学及疾病负担研究; 北京市卫生健康委员会高层次公共卫生技术人才建设项目（项目号：学科带头人-02-20）,题目：儿童重症呼吸道感染病毒病原谱变迁及新发病毒病原预警体系建立~~