2019年云南省手足口病相关的柯萨奇病毒A组10型分离株的全基因组分析

Complete genome analysis of coxsackievirus A10 isolates associated with hand,foot and mouth disease in Yunnan province,2019

目的分析2019年云南省昆明市手足口病相关的2株柯萨奇病毒A组10型(coxsackievirus A10,CVA10)分离株3R3/YN/CHN/2019(简称3R3)和4R3/YN/CHN/2019(简称4R3)的基因组特征。方法对云南省2019年2例手足口病患儿的临床样本中分离到的2株CVA10毒株进行全基因组序列测定。利用MEGA7.0.26、Geneious9.1.4和SimPlot3.5.1软件分析全基因序列。结果3R3和4R3毒株的基因组全长均为7413 nt,全基因组核苷酸和氨基酸序列相似性分别为97.5%和99.4%。与CVA10原型株AF081300/Kowalik/USA全基因组进行比对分析,核苷酸序列相似性均为79.6%,而氨基酸序列相似性分别为95.1%和95.3%;与其他中国大陆CVA10全基因组序列的核苷酸相似性为93.2%~98.2%,氨基酸相似性为98.5%~99.4%。进化分析发现,2株毒株与近年来中国大陆CVA10流行株同属F基因型,位于F3亚型,与分离株KF999764/JL12-51/CHN/2012的同源性最高,形成一个小分支。经Simplot软件分析未发现明显的基因重组。结论3R3和4R3株属F3基因亚型。CVA10在中国大陆有不同传播链存在。

Objective To understand the genomic characteristics of two coxsackievirus A10(CVA10)isolates 3 R3/YN/CHN/2019(3 R3)and 4 R3/YN/CHN/2019(4 R3)associated with hand,foot and mouth disease(HFMD)in Kunming,Yunnan province in 2019.Methods Whole genome sequencing of two CVA10 strains isolated from clinical samples of two child cases of HFMD in Yunnan province in 2019 was performed.Mega 7.0.26,Geneious 9.1.4 and Simplot 3.5.1 software were used to analyze the complete gene sequence.Results The genomes of strains 3 R3 and 4 R3 were 7413 nt in length,and the nucleotide and amino acid sequence similarities were 97.5%and 99.4%,respectively.Compared with the whole genome of CVA10 prototype strain AF081300/Kowalik/USA,the nucleotide sequence similarity was 79.6%,while the amino acid sequence similarity was 95.1%and 95.3%,respectively.The nucleotide similarity and amino acid similarity were 93.2%—98.2%and 98.5%—99.4%compared with other Chinese mainland CVA10.Phylogenetic analysis showed that the two strains belonged to the same F genotype as the CVA10 epidemic strain circulating in Chinese mainland in recent years,both located in the F3 subtype,and had the highest homology with the isolate KF999764/JL12-51/CHN/2012,forming a small branch.No significant gene recombination was found by Simplot 3.5.1 software analysis.Conclusions Strains 3 R3 and 4 R3 belong to F3 genotype.CVA10 has different transmission chains in Chinese mainland.