一株埃可病毒16型510/YN/CHN/2010的全基因组分析

Complete nucleotide sequence of an Echovirus 16 strain 510/YN/CHN/2010 isolated in Yunnan, China

目的分析一株埃可病毒16型(Echovirus 16,E16)云南分离株510/YN/CHN/2010全基因组序列及其遗传特性。方法设计针对E16的引物,提取病毒RNA,RT-PCR扩增病毒目的基因并测序,利用BioEdit 7.2.3、MEGA 7.0和Simplot 3.5.1软件分析其全基因组。结果E16510/YN/CHN/2010全基因组核苷酸序列全长7432 nt,是编码含2196个氨基酸的多聚蛋白。其全VP1和全基因组与原型株Harrington的核苷酸和氨基酸同源性分别为80.68%、49.33%和81.26%、97.26%。与其他埃可病毒原型株的全基因组核苷酸和氨基酸同源性分别为75.72%~88.44%和83.01%~87.65%。系统进化分析将E16分为3个基因型,分离株510/YN/CHN/2010和其他中国分离株均属于B基因型。重组分析显示,510/YN/CHN/2010株可能在非结构编码区的P2段重组。结论510/YN/CHN/2010分离株为E16 B基因型,可能为重组株。

Objective To analyze the genomic sequence of the 510/YN/CHN/2010 strain of Echovirus type 16(E16)and its genetic characteristics.Methods Primers targeting E16 were designed,and viral RNA was extracted and amplified using RT-PCR.The products of amplification were directly sequenced.The genome was analyzed using BioEdit 7.2.3,MEGA 7.0,and Simplot 3.5.1.Results The genomic nucleotide sequence of the 510/YN/CHN/2010 strain of E16 is 7432 nt in length and it encodes a polyprotein containing 2,196 amino acids.The nucleotide similarity of its VP1 and its genome to the prototype Harrington strain was 80.68%and 49.33%and the amino acid similarity of its VP1 and its genome to the prototype Harrington strain was 81.26%and 97.26%.The genome-wide nucleotide similarity to other prototype strains of echovirus ranged from 75.72%to 88.44%and the amino acid similarity to other prototype strains of echovirus ranged from 83.01%to 87.65%.A phylogenetic analysis resulted in the classification of E16 into three types,with 510/YN/CHN/2010 isolates and other Chinese isolates belonging to genotype B.Amino acid analysis indicated that the isolates had five mutations specific to genotypes B and C compared to the prototype Harrington strain(R78 K,V145 I,N157 K,I272 V,and L277 Q).Recombination analysis revealed that the 510/YN/CHN/2010 strain might recombine in the P2 segment of the non-structural coding region.Conclusion The 510/YN/CHN/2010 isolate was identified as the B genotype of a recombinant strain of E16.