天津市输入性基孔肯亚病毒全基因组序列分析

Complete genome analysis of a Chikungunya virus imported into Tianjin,China

目的分析天津市1例输入性基孔肯亚病毒(CHIKV)的全基因组序列特征与进化,为CHIKV的监测与防控提供科学依据。方法收集2019年11月4日于天津市第二人民医院采集的血清标本200μl提取核酸,设计叠瓦式引物扩增CHIKV基因组全长,然后利用Illumina Miniseq平台进行高通量测序。结果本研究的CHIKV属于ECSA基因型印度洋分支,与大部分中国分离株一致,相似性为92.72%~99.86%,在国际上与巴基斯坦分离株亲缘关系最近(99.74%)。天津CHIKV在关键位点E1-D284E和E2-I211T处有两处突变,与ECSA基因型一致。此外,天津CHIKV还具备两个关键毒力位点E2-12T和E2-82G,以及nsP3-R524Opal终止子突变。结论天津CHIKV具备较强毒力,且具备在白纹伊蚊中传播的能力,提示应继续加强对CHIKV的监测。

Objective To study the characteristics and evolution of the whole genome sequence of an imported Chikungunya virus(CHIKV)case in Tianjin,China,and to provide a scientific basis for the surveillance and control of CHIKV.Methods The serum specimen of CHIKV was collected at Tianjin Second People's Hospital,on November 4th,2019,and the viral RNA was extracted.Eleven overlapping primers were used to amplify the complete genome of CHIKV by RT-PCR.The amplification products were then subjected to next generation sequencing(NGS)using Illumina Miniseq platform.Results The complete genome sequence of the Tianjin CHIKV obtained had similarities ranging from 92.72%to 99.86%with other Chinese isolates.Phylogenetic analysis indicated that the Tianjin CHIKV belonged to the Indian Ocean Lineage(IOL),East/Central/South African(ECSA)cluster,consistent with most strains from China.The Tianjin CHIKV is most similar(99.74%)to a Pakistan strain.Compared with the reference strain S27,37 non-structural and 28 structural protein amino acid substitutions had been detected in Tianjin CHIKV genome,including two key site mutations,E1-D284E and E2-I211T,in accordance with other strains in the ECSA cluster.Besides,Tianjin CHIKV possessed two point virulent residues at position 12 and 82 in E2,and also a nsP3-R524Opal nonsense mutation.Conclusions Tianjin CHIKV showed stronger virulence and greater transmissibility in Aedes albopictus.Therefore,the surveillance and monitoring of CHIKV in China should be strengthened.