Complete genome characterization and source tracking of Dengue virus from the first local dengue outbreak in Sichuan province, China

doi:10.11853/j.issn.1003.8280.2022.02.014

Abstract

Abstract: Objective To sequence the complete genome of Dengue virus from the first local dengue outbreak in Sichuan province, China, 2019, and to analyze its molecular biological characteristics and possible origin. Methods Nucleic acids were extracted and whole genome sequences were amplified and sequenced from local case specimens that tested positive by real-time PCR, followed by homology analysis, phylogenetic analysis, and variation analysis. Results The complete genome sequence of one virus strain and the partial genome sequences (containing the E gene) of two virus strains were obtained. The complete genome was 10 706 bp long, encoding 3 393 amino acids. Homology and phylogenetic analyses showed that the epidemic strain in Sichuan province had high homology to the Guangzhou (China) strain isolated in 2019, the Guangzhou strain imported from Cambodia in 2019, the Yunnan province (China) strains isolated in 2019, the Vietnam strain isolated in 2017, and the Singapore strain isolated in 2016, belonging to the same branch in the phylogenetic tree. Compared with the prototype strain of Dengue virus type 1, the Sichuan strain had 589 nucleotide variations and 64 amino acid mutations that were scattered, but no alteration occurred at the key amino acid sites affecting virulence. Conclusion The first local dengue fever outbreak in Sichuan province, 2019 may be caused by imported cases from Cambodia, and the pathogen was the Dengue virus type 1, genotypeⅠ. The strain of Dengue virus isolated from Sichuan province has no marked alteration in virulence-related genes, but the biological significance of the point mutations in some sites remains to be further studied.

Key words: Dengue fever, Local outbreak, Dengue virus, Molecular source tracking, Complete genome characteristic

摘要： 目的对2019年四川省发生的首起本地传播登革热疫情中检出的登革病毒进行全基因组测序，分析病毒分子生物学特征并探讨其可能的来源。方法对实时荧光定量PCR（RT-qPCR）检测为阳性的本地病例标本提取核酸并扩增全基因组序列和测序，测序后进行同源性、系统进化分析和变异分析。结果通过基因扩增和序列测定获得1株病毒全基因组序列和2株包括E基因的全基因组部分序列，全基因组序列全长10 706 bp，编码3 393个氨基酸；同源性和系统进化分析显示，本次疫情流行株与2019年我国广州市分离株、2019年广州市分离的柬埔寨输入株、2019年云南省分离株、2017年越南分离株以及2016年新加坡分离株的同源性较高，系统进化属于同一分支；与登革1型原型株相比本次流行株散在分布有589个核苷酸变异和64个氨基酸突变，但影响毒力的主要氨基酸位点没有改变。结论 2019年四川省首起登革热本地暴发疫情可能由柬埔寨输入病例引起，其病原体为登革1型病毒基因Ⅰ型；本次四川省流行株的毒力相关基因没有明显改变，但其在某些相关区域发生点突变的生物学意义有待进一步研究。

关键词: 登革热, 本地疫情, 登革病毒, 分子溯源, 全基因组特征

CLC Number:

R373.3⁺3

FENG Yu-liang, LIN Shi-hua, PAN Ming, CAO Yi-ou, LI Wei. Complete genome characterization and source tracking of Dengue virus from the first local dengue outbreak in Sichuan province, China[J]. Chinese Journal of Vector Biology and Control, 2022, 33(2): 239-244.

冯玉亮, 林世华, 潘明, 曹一鸥, 李伟. 四川省首起登革热本地传播疫情登革病毒全基因组特征及溯源分析[J]. 中国媒介生物学及控制杂志, 2022, 33(2): 239-244.

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