Complete genome analysis of a Chikungunya virus imported into Tianjin, China
10.3760/cma.j.cn114452-20210427-00271
- VernacularTitle:天津市输入性基孔肯亚病毒全基因组序列分析
- Author:
Zhaolin TAN
1
;
Likun LYU
;
Tong XIE
;
Li LI
;
Jie LYU
;
Xiaoyan LI
Author Information
1. 天津市疾病预防控制中心病原生物研究室，天津300011
- Keywords:
High-throughput nucleotide sequencing;
Chikungunya virus;
Virulence
- From:
Chinese Journal of Laboratory Medicine
2022;45(2):174-179
- CountryChina
- Language:Chinese
-
Abstract:
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.
