Source-tracking of the Chinese Chikungunya viruses suggests that Indian subcontinent and Southeast Asia act as major hubs for the recent global spread of Chikungunya virus

Virology Journal

Liang Wen¹  Peng Li¹  Xinying Du¹  Hua Shi¹  Ligui Wang¹  Peihan Li¹  Sai Tian¹  Chaojie Yang¹  Hongbin Song¹  Jinpeng Guo¹  Rongzhang Hao¹  Hongbo Liu¹  Qi Wang¹  Haoran Zhang¹  Daizhi An¹  Shaofu Qiu¹  Changjun Wang¹  Xiaoyuan An²  Xiaocui Yang² 

[1] The Chinese PLA Center for Disease Control and Prevention;The Fourth People’s Hospital of Zunyi;

关键词: Chikungunya virus;    Whole-genome sequencing;    Phylogenetic analysis;    Evolution;    Adaptive mutation;   

DOI  :  10.1186/s12985-021-01665-2

来源: DOAJ

【 摘 要 】

Abstract Background Chikungunya fever, caused by the Chikungunya virus (CHIKV), has become a major global health concern, causing unexpected large outbreaks in Africa, Asia, Europe, and the Americas. CHIKV is not indigenous to China, and its origin in the country is poorly understood. In particular, there is limited understanding of the recent global spread of CHIKV in the context of the CHIKV epidemic. Methods Here we investigated a novel Chikungunya patient who came from Myanmar to China in August, 2019. Direct genome sequencing was performed via combined MinION sequencing and BGISEQ-500 sequencing. A complete CHIKV genome dataset, including 727 CHIKV genomes retrieved from GenBank and the genome sequenced in this study, was constructed. An updated and comprehensive phylogenetic analysis was conducted to understand the virus’s origin, evolution, transmission routes and genetic adaptation. Results All globally distributed CHIKV genomes were divided into West Africa, East/Central/South African and Asian genotypes. The genome sequenced in this study was located in the Indian Ocean lineage, and was closely related to a strain isolated from an Australian patient who returned from Bangladesh in 2017. A comprehensive phylogenetic analysis showed that the Chinese strains mainly originated from the Indian subcontinent and Southeast Asia. Further analyses indicated that the Indian subcontinent and Southeast Asia may act as major hubs for the recent global spread of CHIKV, leading to multiple outbreaks and epidemics. Moreover, we identified 179 distinct sites, including some undescribed sites in the structural and non-structural proteins, which exhibited apparent genetic variations associated with different CHIKV lineages. Conclusions Here we report a novel CHIKV isolate from a chikungunya patient who came from Myanmar to China in 2019, and summarize the source and evolution of Chinese CHIKV strains. Our present findings provide a better understanding of the recent global evolution of CHIKV, highlighting the urgent need for strengthened surveillance against viral diversity.

【 授权许可】

Unknown