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
Abstract BackgroundChikungunya fever caused by Chikungunya virus (CHIKV) has become a major global health concern, which has caused unexpected large outbreaks in Africa, Asia, Europe, and the Americas. China is a non-indigenous region of CHIKV, and the origin of the Chinese CHIKV strains is not well understood. Especially, there is limited understanding of the recent global spread of CHIKV in the context of recent worldwide epidemic of CHIKV.MethodsHere we investigated a novel Chikungunya patient imported from Myanmar into China in August, 2019. The genome was sequenced directly from the serum sample by combined MinION sequencing with BGISEQ-500 sequencing. We constructed a complete CHIKV genome dataset, including 727 CHIKV genomes retrieved from Genbank and the genome sequenced in this study, and conducted an updated and comprehensive phylogenetic analysis to understand the origin, evolution, transmission routes and genetic adaptation of the virus.ResultsAll of the globally distributed CHIKV genomes were divided into three genotypes, including West Africa (WA), East/Central/South African (ECSA) and Asian genotypes. The genome sequenced in this study was located in the Indian Ocean lineage (IOL), and closely related to a strain isolated from a patient in Australia who returned from Bangladesh in 2017. Comprehensive phylogenetic analysis showed that the Chinese strains were mainly sourced from Indian subcontinent and Southeast Asia. Further analyses indicated that Indian subcontinent and Southeast Asia may act as major hubs for the recent global spread of CHIKV, leading to widespread epidemics and even many large outbreaks. Moreover, we identified 179 distinct sites containing some undescribed sites in the sP and nsP proteins, showing obvious genetic varieties associated with different CHIKV lineages.ConclusionsHere we reported a novel CHIKV isolate from a Chikungunya patient imported from Myanmar into China in 2019, and summarized the source and evolution of Chinese CHIKV strains. The present findings provided better understanding of the recent global evolution of CHIKV, highlighting the urgent need for the strengthened surveillance including the viral diversity surveillance.