What question did this study set out to answer?

The study aims to trace the origins and genetic diversity of chikungunya virus (CHIKV) in Yunnan Province from travelers.

April 27, 2026Open Access

Genomic surveillance reveals multiple origins and local transmission of travel-associated chikungunya virus in Yunnan, China

MZMengyuan ZhengKunming University of Science and Technology JLJie LiKunming University of Science and Technology WCWei ChangKunming University of Science and Technology

Key Points

The study aims to trace the origins and genetic diversity of chikungunya virus (CHIKV) in Yunnan Province from travelers.
Retrospective analysis of 447 blood samples from febrile travelers at Kunming Airport.
Viral detection by RT-qPCR and near-complete genome sequencing via RT-nested PCR and Sanger sequencing.
Phylogenetic and phylodynamic analysis integrating 28 new genomes with 66 publicly available sequences.],
32 (7.2%) out of 447 travelers were CHIKV-positive, with 28 near-complete genomes sequenced.
Phylogenetic analysis revealed all strains belonged to the Indian Ocean lineage of the ECSA genotype with significant mutations enhancing transmission.
Three genotypes (Indian Ocean lineage, Asian, and West African) circulated in Yunnan, with close associations to strains from Thailand and Indonesia.

Abstract

Chikungunya virus (CHIKV) is a mosquito-borne arbovirus causing debilitating arthralgia, posing a significant public health threat in Southeast Asia. Bordering multiple endemic countries, Yunnan Province, China, is at high risk for CHIKV introduction. We conducted a retrospective analysis of 447 blood samples from febrile travelers arriving at Kunming Airport between May 2019 and January 2020. Viral detection was conducted by RT-qPCR, and near-complete genome sequences were subsequently obtained through RT-nested PCR and Sanger sequencing. To map genetic diversity and trace origins, we integrated 28 newly generated genomes with 66 publicly available sequences from local outbreaks and mosquitoes for phylogenetic and phylodynamic analysis. Among the travelers, 32 (7.2%, 32/447) were CHIKV-positive, with 28 near-complete genomes successfully sequenced. Phylogenetic analysis revealed that all strains studied belonged to the Indian Ocean lineage (IOL) of the East/Central/South African (ECSA) genotype and contained the E1-211E, E1-226 A, and E2-264 A mutations, which are known to enhance Aedes albopictus transmission. By integrating publicly available GenBank records (n = 66), including local outbreaks (n = 56) and mosquito vector samples (n = 10), our comprehensive analysis identified three circulating genotypes in Yunnan: IOL, Asian, and West African. Phylodynamic analysis suggested that the IOL strains were closely related to sequences reported from Thailand, while the Asian genotype showed close genetic association with strains from Indonesia. The co-circulation of multiple genotypes, detected in air travelers, local cases, and mosquitoes, underscores the role of international travel in seeding CHIKV transmission in Yunnan. Our findings highlight the need for enhanced airport screening, genotype-aware surveillance, and coordinated vector control to mitigate this public health challenge in southwestern China.

اسأل الذكاء الاصطناعي

Bookmark

View Full Paper