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

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.