Genomic epidemiology reveals the origins and transmission dynamics of chikungunya virus in China

Background: The chikungunya virus (CHIKV) poses a significant public health threat in China, driven by travel-related introductions and local outbreaks. A comprehensive understanding of the spatiotemporal dynamics, viral genetic diversity, and origins of these outbreaks is imperative for surveillance and control measures. This study aimed to characterize the spatiotemporal dynamics of CHIKV in China and elucidate the evolutionary origins of outbreak lineages. Methods: A systematic collection of epidemiological data on CHIKV cases in China was conducted up to December 2025, resulting in the identification of 416 imported cases and 25,948 local cases. A comprehensive retrieval of all publicly available CHIKV genomes from China was conducted. The composition of viral lineages was determined by employing maximum likelihood phylogeny. Substitution rates were estimated, and time-scaled transmission clusters were generated using Bayesian evolutionary analysis. Discrete phylogeographic reconstruction was used to infer spatial diffusion pathways, with statistical support evaluated using Bayes Factors. Results: From 1987 to 2025, imported chikungunya cases in China mainly originated from Southeast Asia, especially Myanmar, and were accompanied by several major local outbreaks. Significant outbreaks were reported in Guangdong (2010 and 2025), Yunnan (2019), and Taiwan (2019), with the largest outbreak occurring in Guangdong in 2025 and involving 25,335 cases. Genomic analysis of 314 sequences revealed that the East/Central/South African lineage was the most prevalent, accounting for 92.0% of cases. This lineage includes the Indian Ocean (IOL) and Central African clades. The Asian lineage accounted for the remaining 8.0%. Bayesian analysis identified four independent outbreak clusters. Phylogeographic data supported the conclusion that there were multiple introductions. The IOL clusters spread from Africa and South Asia to Southeast Asia. The 2025 Guangdong outbreak cluster (Central African clade) suggests a possible association with introduction from Africa. The Asian lineage circulated persistently in Southeast Asia before entering Yunnan Province. Conclusions: CHIKV outbreaks in China are linked to imported cases, and outbreak lineages consistently match recent imports. The virus entered through various, geographically independent routes. These findings underscore the need for genomic-informed surveillance at key entry points and in high-risk regions to anticipate and prevent local epidemics.