Summary
In 2025, a large chikungunya virus (CHIKV) outbreak in southern China resulted in more than 25,000 confirmed cases, representing the largest documented CHIKV epidemic in southern China to date. To resolve its origins and transmission history, we generated 1,264 near-complete CHIKV genomes from Guangdong Province and integrated viral genomic, epidemiological, entomological, and human mobility data:
Single Dominant ECSA Introduction & Cryptic Pre-Detection Spread: Phylodynamic analyses traced the epidemic to a single dominant introduction of a Reunion-associated East/Central/South African (ECSA) lineage, dating the ancestor of the Guangdong outbreak clade to late April–early May 2025. The lag between the estimated viral origin and the first reported case points to a window of undetected local transmission, highlighting the limitations of passive surveillance for early arbovirus detection.
Two Contrasting Epidemic Waves: Spatiotemporal phylogeographic reconstruction uncovered two distinct epidemic waves with markedly different dispersal patterns: the Foshan wave was characterized by frequent medium- to long-distance viral movements across districts, whereas the Jiangmen wave remained comparatively localized.
Implications for Surveillance: These findings demonstrate the critical role of active genomic surveillance and rapid sequencing at the geographic fringe of endemic arbovirus transmission to detect introductions early and guide targeted vector control.
