Genomic epidemiology reconstructs the pre-detection transmission and establishment of chikungunya virus in Guangdong, China

In 2025, a chikungunya outbreak in southern China resulted in more than 25,000 confirmed cases, but its origins and transmission history remain unresolved. As part of the public health investigation, we generated 1,264 near-complete chikungunya virus (CHIKV) genomes from Guangdong Province and integrated genomic, epidemiological, entomological, and human mobility data to reconstruct the emergence and spread of this outbreak. Our analyses traced the outbreak to a single dominant introduction of a Reunion-associated East/Central/South African (ECSA) virus lineage and dated the origin of the sampled Guangdong outbreak lineage from late April to early May 2025. The interval between the estimated origin of the outbreak lineage and the first reported case was consistent with a period of undetected local transmission and exposed limitations in passive surveillance for early arboviral outbreak detection. Spatiotemporal reconstruction showed two distinct epidemic waves with contrasting transmission dynamics. The Foshan wave involved frequent medium- to long-distance viral movement, while the Jiangmen wave remained relatively localized. Together, these findings reconstruct the early establishment and spatially heterogeneous spread of the largest documented CHIKV epidemic in southern China to date and demonstrate the necessity of expanding active genomic surveillance in areas at the fringe of CHIKV endemic transmission for timely detecting and characterizing emerging epidemics.