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 samp

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