Genomic characterization of a large-scale chikungunya outbreak in China

In July 2025, a large chikungunya outbreak occurred in southern China, with more than 5000 cases reported within a single month. However, the genomic basis of this urban outbreak remains poorly characterized.

A total of 804 CHIKV-positive clinical specimens were collected through routine surveillance and outbreak investigations by the Shenzhen Center for Disease Control and Prevention. Following whole-genome sequencing and quality control, 614 genomes were retained and analyzed in combination with 1105 publicly available CHIKV genomes sampled globally between 1953 and 2025. Comprehensive genetic analyses were performed to characterize lineage origin, transmission dynamics, and short-term genomic diversification across local and global scales.

All outbreak sequences belonged to the East/Central/South African (ECSA) lineage, specifically clustering within the Middle African lineage (MAL) sub-lineage, and formed a well-supported, genetically compact monophyletic group. Within this cluster, genomes diversified rapidly into multiple co-circulating subclusters over a short time window (August-October), indicating continued regional transmission and geographic structuring during outbreak expansion. Despite this rapid expansion, genetic variation remained limited, with only a small number of characteristic amino-acid substitutions identified, most of which were present at low to moderate frequencies and showed no evidence of widespread fixation across the outbreak population. The inferred substitution rate for the outbreak-associated lineage was 9.90 × 10⁻⁴ substitutions per site per year (95% HPD: 8.28-11.69 × 10⁻⁴).

These findings suggest that large CHIKV outbreaks in highly connected metropolitan settings can arise from the rapid expansion of a single contemporary genetic background, even in the absence of extensive adaptive change. This study provides a high-resolution genomic perspective on CHIKV spread and highlights key features of short-term viral diversification during outbreaks.