Virome dynamics of Aedes albopictus during the 2025 chikungunya outbreak in Foshan

Chikungunya virus (CHIKV) has re-emerged globally, yet little is known about how natural CHIKV transmission influences the resident virome of mosquito vectors under field conditions. Here, we combined continuous entomological surveillance, viral genomics and metagenomic sequencing to characterize CHIKV transmission and virome dynamics in Aedes albopictus during the 2025 chikungunya outbreak in Foshan, China. Mosquitoes were continuously collected throughout the outbreak using pooled and individual sampling strategies, and viral metagenomic sequencing was performed to compare virome composition between CHIKV-positive and CHIKV-negative mosquitoes. CHIKV-positive mosquitoes first appeared shortly after the onset of local human transmission and expanded geographically in parallel with the epidemic. Mosquito- and human-derived CHIKV genomes were nearly identical and belonged to a genetically homogeneous East/Central/South African (ECSA) lineage, supporting sustained local mosquito–human transmission. Despite widespread CHIKV circulation, the resident mosquito virome remained broadly stable, with sampling time contributing more to virome variation than CHIKV infection status. Only two resident viruses, Orthophasmavirus barstukorius and Guato virus, were significantly associated with CHIKV infection. Integration of pooled and individual sequencing further showed that pooled samples reliably represented the population-level core virome, whereas individual mosquitoes revealed substantial inter-individual heterogeneity. Five previously undescribed RNA viruses were also identified, expanding the known virosphere of Ae. albopictus. Together, our findings show that natural CHIKV emergence is accompanied by limited species-specific shifts rather than wholesale restructuring of the resident mosquito virome, and highlight the value of integrating genomic and metagenomic surveillance into vector-borne disease monitoring.