Isolation and genomic characterization of Chikungunya virus during the 2025 outbreak in Foshan, China
Changyun Sun, Lu Zhang, Haisu Yi, Shuichun Wan, Airu Zhu, Bin Yuan, Qihong Yan, Xiaofang Peng, Chao Yu, Xin Zhang, Kangkang Fu, Jianwen Zeng, Yongxia Shi, Lifen Huang, Yanqun Wang, Jincun Zhao, Baisheng Li
Abstract
Chikungunya virus (CHIKV) caused more than 10,000 infections in Foshan, Guangdong, in 2025. Using plasma from acute-phase patients, we successfully isolated infectious CHIKV, confirmed by focus-forming assay and transmission electron microscopy. Whole-genome sequencing revealed that all isolates belonged to the ECSA-2 sub-lineage and were closely related to strains circulating on Réunion Island in 2024-2025, carrying adaptive mutations including C:T143A, E1:A226 V, and E2:I211 T/L210Q. Based on Foshan's 2025 population (∼9.6 million), the outbreak corresponded to a cumulative incidence of ∼104 cases per 100,000 inhabitants, highlighting intense transmission. Integrated virological, genomic, and epidemiological analyses characterize the rapid expansion of a single ECSA-2 genotype and underscore the need for strengthened arbovirus and genomic surveillance in southern China.