Whole-genome phylogenetics of chikungunya virus from a clustered outbreak in China reveals IOL circulation.

Chikungunya virus (CHIKV) is an arthropod-borne Alphavirus of the family Togaviridae. In this study, four CHIKV whole-genome sequences (JH01/China Jinhua/2025 to JH04/China Jinhua/2025) were obtained from a clustered outbreak in Jinhua City, China, using Nanopore sequencing. Phylogenetic relationships were inferred via a maximum likelihood (ML) approach implemented in IQ-TREE, and genomic variation was characterized through analyses of nucleotide substitutions, amino acid changes, and codon-level selective pressures. All four isolates clustered with strong statistical support within the India Ocean lineage (IOL). Comparative genomic analysis identified several amino acid substitutions, including E1-A226V, E2-L210Q, and E2-I211T. E1-A226V has previously been reported as an adaptive mutation associated with the expansion of some IOL lineages. Codon-based selection analyses indicated that the E1 protein within the IOL genetic background is predominantly subject to purifying selection. Together, these results confirm the classification of the Jinhua isolates as IOL and provide molecular evidence for the circulation and evolutionary stability of this lineage in China.