Global genomic epidemiology of chikungunya virus: E1-based phylodynamics, recombination screening, and structural...

The chikungunya virus (CHIKV) is re-emerging worldwide, yet integrative analyses combining E1-based phylodynamics, full-genome recombination screening, and genomic characterization of Chinese isolates remain limited.

We curated 1291 high-quality CHIKV full genomes from GenBank (through September 2025). Alignments were generated with Multiple Alignment using Fast Fourier Transform (MAFFT) and models selected using ModelFinder. Time-scaled phylogenetic reconstruction and Bayesian skyline analyses were conducted in BEAST using the E1 coding region. Recombination was screened across complete genomes using Recombination Detection Program version 4 (RDP4) and further evaluated using SimPlot. Codon-based selection analyses of the Chinese structural coding region subset were performed using Genetic Algorithm for Recombination Detection (GARD), Branch-site Unrestricted Statistical Test for Episodic Diversification (BUSTED), Mixed Effects Model of Evolution (MEME), and Single-Likelihood Ancestor Counting (SLAC). For 84 Chinese isolates, variation in the structural protein region was quantified, and amino acid substitutions were mapped onto AlphaFold-predicted protein structures.

Root-to-tip regression of the E1 data set showed apparent temporal structure, but this signal was interpreted cautiously because of lineage structure and uneven outbreak-driven sampling. Three of 16 recombination candidates were retained as sequence-supported signals after additional evaluation, with retained break points localized mainly to nsP2 and E2. Among available recent genomes, the ECSA lineage was prominently represented, including genomes associated with recent outbreaks in China. Structural proteins were overall conserved, with amino acid variability concentrated mainly in E2 and E1.

The E1-based analyses provided a cautious time-calibrated framework for CHIKV evolutionary history. Recombination signals were rare after validation, with retained break points localized mainly to nsP2 and E2, and the East/Central/South African lineage was prominently represented among recent available genomes. In Chinese isolates, structural proteins were overall conserved, with amino acid variability concentrated in E2 and E1. Codon-based analyses supported predominant purifying selection with limited evidence of episodic selection at a subset of sites.