Global Genomic Epidemiology of Chikungunya Virus: E1-Based Phylodynamics, Recombination Screening, and Structural Variation in Chinese Isolates.

Authors

Yu Chen, Meng Shang, Shengping Dou, Xiaoxu Wang, Haoqiang Ji, Qiyong Liu

Published in

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases. Pages 108908. Jun 23, 2026. Epub Jun 23, 2026.

Abstract

Chikungunya virus (CHIKV) is re-emerging globally, yet integrative analyses combining E1-based phylodynamics, full-genome recombination screening, and genomic characterization of Chinese isolates remain limited.
We curated 1,291 high-quality CHIKV full genomes from GenBank (through September 2025). Alignments were generated with 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 RDP4 and further evaluated using SimPlot. Codon-based selection analyses of the Chinese structural coding-region subset were performed using GARD, BUSTED, MEME, and 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 dataset showed apparent temporal structure, but this signal was interpreted cautiously because of lineage structure and uneven outbreak-driven sampling. Three of sixteen recombination candidates were retained as sequence-supported signals after additional evaluation, with retained breakpoints 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 breakpoints localized mainly to nsP2 and E2, and the ECSA 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.

PMID:
42336193
Bibliographic data and abstract were imported from PubMed on 24 Jun 2026.

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