<p>Abbreviations used in this study.</p>

The East/Central/South African (ECSA) genotype has increasingly predominated in multiple regions, yet the molecular basis of its competitive advantage remains unresolved. Here, we demonstrate that three ECSA sub-lineages—ECSA-IOL, ECSA-2.1, and ECSA-2.2—have independently evolved distinct vector-associated evolutionary patterns that underlie their divergent geographic dominance.

Using comparative phylogenomic analyses of complete CHIKV genomes and selection pressure analyses (RELAX/BUSTED/Contrast-FEL), we found that ECSA-2.1 showed intensified selection on structural-protein genes and accumulated substitutions previously associated with <i>Aedes aegypti</i>, explaining its rapid displacement of the Asian genotype across the Americas. In contrast, ECSA-IOL underwent adaptation strategy switching from <i>Aedes albopictus</i> to <i>Ae. aegypti</i>, maintaining its dominance across South and Southeast Asia, while ECSA-2.2 convergently acquired <i>Ae. albopictus</i> adaptation with additional envelope protein mutations, suggesting enhanced adaptive potential.