Global patterns of genetic diversity and evolution in chikungunya virus E2 glycoprotein

The E2 glycoprotein of chikungunya virus (CHIKV) mediates host-cell attachment and entry and contains key antigenic determinants targeted by host immune responses. Variation in E2 can influence host interaction, immune recognition, lineage diversification, and epidemic fitness, it represents a biologically relevant target for assessing evolutionary pressures and epidemic dynamics. In this study, we conducted a comprehensive analysis of E2 genetic diversity using a dataset of sequences collected across regions, hosts, and epidemic periods. Diversity indices, neutrality tests, and haplotypes network analysis were applied to characterize evolutionary pressures acting on E2 glycoprotein. To assess the influence of geography, host, and time on viral population structure, we performed spatial–temporal stratification and analysis to assess clustering patterns across lineages and regions using Fixation index test (Fst). Nucleotide diversity varied considerably across time, with the pre-expansion period (pre-2004) showing the highest diversity (Pi = 0.085), while more recent outbreak periods exhibited comparatively reduced diversity (Pi = 0.012). Neutrality tests revealed signatures of both purifying and positive selection across the three CKIKV E2 lineages (negatively statistically significant Tajima D, Fu and Li’s D, and Fu and Li’s F tests, p -values < 0.05) supported by codon‑based analyses showing pervasive purifying constraint across the E2 gene but recurrent diversifying signals at lineage‑specific sites, notably codon 146 in the West African lineage, codons 220, 245, 247, and 254 in the Asian lineage, and codons 54, 56, 102, 145, 163, 177, and 350 in the East/Central/South/African lineage. Population structure analyses using Fst indicated significant genetic differentiation between regional populations, reflecting restricted gene flow and localized evolutionary trajectories. Haplotype network analysis highlighted distinct clustering patterns shaped by geography and epidemic waves, reflecting the persistence of lineage-specific signatures across regions. At the same time, reduced connectivity among recent outbreak strains point to more discrete intercontinental movement events, likely driven by human-mediated vector dispersal or travel-associated introductions. Collectively, these findings underscore the spatiotemporal evolution of CHIKV E2 glycoprotein and its implications for viral adaptation and immune evasion.