From emergence to resurgence: evolutionary dynamics of chikungunya virus in Bangladesh, 2008-2025

Chikungunya virus (CHIKV) remains a growing public health concern in tropical regions, yet its long-term evolutionary dynamics in Bangladesh are not well defined.

This study analyzes genomic data from 2008 to 2025 to characterize evolutionary relationships, genetic structure, and demographic trends underlying recurrent outbreaks.

Phylogenetic analysis shows all isolates cluster within the Indian Ocean Lineage of the East/Central/South African genotype, forming distinct temporal groups aligned with outbreak periods. Time-scaled phylogeny suggests a common ancestor around mid-2007, with short internal branches indicating rapid epidemic expansion. Population genetic results reveal high haplotype diversity (Hd = 0.90 ± 0.03) but low nucleotide diversity (π = 0.008), consistent with expansion from limited ancestral variants and supported by significantly negative neutrality tests. Haplotype networks display star-like patterns, and Bayesian skyline analysis indicates a sharp population increase in 2017 followed by stabilization and a modest recent rise. The estimated evolutionary rate (1.28 × 10^-3 substitutions/site/year) is consistent with other arboviruses, with selection analyses indicating predominant purifying pressure alongside persistence of key mutations.

Overall, the findings support sustained local circulation with periodic amplification rather than repeated external introductions, underscoring the need for continuous genomic surveillance.