Poster #53 - Md Nazmul Hasan

Unraveling Dengue Virus Adaptation: Insights from Near-Neutral Balanced Selectionist Theory (NNBST) and Evolutionary Model Comparison

Md Nazmul Hasan, Department of Chemistry & Biochemistry, Rowan University, USA Dr. Chun Wu,  Department of Chemistry and Biochemistry & Department of Biological & Biomedical Sciences, Rowan University, USA

Dengue virus serotype 1 (DENV1), a mosquito-borne flavivirus, causes severe disease due to antibody-dependent enhancement (ADE), limited vaccine efficacy, and the lack of specific antivirals. An unresolved question is whether fixed mutations in DENV1 are governed by neutrality, selection, or a balanced interplay of both. Conventional Ka/Ks (dN/dS) analyses report pervasive negative selection, yet conflict with evidence of molecular clock behavior and adaptive mutations. To resolve this paradox, we applied our substitution-mutation rate ratio (c/µ) framework, where c is the substitution rate in populations and µ the spontaneous mutation rate in individuals, to DENV1 full-genome sequences. The c/µ framework directly compares substitution and mutation rates, enabling genome-wide detection of purifying (c/µ < 1), neutral (c/µ ≈ 1), and adaptive (c/µ > 1) sites across coding and noncoding regions. Our analysis revealed two recurrent evolutionary features: (i) near-constant substitution accumulation consistent with molecular clock behavior, and (ii) an L-shaped distribution of fitness effects (DFE), showing that strictly neutral mutations are rare. Segment-level analyses showed mixtures of adaptive and purifying sites across all regions. Adaptive residues were enriched in E, NS1, NS2A/B, NS4A/B, and NS5, while conserved sites were more common in C, NS3, and UTRs. Top mutations identified by elevated c/µ values mapped to residues with literature-reported roles in replication, host adaptation, and immune evasion. Structural modeling suggested differences between wild-type and mutant residues in NS3 helicase and NS5 polymerase, implying viral fitness and drug susceptibility. These findings support the Near-Neutral Balanced Selectionist Theory (NNBST), where balanced weakly deleterious and advantageous mutations sustain effective neutrality and molecular clock behavior. The c/µ framework resolves contradictions left by Ka/Ks analyses by identifying conserved regions for vaccine design and adaptive sites for anticipating vaccine escape, thereby providing a mechanistic link between viral genotypes and phenotypic fitness effects.