Dominance of dengue virus serotype-2 in Pakistan (2023–2024): Molecular characterization of the envelope gene and exploration of antiviral targets

Dengue virus infection, caused by a single positive-stranded RNA virus from the Flaviviridae family, represents a significant public health challenge in tropical and subtropical regions. This virus has four serotypes (DENV-1, 2, 3, and 4), primarily transmitted by Aedes mosquitoes. Despite extensive research, effective antiviral treatments and vaccines remain elusive due to the viral diversity and the complex mechanisms such as antibody-dependent enhancement (ADE). In the current study, NS1-positive serum samples from dengue cases in Pakistan (2023–2024), were analyzed to determine the predominant serotype and characterize the envelope (E) gene for further exploration of antiviral targets. Out of 100 samples, 63 (63%) tested positive for DENV-2, indicating its predominance during this period, while two samples showed mixed infections with DENV-2 and DENV-3. The envelope gene was successfully amplified using nested PCR, validated through gel electrophoresis and sanger sequencing. Phylogenetic analysis revealed high similarity of the DENV-2 isolates to strains from China and India. Computational modeling of the envelope protein structure identified potential antiviral binding sites and further molecular docking studies suggested that specific antiviral compounds like Arbidol and Quercetin can inhibit early steps in viral infection. Additionally, BepiPred-3.0 predicted several B-cell epitopes, which could be useful for vaccine development. These findings enhance our understanding of dengue epidemiology in Pakistan and contribute to the development of targeted antiviral therapies, potentially informing future vaccination strategies and outbreak management.