Development of a highly specific PrM-based diagnostic marker for dengue virus detection: minimizing cross-reactivity with other flaviviruses and SARS-CoV-2

Accurate diagnosis is the key to effective treatment, ensuring that the proper treatment is delivered to the right patient at the right time. In the case of the dengue virus, the virus's habitat resemblance to other flaviviruses makes diagnosis difficult. Serological cross-reactivity between these flaviviruses leads to lower specificity in the current diagnostic tests. In this study, we have mapped the putative B-cell-specific PrM epitopes from DENV serotypes with comprehensive bioinformatics analysis (epitope predictions, protein-protein interactions, MD simulation, etc.) to reduce the cross-reactivity. Understanding the sequential and structural characteristics of B-cell epitopes is crucial for designing successful vaccinations and developing reliable diagnostic assays. We predicted B-cell epitopes from all dengue proteins and checked their antigenicity, immunogenicity, and conservancy. We found that only PrM proteins are highly conserved among dengue serotypes, whereas they are less conserved among other species of the Flaviviridae family. For comparison with the existing NS1-based diagnosis assays, we performed in silico molecular docking. Also, the MD simulations confirm that the designed DENV antigen shows specificity towards the DENV PrM antibody. We found that the PrM antibody is less likely to show interaction with the PrM antigen of other flaviviruses. Therefore, these PrM-based epitopes can be utilized in novel rapid diagnostic tests to accurately diagnose dengue virus, thereby eliminating cross-reactivity and false-positive detection.