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Integrative genomic and immunoinformatic approach for characterizing HIV-1 pol, vpr, and Nef genes and designing a multi-epitope vaccine

Akmal Zubair,Muhammad Ali,Ahmed Al-Emam,R. M. Elmagzoub

Published 2025 in Scientific Reports

ABSTRACT

The study aims to characterize the Pol, Vpr, and Nef genes, as well as to explore the development of vaccines using computational tools. In this study, blood was extracted from HIV-positive samples, followed by RNA extraction. The RNA was converted into complementary DNA (cDNA) and processed for PCR amplification of the Pol, Vpr, and Nef genes using gene-specific primers. Consensus sequences were generated using CLC software. Additionally, we design an in-silico vaccine by using computational tools. We have successfully sequenced several samples, among them 9 for Pol gene, 5 for Vpr gene, and 8 for Nef gene. The consensus sequences generated from these genes were utilized for vaccine development. We created computational vaccines that include 8 B-cell epitopes, 9 CTL epitopes, and 11 HTL epitopes. The final vaccine construct consists of 555 amino acids, with a molecular weight of 60,226.49 amu. Molecular docking studies indicate that our vaccine construct exhibits a strong binding affinity with the TLR4 receptor. Our HIV vaccine construct covers 96.21% population of the world. Immune stimulation and molecular dynamics simulations demonstrate that our vaccine is stable and elicits a robust immune response. Our study indicates that our vaccine is a potentially strong and stable HIV vaccine for the Pakistani population by utilizing consensus amino acids from the Pol, Vpr, and Nef genes. Further in vivo and in vitro studies are necessary to evaluate the vaccine’s potential impact.

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