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Highly conserved and associated HIV-1 CTL and T-Helper epitopes in global HIV-1 population: potential candidates for multi-epitope HIV-1 vaccine

Published: 02 August 2010 Publication History

Abstract

Human Immunodeficiency Virus (HIV-1), one of the fastest evolving organisms, is a leading cause of death in the world today. But regardless of isolated stories about HIV cure in one patient and a modest success in a clinical vaccine trial, a perfect vaccine that can give total protection or a drug for a complete cure still remains intangible. Epitope vaccines have been suggested as a strategy to counteract viral escape and development of drug resistance. Multiple studies have shown that Cytotoxic T-Lymphocyte (CTL) and T-Helper (Th) epitopes can generate strong immune responses in HIV-1. However, not much is known about the relationship among different types of HIV-1 epitopes, particularly those epitopes that can be considered potential candidates for inclusion in the multi-epitope vaccines. In this study we used association rule mining to examine relationship between different types of epitopes (CTL, Th and Antibody epitopes) from nine protein-coding HIV-1 genes. Our results identified 137 association rules that were consistently present in the majority of reference and non-reference HIV-1 genomes from worldwide HIV-1 population and included epitopes of two different types (CTL and Th) from three different genes (Gag, Pol and Nef). These epitope association rules involved 14 non-overlapping epitope regions that frequently co-occurred despite high mutation and recombination rates of HIV-1, including genomes of circulating recombinant forms. These epitope regions were also highly conserved at both the amino acid and nucleotide levels indicating strong purifying selection driven by functional and/or structural constraints and hence, the diminished likelihood of successful escape mutations. Thus, these associated epitopes should be considered as potent candidates for inclusion in multi-epitope vaccines.
  1. Highly conserved and associated HIV-1 CTL and T-Helper epitopes in global HIV-1 population: potential candidates for multi-epitope HIV-1 vaccine

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    cover image ACM Conferences
    BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
    August 2010
    705 pages
    ISBN:9781450304382
    DOI:10.1145/1854776
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    Published: 02 August 2010

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