Based on the type of recognizing

receptors, there are three types of epitopes, namely CTL/CD8+ epitopes (CTL), T-Helper/CD4+ epitopes (Th) and neutralizing antibody (Ab) epitopes. Single and multi-epitope vaccines containing CTL, Th and Ab epitopes Fludarabine have been described [33, 34]. Inclusion of highly conserved epitopes from different genomic regions in a multi-epitope vaccine has been suggested as a strategy to induce a broader cellular immune response that targets the majority of the virus variants [33, 35, 36]. However, identification of good vaccine candidates based on the extent of sequence conservation in HIV is a challenging problem, compounded by the fast mutation [37, 38] and recombination rates [39–41], overlapping reading frames [42] and overall high degree of sequence divergence among the global HIV-1 population [43]. Recently, we reported a series of highly conserved, co-occurring CTL epitopes from three different genes (Gag, Pol and Nef) that are frequently found in association with each other and therefore can be considered strong candidates for inclusion in CTL multi-epitope vaccines [44]. However, to further improve the vaccine efficiency, the use of adjuvants capable of inducing a strong cellular response and

potentially augmenting these responses should be considered (e.g., [45–48]), including use of multiple types of epitopes [49]. For example, Gram et al. (2009) [49] LY3039478 in vivo recently showed that while the use of immune-stimulating adjuvant CAF01 induces strong a CTL response, inclusion of a CD4 T-Helper epitope further improves this this website CTL response. Thus, this study was focused on identifying strong associations between different types of epitopes from multiple genes in search of potent multi-epitope vaccine candidates. Our results identified several highly conserved T-Helper epitopes that frequently co-occur

with particular highly Reverse transcriptase conserved CTL epitopes and that these epitopes co-occur in the majority of HIV-1 genomes of different subtypes and groups as well as circulating recombinant forms. Here we report 137 unique CTL and T-Helper epitope associations (also referred to as association rules) that involve epitopes from 14 non-overlapping genomic regions from three different genes, namely, Gag, Pol and Nef. Widespread presence of these epitope combinations across highly divergent HIV-1 genomes sampled worldwide, including circulating recombinant forms, coupled with a high degree of evolutionary sequence conservation likely reflective of substantial fitness impacts of escape mutations [50] makes them potent candidates for a multi-epitope vaccine. Methods HIV-1 genomic sequence data and sequence alignment HIV-1 sequences in the primary analysis included 90 HIV-1 reference sequences from the 2007 subtype reference set of the HIV Sequence database (Los Alamos National Laboratory (LANL), http://​www.​hiv.​lanl.