Although the exact nature of these selection constraints remains to be elucidated, it may be related with the structural constraints at the level of RNA structure, including potential regulatory RNA elements that are NVP-AUY922 ic50 yet to be described in the HIV genome [83]. Interestingly, when the number of sites characterized as “”structured”" and “”non-structured”" in Watts et al. (2009) [83] study was compared among regions classified as associated epitopes and non-epitopes in this study, the results showed that associated epitope regions tend to harbor a significantly larger proportion of structured than non-structured sites while non-epitopes

harbor more non-structured than structured sites (Fisher’s MLN0128 purchase exact test, p < 0.05). Because structured regions are expected to be more evolutionary conserved at the nucleotide level to preserve the ability to form secondary or higher-order RNA structures, this is consistent with the overall lower degree of sequence divergence observed among associated epitopes. However, no statistically significant difference was observed when the numbers of structured and unstructured sites were compared between associated epitopes and epitope regions not included in the association rule mining (p > 0.05). This can be attributed to a variety of factors,

including that the latter epitope category is a heterogeneous mixture of epitopes that are evolving with different rates under different selection Adenosine pressures [78, 79]. Likewise, as pointed out by Watts et al.

(2009) [83], while most structures in their studied HIV-1 model have been well characterized, some structural RNA elements may still require further refinement. Discussion Overall, our results identified a set of strong associations between CTL and T-Helper epitopes that co-occur in the majority of the HIV-1 genomes worldwide and can be considered strong candidates for multi-epitope vaccine and/or treatment targets. There have been several attempts to design multi-epitope vaccines using different strategies for the epitope selection, which is one of the most important steps in a multi-epitope vaccine design. Some studies have suggested computer based epitope prediction methods (e.g., [23, 84–86]) for such selection, although accuracy of in-silico methods for “”prediction of epitopes”" is still debated [87]. It has been proposed that a mixture of epitopes representing variable regions or potential escape variants can be used to overcome enormous viral diversity of HIV (e.g., [88, 89]). Indeed, some of the hypervariable regions have been shown to be strongly immunogenic eliciting broad cross-subtype-specific responses [90, 91].