The results of these analyses suggest that a T cell based vaccine containing gag/pol/nef would require four or more epitope responses to be elicited in order to expect 90% coverage by 1 or more epitopes. As epitope escape early in infection has been reported, it is desirable to have multiple epitopes present; our analysis indicates that two or more epitopes at 90% coverage need 6 or more epitopes to be recognized, and three or more epitopes need 8 to 9 epitopes. This prediction assumes the same degree of conservation of epitopes as observed in the current data. However, if responses to more highly conserved epitopes are elicited by vaccination, the number of epitopes required to achieve coverage may be markedly reduced. Development of a more detailed predictive model of vaccine coverage as a function of both breadth and epitope-level frequency would be useful for guiding future insert designs and for assessment of coverage by future candidate vaccines. The above analysis of epitope coverage implicitly assumes that T-cell epitopes have equal efficacy. For example, recent studies suggest that epitopes restricted by some HLA alleles are more likely to be associated with reduced viral load than other epitopes. Our analyses provide an important series of observations about the outcome of the Step trial and future immunogen design. It is clear that while immunogenic in most individuals, the Merck gag/ pol/nef vaccine tended to elicit responses to fewer highly conserved epitopes and more less-conserved epitopes than would be predicted from the vaccine sequences alone. An interesting question is raised as to how generic this bias towards lessconserved epitopes may be. The mechanism for these observations are unclear; Pazopanib potential explanations include that such highly conserved but relatively immunologically silent regions could be the consequence of Y-27632 dihydrochloride side effects retroviruses evolving to evade epitope processing in regions where mutations have a very high fitness cost, or could be due to very conserved domains also being conserved in HERVs, causing such regions to be seen as ����self����. To our knowledge, this is the first study to analyze this question in the context of high-resolution epitope mapping with a high number of patients and a clinical HIV-1 candidate.