Comparisons of Nef effects on CTL-recognizing late protein versus early protein epitopes. For the 8 epitopes shown (5 from the late proteins RT, Gag, and Env, and 3 from the early proteins Nef and Rev), CTL clones were tested for Nef effects as described in Figure 1. The bar plots represent average results for each epitope. In the case that there were multiple repeats of individual clones (as described in Figure 2 and Table 1), these were averaged; if there were multiple clones from the same HIV-1–infected person, these were then again averaged (to apply equal weight to CTL clones from different persons). Finally, results across all persons were averaged (if clones recognizing the same epitope from multiple persons were tested) to generate the single values plotted for each epitope. MEAN LATE indicates the average for the 5 late protein-derived epitopes (± 1 SD) and MEAN EARLY indicates the average for the 3 early protein-derived epitopes.