CD8 and CD4 epitopes predicted to be strong binders matched against different vaccine inserts.

Epitopes were predicted in all HIV-1 proteome sequences derived from RV144 breakthrough infections. The epitopes were matched against epitopes derived from the RV144 vaccine inserts of subtype B (MN, LAI) or CRF01_AE (CM244, 92TH023); two epitope characteristics were used to compare epitopes from the breakthrough to the vaccine: the predicted binding affinity for each epitope and the protein distance between the epitope sequences. One summary measure was computed for each protein and each subject, and comparisons were done between the vaccine (V) and placebo (P) groups (the number of vaccine and placebo recipients included in each group is in parenthesis) with Mann-Whitney tests for proteins corresponding to those included in the RV144 vaccine insert (Gag, Pro, gp120 (including V2)) and those not part of the RV144 vaccine (RT-IN, Nef).CD8 and CD4 epitopes predicted to be strong binders matched against different vaccine inserts.