HIV sequence variations in regions targeted by the shRNAs. HIV sequences in the Los Alamos HIV Sequence Database were analyzed for sequence variation at each of the 19 nt residues in the rev-, gag-, and vif-targeted regions. The number of isolates within each clade (A, B, C, D, or E) that contain mutations relative to the total number of isolates were determined and expressed as a percentage. For each sequence, 41 to 45 clade A isolates, 31 clade B isolates, 61 to 66 clade C isolates, 33 clade D isolates, and 9 clade E isolates were available.