The importance of the repertoire of a primed, AIDS virus-specific population of CTL in the recognition of emerging mutant viruses was assessed in simian immunodeficiency virus (SIV)-infected rhesus monkeys. These studies were done by using the well-characterized CTL recognition of the SIVmac Gag peptide 11C (p11C) epitope in rhesus monkeys expressing the MHC class I molecule Mamu-A*01. Lysis of peptide-pulsed targets by bulk PBL effector cells from SIVmac-infected, Mamu-A*01+ monkeys was significantly decreased by mutations at residues 2, 3, and 5 of the nine-amino-acid Gag p11C epitope. However, effector cell lysis of targets pulsed with p11C containing substitutions at residues 3 or 5 was substantially increased by in vitro incubation of the monkeys' PBL with these mutant peptides. This suggested that expandable populations of cells exist in the primed CTL of infected monkeys capable of recognizing mutant peptide sequences. In fact, without in vitro exposure of PBL to mutant peptides, SIVmac Gag-specific CTL could be cloned from PBL of infected monkeys that lysed targets pulsed with mutant peptides. These observations suggest that clones of effector cells capable of recognizing many viral mutants may be able to expand in vivo to control the spread of emerging variant AIDS viruses.