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Methods Analysis was performed in 2003 on 10,803 HIV-1 sequences, and again in 2009, on an expanded set of 43,822 sequences. These were searched for conserved 910-mer segments with the EpiMatrix suite of immunoinformatic algorithms. From the most highly conserved (>5% isolates) or top 1,000 scoring 9-mers, HLA Class I binding sequences and Class II immunogenic consensus sequences (ICS) were identified for vaccine design. Validation was performed in Thailand, the USA, and Mali via in vitro binding and IFN-g ELISpot assays, using HIV-infected donor peripheral blood. HLA transgenic mice were immunized in DNA-prime/peptide-boost vaccine studies including these epitopes.

Further confirmation of broadly conserved, highly immunogenic cross-clade HIV CTL epitopes for inclusion in the GAIA HIV vaccine