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Table 5 Predicted CTL epitopes in HIV-1 gag and env-V3 (according to the patients HLA type) and their evolution

From: HIV-1 sequence evolution in vivo after superinfection with three viral strains

Protein, position CTL epitope HLA-I type Subtype B1 2001 Subtype B2 2002 Subtype AE 2003
Gag p17, 18–28 KIRLRPGGK
or RLRPGGKKK
A3 KIRLRPGGKKR*
K→R (42%) in 2005
KIRLRPGGKKS
S→R (100%) in 2005
KIRLRPGGKKQ, no changes over time
Gag p17, 74–82 ELRSLYNTV B8 ELKSLYNTV, 50% V→I in 2005 ELKSLFNTV, 67% F→Y in 2005 ELKSLYNTV, no changes over time
Gag p17, 93–101 EIKDTKEAL B8 EVKDTKEAL, 83% V→I in 2005 DVKDTKEAL, no changes over time EILDTKEAL, no changes over time
Gag p24, 8–21 GQMVHQAISPRTLN A3- supertype Cw3 GQMVHQPISPRTLN, no changes over time GQMVHQPISPRTLN, no changes over time GQMVHQPVSPRTLN, no changes over time
Gag p24, 41–60 SALSEGATPQDLNTMLNTVG unknown SALSEGATPQDLNTMLNTVG 92% S→T in 2005 SALSEGATPQDLNTMLNTVG 96% S→T in 2005 SALSEGATPQDLNMMLNIVG, no changes over time
Env-V3, 296–305 CTRPNNNTRK A3 CTRPSNNTRK, no changes over time CTRPSNNTRK, no changes over time CTRPSNNTRT, no changes over time
Env-V3, 308–322 RIQRGPGRAFVTIGK A3 SIHIAPGRAFYATGE, no changes over time SIHMGPGKAFFTTGE, no changes over time SIHMGPGQVFYRTGD, no changes over time
  1. * Underlined amino acids are deviations from the consensus epitope sequence. Changes over time are marked in bold.