Nef effects on inhibition of HIV-1 replication by CTL clones
Clone . | Epitope (location) . | HLA . | Nef ratio (SD) . | No. of repeats . |
|---|---|---|---|---|
| Late protein/A or B restricted | ||||
| S1-SL9-3.23T | SLYNTVATL (Gag p17 77-85) | A*02 | 0.21 (0.15) | 5 |
| S36-SL9-10.18T | SLYNTVATL (Gag p17 77-85) | A*02 | 0.47 (0.38) | 2 |
| S36-SL9-10.26T | SLYNTVATL (Gag p17 77-85) | A*02 | 0.30 | 1 |
| 18030D23 | SLYNTVATL (Gag p17 77-85) | A*02 | 0.12 (0.14) | 4 |
| S42953-SL9-10.18 | SLYNTVATL (Gag p17 77-85) | A*02 | -0.08 | 1 |
| 161J×A12 | SLYNTVATL (Gag p17 77-85) | A*02 | -0.08 | 1 |
| 115D3 | SLYNTVATL (Gag p17 77-85) | A*02 | 0.06 | 1 |
| S14-KF11-1.3 | KAFSPEVIPMF (Gag p24 30-40) | B*57 | 0.46 | 1 |
| S14-KF11-10.6 | KAFSPEVIPMF (Gag p24 30-40) | B*57 | 0.62 | 1 |
| 68A62 | ILKEPVHGV (RT 309-317) | A*02 | 0.24 (0.24) | 8 |
| S34-KW10-10.38T | KIATESIVIW (RT 374-383) | B*57 | 0.03 | 1 |
| S34-KW10-10.55T | KIATESIVIW (RT 374-383) | B*57 | 0.26 | 1 |
| KS7 | IPRRIRQGL (Env gp41 332-340) | B*07 | 0.29 | 1 |
| Early protein/A or B restricted | ||||
| S42758-RL10-3.22T | RPAEPVPLQL (Rev 66-75) | B*07 | 0.23 (0.20) | 4 |
| S14-HQ10-1.1 | HTQGYFPDWQ (Nef 116-125) | B*57 | 0.46 (0.11) | 2 |
| S14-HQ10-1.3 | HTQGYFPDWQ (Nef 116-125) | B*57 | 0.37 | 1 |
| S14-YT9-10.4 | YFPDWQNYT (Nef 120-128) | B*57 | 0.50 (0.01) | 2 |
| S14-YT9-10.8 | YFPDWQNYT (Nef 120-128) | B*57 | 0.47 | 1 |
| S36-YT9-3.36 | YFPDWQNYT (Nef 120-128) | B*57 | 0.75 | 1 |
| C restricted | ||||
| 161J×B28 | RAIEAQQHL (Env gp41 46-54) | C*03 | 0.95 | 1 |
| 161J-JD19 | RAIEAQQHL (Env gp41 46-54) | C*03 | 0.76 | 1 |
| SE7/126E | RAIEAQQHL (Env gp41 46-54) | C*15 | 1.10 | 1 |
| S22-AL9-3.7 | AAVDLSHFL (Nef 83-91) | C*03 | 0.94 (0.11) | 2 |
| S16-RY11-10.41 | RRQDILDLWVY (Nef 105-115) | C*07 | 1.05 (0.10) | 3 |
Clone . | Epitope (location) . | HLA . | Nef ratio (SD) . | No. of repeats . |
|---|---|---|---|---|
| Late protein/A or B restricted | ||||
| S1-SL9-3.23T | SLYNTVATL (Gag p17 77-85) | A*02 | 0.21 (0.15) | 5 |
| S36-SL9-10.18T | SLYNTVATL (Gag p17 77-85) | A*02 | 0.47 (0.38) | 2 |
| S36-SL9-10.26T | SLYNTVATL (Gag p17 77-85) | A*02 | 0.30 | 1 |
| 18030D23 | SLYNTVATL (Gag p17 77-85) | A*02 | 0.12 (0.14) | 4 |
| S42953-SL9-10.18 | SLYNTVATL (Gag p17 77-85) | A*02 | -0.08 | 1 |
| 161J×A12 | SLYNTVATL (Gag p17 77-85) | A*02 | -0.08 | 1 |
| 115D3 | SLYNTVATL (Gag p17 77-85) | A*02 | 0.06 | 1 |
| S14-KF11-1.3 | KAFSPEVIPMF (Gag p24 30-40) | B*57 | 0.46 | 1 |
| S14-KF11-10.6 | KAFSPEVIPMF (Gag p24 30-40) | B*57 | 0.62 | 1 |
| 68A62 | ILKEPVHGV (RT 309-317) | A*02 | 0.24 (0.24) | 8 |
| S34-KW10-10.38T | KIATESIVIW (RT 374-383) | B*57 | 0.03 | 1 |
| S34-KW10-10.55T | KIATESIVIW (RT 374-383) | B*57 | 0.26 | 1 |
| KS7 | IPRRIRQGL (Env gp41 332-340) | B*07 | 0.29 | 1 |
| Early protein/A or B restricted | ||||
| S42758-RL10-3.22T | RPAEPVPLQL (Rev 66-75) | B*07 | 0.23 (0.20) | 4 |
| S14-HQ10-1.1 | HTQGYFPDWQ (Nef 116-125) | B*57 | 0.46 (0.11) | 2 |
| S14-HQ10-1.3 | HTQGYFPDWQ (Nef 116-125) | B*57 | 0.37 | 1 |
| S14-YT9-10.4 | YFPDWQNYT (Nef 120-128) | B*57 | 0.50 (0.01) | 2 |
| S14-YT9-10.8 | YFPDWQNYT (Nef 120-128) | B*57 | 0.47 | 1 |
| S36-YT9-3.36 | YFPDWQNYT (Nef 120-128) | B*57 | 0.75 | 1 |
| C restricted | ||||
| 161J×B28 | RAIEAQQHL (Env gp41 46-54) | C*03 | 0.95 | 1 |
| 161J-JD19 | RAIEAQQHL (Env gp41 46-54) | C*03 | 0.76 | 1 |
| SE7/126E | RAIEAQQHL (Env gp41 46-54) | C*15 | 1.10 | 1 |
| S22-AL9-3.7 | AAVDLSHFL (Nef 83-91) | C*03 | 0.94 (0.11) | 2 |
| S16-RY11-10.41 | RRQDILDLWVY (Nef 105-115) | C*07 | 1.05 (0.10) | 3 |
CTL clones were tested as described in Figure 1, comparing suppression of Nef-competent (NL4-3 wild-type Nef) to Nef-defective (the same virus with either a large deletion in nef or a mutation resulting in a methionine to alanine mutation at amino acid 20, M20A) HIV-1 for approximately 7 days. The effect of Nef was calculated as an inhibition ratio, as described in Figure 1 (mean, SD, and number of repeats given when multiple independent experiments were performed with the same clone).