CEs predicted based on HLA-I–associated HIV-1 polymorphisms
| ARF | Protein | HLA | Best epitopea | Peptide | PPb | PHIc | CHIc |
| % | |||||||
| 2 | pol | B*3910 | −−−ELKTFGRF+−−− | EF8 | 30 | 1 (0) | 0 (0) |
| 3 | gag | A*01 | −−−SSHANvKRY−−− | SY9* | 54 | 7 (0) | 7 (0) |
| 3 | pol | B*15 | −−−YRYSISRtY−−− | YY9 | 40 | 1 (0) | 3 (0) |
| 3 | pol | C*07 | −−−YRfSISRAY−−− | YY9* | 20 | 13 (1) | 17 (1) |
| 3 | pol | C*07 | −−−NLWKKGYRf−−− | NF9 | 30 | 13 (0) | 17 (2) |
| 4 | pol | A*3001 | −−−FcFPPWYYL−−− | FL9 | 51 | 2 (0) | 9 (0) |
| 4 | pol | A*34 | −−−NIPCFSYf−−−− | NF8* | 26 | 2 (0) | 4 (0) |
| 4 | pol | B*15 | −−−LCFYVATgY−−− | LY9 | 31 | 1 (0) | 3 (2) |
| 4 | pol | B*35 | −−+SPAILFWQL−−− | SL9 | 30 | 4 (0) | 7 (0) |
| 4 | pol | B*42 | −−−LPKSDLREv−−− | LV9 | 51 | 1 (0) | 2 (0) |
| 5 | pol | A*0205 | −−−SVnCFTSLV−−− | SV9* | 35 | 14 (0) | 20 (0) |
| 5 | gag | A*3001 | −+−CLQPSDVSK−−− | CK9* | 29 | 2 (1) | 9 (0) |
| 5 | pol | A*3002 | −+−AYFPVFRFL−−− | AL9* | 28 | 2 (0) | 9 (1) |
| 5 | pol | A*33 | −−−TGHLPANF+−−− | TF8 | 26 | 1 (0) | 4 (0) |
| 5 | nef | A*6801 | −−−SLTaGHPTM−−− | SM9 | 30 | 1 (0) | 8 (0) |
| 5 | gag | B*08 | −−−FPHFQQPf−−−− | FF8* | 36 | 5 (1) | 9 (0) |
| 5 | pol | B*35 | −−−IPNAYcESV−−− | IV9 | 42 | 4 (0) | 7 (1) |
| 5 | pol | B*5802 | −−−ASFIWPPTF−+− | AF9 | 40 | 4 (1) | 5 (1) |
| 5 | gag | C*0801 | −−−NVAPGPNAL−−+ | NL9* | 58 | 1 (0) | 2 (0) |
| 5 | pol | C*0804 | −−+FPTNFCISL−−− | FL9 | 27 | 1 (0) | 2 (0) |
| 5 | pol | C*18 | −−−DPTYkSSI−−− | DI8* | 26 | 0 (0) | 1 (0) |
| 6 | pol | A*0205 | −−+SLLVHVWLPL−− | SL10 | 29 | 14 (1) | 20 (1) |
| 6 | pol | A*29 | −−−NMHPPHPVL−−+ | NL9 | 69 | 4 (0) | 1(1) |
| 6 | pol | B*5802 | −−−LPSPFLHkL−−− | LL9 | 28 | 4 (1) | 5 (2) |
| ARF | Protein | HLA | Best epitopea | Peptide | PPb | PHIc | CHIc |
| % | |||||||
| 2 | pol | B*3910 | −−−ELKTFGRF+−−− | EF8 | 30 | 1 (0) | 0 (0) |
| 3 | gag | A*01 | −−−SSHANvKRY−−− | SY9* | 54 | 7 (0) | 7 (0) |
| 3 | pol | B*15 | −−−YRYSISRtY−−− | YY9 | 40 | 1 (0) | 3 (0) |
| 3 | pol | C*07 | −−−YRfSISRAY−−− | YY9* | 20 | 13 (1) | 17 (1) |
| 3 | pol | C*07 | −−−NLWKKGYRf−−− | NF9 | 30 | 13 (0) | 17 (2) |
| 4 | pol | A*3001 | −−−FcFPPWYYL−−− | FL9 | 51 | 2 (0) | 9 (0) |
| 4 | pol | A*34 | −−−NIPCFSYf−−−− | NF8* | 26 | 2 (0) | 4 (0) |
| 4 | pol | B*15 | −−−LCFYVATgY−−− | LY9 | 31 | 1 (0) | 3 (2) |
| 4 | pol | B*35 | −−+SPAILFWQL−−− | SL9 | 30 | 4 (0) | 7 (0) |
| 4 | pol | B*42 | −−−LPKSDLREv−−− | LV9 | 51 | 1 (0) | 2 (0) |
| 5 | pol | A*0205 | −−−SVnCFTSLV−−− | SV9* | 35 | 14 (0) | 20 (0) |
| 5 | gag | A*3001 | −+−CLQPSDVSK−−− | CK9* | 29 | 2 (1) | 9 (0) |
| 5 | pol | A*3002 | −+−AYFPVFRFL−−− | AL9* | 28 | 2 (0) | 9 (1) |
| 5 | pol | A*33 | −−−TGHLPANF+−−− | TF8 | 26 | 1 (0) | 4 (0) |
| 5 | nef | A*6801 | −−−SLTaGHPTM−−− | SM9 | 30 | 1 (0) | 8 (0) |
| 5 | gag | B*08 | −−−FPHFQQPf−−−− | FF8* | 36 | 5 (1) | 9 (0) |
| 5 | pol | B*35 | −−−IPNAYcESV−−− | IV9 | 42 | 4 (0) | 7 (1) |
| 5 | pol | B*5802 | −−−ASFIWPPTF−+− | AF9 | 40 | 4 (1) | 5 (1) |
| 5 | gag | C*0801 | −−−NVAPGPNAL−−+ | NL9* | 58 | 1 (0) | 2 (0) |
| 5 | pol | C*0804 | −−+FPTNFCISL−−− | FL9 | 27 | 1 (0) | 2 (0) |
| 5 | pol | C*18 | −−−DPTYkSSI−−− | DI8* | 26 | 0 (0) | 1 (0) |
| 6 | pol | A*0205 | −−+SLLVHVWLPL−− | SL10 | 29 | 14 (1) | 20 (1) |
| 6 | pol | A*29 | −−−NMHPPHPVL−−+ | NL9 | 69 | 4 (0) | 1(1) |
| 6 | pol | B*5802 | −−−LPSPFLHkL−−− | LL9 | 28 | 4 (1) | 5 (2) |
CD8 T cell epitopes were predicted by Epipred. Bolded and underlined amino acids were recognized in primary (PHI) and chronic (CHI) HIV-1 infections, respectively. Lowercase letters and plus signs represent HLA-associated HIV-1 polymorphisms within and outside the predicted epitope, respectively. The asterisks indicate evidence for reversion in the predicted epitope.
Predicted epitope from an input 27mer sequence.
PP indicates the percent probability that the predicted epitope represents a real epitope.
Number of patients with the allele that were tested (number of responses).