Table 1.
Associations between supertype members and polymorphisms in optimal epitopes at a q value of <0.2
| Protein | Epitope | Sequence |
Location | HLAc | Associationsd | Supertype(s)e | |
|---|---|---|---|---|---|---|---|
| Optimala | Consensusb | ||||||
| Gag | KK9 | KIRLRPGGK | KIRLRPGGK | 18–26 | A*03:01 | A*03:01(R18K, K28X), A*30:01(X20S, C/K28Q), A*31:01(X18Q), A*33:01(X18Q, X28Q), A*74:01(R20K, R28X, Q30X) | A3 |
| RLRPGGKKK | RLRPGGKKH | 20–28 | |||||
| RLRPGGKKKY | RLRPGGKKHY | 20–29 | |||||
| KW9 | KYKLKHIVW | HYMLKHLVW | 28–36 | A*24:02 | A*23:01(R28X, L34I), A*24:02(R28X) | A24 | |
| RY11 | RSLYNTVATLY | RSLYNTVATLY | 76–86 | A*30:02, B58, B63 | A*01:01(E73K, Y79F/H), A*29:02(L85I), A*29:11(C87X), A*30:02(T81A), A*36:01(Y79H), B*58:02(C87X) | A1, A24 | |
| LY9 | LYNTVATLY | LYNTVATLY | 78–86 | A*29:02, B*44:03 | A*01:01(Y79F/H), A*29:02(L85I), A*29:11(C87X), A*30:02(T81A), A*36:01(Y79H) | A1, A24 | |
| TK8 | TLYCVHQK | TLYCVHEK | 84–91 | A*11:01 | A*03:01(X91S), A*34:02(K90R), A*68:01(K90X), A*66:03(T81A, A83V), A*74:01(R91K, V94I) | A3 | |
| IL10 | IEIKDTKEAL | IEVRDTKEAL | 92–101 | B*40:01 | B*41:01(E93V), B*44:03(X91Q), B*45:01(E93X) | B44 | |
| VL10 | VHQAISPRTL | VHQAISPRTL | 143–152 | B*15:10 | B*14:02(V143I, L147I), B*15:10(A146S) | B27 | |
| IW9 | ISPRTLNAW | ISPRTLNAW | 147–155 | B*57:01, B63 | B*57:02(A146P, I147L), B*57:03(A146P, I147L/M), B*58:01(X146P), B*58:02(S146X) | B58 | |
| KF11 | KAFSPEVI | KAFSPEVI | 162–169 | B*57:03 | B*57:03(X161D, A163G/S, S165K/N), B*58:01(V168X) | B58 | |
| KAFSPEVIPMF | KAFSPEVIPMF | 162–172 | |||||
| EL9 | EVIPMFSAL | EVIPMFTAL | 167–175 | A*26:01 | A*26:01(V168X, T173 M), A*29:02(X173 M) | A1 | |
| TL9 | TPQDLNTML | TPQDLNTML | 180–188 | B*07:02, B*39:10, B*42:01, B*81:01, C*08:02 | B*39:10(E177D, T186X), B*42:01(X182T), B*67:01(T190A), C*08:02(X182H), B*81:01(E177D, Q/T182E/G/S, T186S, L188F, T190X, V191I) | B7 | |
| TPYDINQML | TPQDLNTML | ||||||
| TW10 | TSTLQEQIGW | TSTLQEQIAW | 240–249 | B*57:01, B*58:01 | B*57:02(T242N, X247 M), B*57:03(T242N, I247V), B*58:01(T242N, L243X, X248A) | B58 | |
| NY10 | NPPIPVGDIY | NPPIPVGDIY | 253–262 | B*35:01 | B*35:01(D260E), B*39:10(I250 M), B*53:01(X256T, R264X), B*81:01(X252A) | B7 | |
| QW9 | QASQEVKNW | QATQDVKNW | 308–316 | B*53:01, B*57:01 | B*53:01(A309X, N315G), B*58:01(S309A, T310S) | ||
| Pr | DL9 | DTVLEEWNL | DTVLEEINL | 30–38 | A*68:02 | A*02:02(X39S), A*02:05(X36V) | A2 |
| RT | AM9 | ALVEICTEM | ALTAICEEM | 33–41 | A*02:01 | A*02:01(X35I, X36V, X40D), A*02:02(E36A, X41I) | A2 |
| TI8 | TAFTIPSI | TAFTIPSI | 128–135 | B*51:01 | B*51:01(I135T), B*81:01(X134G) | B7 | |
| KY9 | KQNPDIVIY | AQNPEIVIY | 173–181 | A*30:02 | A*29:02(178X), A*30:01(E173X), A*36:01(X178V) | A1 | |
| IL9 | IEELRQHLL | IEELREHLL | 202–210 | B*40:01 | B*18:01(E207X), B*44:03(E204X, E207K/N) | B44 | |
| QR9 | QIYPGIKVR | QIYPGIKVR | 269–277 | A*03:01 | A*03:01(K277R), A*30:01(Q278X), A*33:03(X273R), A*34:02(R275X) | A3 | |
| IW9 | IAMESIVIW | IAMESIVIW | 375–383 | B*58:01 | B*15:16(X386V), B*58:01(I375V, X377Q/T, X379A) | B58 | |
| EY9 | ETKLGKAGY | ETKIGKAGY | 449–457 | A*26:01 | A*26:01(K451R, M452X), A*29:01(T450N) | A1 | |
| Nef | RM9 | RPQVPLRPM | RPQVPLRPM | 71–79 | B*42:01, B*07:02 | B*35:01(Y81F), B*81:01(X71T, L76T/V) | B7 |
| TPQVPLRPM | RPQVPLRPM | ||||||
| QK10 | QVPLRPMTYK | QVPLRPMTYK | 73–82 | A*03:01, A*11:01 | A*03:01(A83G, X85L), A*33:01(X71K), A*34:02(A83G), A*66:03(V70I), A*68:01(X82Q) | A3 | |
| RL9 | VPLRPMTY | VPLRPMTY | 74–81 | B*35:01, B*07:02 | B*35:01(Y81F), B*81:01(X71T, L76T/V) | B7 | |
| RPMTYKAAL | RPMTYKAAF | 77–85 | |||||
| PK8 | PLRPMTYK | PLRPMTYK | 75–82 | A*11:01 | A*03:01(A83G, X85L), A*34:02(A83G), A*68:01(X82Q) | A3 | |
| KL10 | KAAFDLSFFL | KAAFDLSFFL | 82–91 | B*57:03 | B*57:02(A83X), B*57:03(A83X), B*58:01(A83G) | B58 | |
| AK9 | AVDLSHFLK | AFDLSFFLK | 84–92 | A*03:01, A*11:01 | A*03:01(A83G, X85L), A*34:02(A83G), A*68:01(X82Q) | A3 | |
| HW9 | HTQGYFPDW | HTQGFFPDW | 116–124 | B*57:01 | B*57:03(H116N), B*58:01(X116N) | B58 | |
| TL10 | TPGPGVRYPL | TPGPGVRYPL | 128–137 | B*07:02, B*42:01 | B*35:01(V133T), B*53:01(V133I) | B7 | |
| RW8 | RYPLTFGW | RYPLTFGW | 134–141 | A*24:02 | A*23:01(F143Y), A*24:02(Y135F/L) | A24 | |
| YY9 | YPLTFGWCY | YPLTFGWCF | 135–143 | B*18:01, B*53:01 | B*35:01(V133T), B*53:01(V133I) | B7 | |
Optimally defined epitopes as defined at http://www.hiv.lanl.gov/content/immunology/tables/optimal_ctl_summary.html. Only optimal epitopes that were restricted by least two HLA alleles are shown. Overlapping optimals with published alleles in the same supertype are grouped together.
Consensus in the present cohort. Underlining marks differences from published optimal epitope.
HLA alleles associated with the epitope as defined in the optimal epitope definitions.
HLA alleles that are related to the published alleles via supertype were tested for associations with polymorphisms within or flanking the optimal epitope. Associations are of the form (YposZ), where Y is a residue that is negatively associated with the HLA allele and Z is a residue that is positively associated with the allele. X indicates no association in the positive/negative direction. All associations with a q value of <0.2 are reported.
Supertypes that are represented by HLA alleles that are associated with escape.