HLA class I allele–associated HIV-1 polymorphisms occurring within or flanking known CTL epitopes in chronically clade C–infected South Africans
| HIV-1 subregion . | Common mutationsa . | Defined epitopesb . | Specific HLA-I associationc . |
|---|---|---|---|
| Gag-p17 | EKIRLRPGGKKHYML | RY10 (Gag 20–29) | B*4201, P = 1.1 × 10−4; q = 0.07 |
| EKIRLRPGGKKHYML | RY10 (Gag 20–29) | B*4201, P = 1.7 × 10−4; q = 0.17 | |
| Gag-p24 | HQAISPRTLNAWVKV | IW9 (Gag 147–155) | B*5703, P = 2.5 × 10−14; q = 0 |
| HQAISPRTLNAWVKV | IW9 (Gag 147–155) | B*5703, P = 1.6 × 10−8; q = 0 | |
| QAISPRTLNAWVKVI | SV9 (Gag 148–156) | B*8101, P = 2.8 × 10−3; q = 0.15 | |
| IEEKAFSPEVIPMFT | KF11 (Gag 162–171) | B*5703, P = 1.4 × 10−15; q = 0 | |
| IEEKAFSPEVIPMFT | KF11 (Gag 162–171) | B*5703, P = 2.9 × 10−4; q = 0.04 | |
| EGATPQDLNTMLNTV | TL9 (Gag 180–188) | B*8101, P = 4.3 × 10−7; q = 0 | |
| EGATPQDLNTMLNTV | TL9 (Gag 180–188) | B*8101, P = 3.6 × 10−5; q = 0.01 | |
| EGATPQDLNTMLNTV | TL9 (Gag 180–188) | B*8101, P = 1.9 × 10−3; q = 0.11 | |
| AGTTSTLQEQIAWMT | TW10 (Gag 240–249) | B*57/5801, P = 1.9 × 10−28; q = 0 | |
| AGTTSTLQEQIAWMT | TW10 (Gag 240–249) | B*5703, P = 1.7 × 10−5; q = 0 | |
| TSNPPIPVGDIYKRW | PY9 (Gag 254–262) | B*35, P = 1.1 × 10−7; q = 0 | |
| DYVDRFFKTLRAEQA | DA9 (Gag 298–306) | B*1401, P = 2.5 × 10−11; q = 0 | |
| FRDYVDRFFKTLRAE | YL9 (Gag 296–304) | Cw*0304, P = 3 × 10−4; q = 0.04 | |
| RAEQATQDVKNWMTD | QW9 (Gag 308–316) | B*5801, P = 3.7 × 10−7; q = 0 | |
| RAEQATQDVKNWMTD | AW11 (Gag 306–316) | B*4403, P = 3 × 10−9; q = 0.03 | |
| TILRALGPGATLEEM | RL9 (Gag 335–343) | Cw*08, P = 9.3 × 10−4; q = 0.09 | |
| TILRALGPGATLEEM | RL9 (Gag 335–343) | Cw*08, P = 8.5 × 10−4; q = 0.09 | |
| GVGGPGHKARVLAEA | GL9 (Gag 355–363) | B*0702/05, P = 6.7 × 10−10; q = 0.03 | |
| Nef | EEEEEVGFPVRPQVP | EV11 (Nef 65–75) | B*4501, P = 8.3 × 10−9; q = 0 |
| FPVRPQVPLRPMTYK | RM9 (Nef 72–80) | B*0702, P = 10−9; q = 0 | |
| FPVRPQVPLRPMTYK | RM9 (Nef 72–80) | B*8101, P = 1.8 × 10−10; q = 0 | |
| RPQVPLRPMTYKAAF | VY8 (Nef 74–81) | B*35, P = 1.1 × 10−7; q = 0 | |
| MTYKAAFDLSFFLKE | KF9 (Nef 82–90) | B*57/5801, P = 7.3 × 10−6; q = 0.07 | |
| FFLKEKGGLEGLIYS | KL9 (Nef 91–100) | B*4403, P = 1.9 × 10−8; q = 0 | |
| YSKKRQEILDLWVYH | KY11 (Nef 105–115) | Cw*0701, P = 7.9 × 10−7; q = 0 | |
| YSKKRQEILDLWVYH | KY11 (Nef 105–115) | B*18, P = 1.4 × 10−9, q = 0 | |
| GVRYPLTFGWCFKLV | YF9 (Nef 135–143) | B*35, P = 6.7 × 10−6; q = 0 | |
| PGVRYPLTFGWCFKL | RW8 (Nef 134–141) | A*2402, P = 10−4; q = 0.20 | |
| PGVRYPLTFGWCFKL | RW8 (Nef 134–141) | A*2301, P = 6.8 × 10−12; q = 0 |
| HIV-1 subregion . | Common mutationsa . | Defined epitopesb . | Specific HLA-I associationc . |
|---|---|---|---|
| Gag-p17 | EKIRLRPGGKKHYML | RY10 (Gag 20–29) | B*4201, P = 1.1 × 10−4; q = 0.07 |
| EKIRLRPGGKKHYML | RY10 (Gag 20–29) | B*4201, P = 1.7 × 10−4; q = 0.17 | |
| Gag-p24 | HQAISPRTLNAWVKV | IW9 (Gag 147–155) | B*5703, P = 2.5 × 10−14; q = 0 |
| HQAISPRTLNAWVKV | IW9 (Gag 147–155) | B*5703, P = 1.6 × 10−8; q = 0 | |
| QAISPRTLNAWVKVI | SV9 (Gag 148–156) | B*8101, P = 2.8 × 10−3; q = 0.15 | |
| IEEKAFSPEVIPMFT | KF11 (Gag 162–171) | B*5703, P = 1.4 × 10−15; q = 0 | |
| IEEKAFSPEVIPMFT | KF11 (Gag 162–171) | B*5703, P = 2.9 × 10−4; q = 0.04 | |
| EGATPQDLNTMLNTV | TL9 (Gag 180–188) | B*8101, P = 4.3 × 10−7; q = 0 | |
| EGATPQDLNTMLNTV | TL9 (Gag 180–188) | B*8101, P = 3.6 × 10−5; q = 0.01 | |
| EGATPQDLNTMLNTV | TL9 (Gag 180–188) | B*8101, P = 1.9 × 10−3; q = 0.11 | |
| AGTTSTLQEQIAWMT | TW10 (Gag 240–249) | B*57/5801, P = 1.9 × 10−28; q = 0 | |
| AGTTSTLQEQIAWMT | TW10 (Gag 240–249) | B*5703, P = 1.7 × 10−5; q = 0 | |
| TSNPPIPVGDIYKRW | PY9 (Gag 254–262) | B*35, P = 1.1 × 10−7; q = 0 | |
| DYVDRFFKTLRAEQA | DA9 (Gag 298–306) | B*1401, P = 2.5 × 10−11; q = 0 | |
| FRDYVDRFFKTLRAE | YL9 (Gag 296–304) | Cw*0304, P = 3 × 10−4; q = 0.04 | |
| RAEQATQDVKNWMTD | QW9 (Gag 308–316) | B*5801, P = 3.7 × 10−7; q = 0 | |
| RAEQATQDVKNWMTD | AW11 (Gag 306–316) | B*4403, P = 3 × 10−9; q = 0.03 | |
| TILRALGPGATLEEM | RL9 (Gag 335–343) | Cw*08, P = 9.3 × 10−4; q = 0.09 | |
| TILRALGPGATLEEM | RL9 (Gag 335–343) | Cw*08, P = 8.5 × 10−4; q = 0.09 | |
| GVGGPGHKARVLAEA | GL9 (Gag 355–363) | B*0702/05, P = 6.7 × 10−10; q = 0.03 | |
| Nef | EEEEEVGFPVRPQVP | EV11 (Nef 65–75) | B*4501, P = 8.3 × 10−9; q = 0 |
| FPVRPQVPLRPMTYK | RM9 (Nef 72–80) | B*0702, P = 10−9; q = 0 | |
| FPVRPQVPLRPMTYK | RM9 (Nef 72–80) | B*8101, P = 1.8 × 10−10; q = 0 | |
| RPQVPLRPMTYKAAF | VY8 (Nef 74–81) | B*35, P = 1.1 × 10−7; q = 0 | |
| MTYKAAFDLSFFLKE | KF9 (Nef 82–90) | B*57/5801, P = 7.3 × 10−6; q = 0.07 | |
| FFLKEKGGLEGLIYS | KL9 (Nef 91–100) | B*4403, P = 1.9 × 10−8; q = 0 | |
| YSKKRQEILDLWVYH | KY11 (Nef 105–115) | Cw*0701, P = 7.9 × 10−7; q = 0 | |
| YSKKRQEILDLWVYH | KY11 (Nef 105–115) | B*18, P = 1.4 × 10−9, q = 0 | |
| GVRYPLTFGWCFKLV | YF9 (Nef 135–143) | B*35, P = 6.7 × 10−6; q = 0 | |
| PGVRYPLTFGWCFKL | RW8 (Nef 134–141) | A*2402, P = 10−4; q = 0.20 | |
| PGVRYPLTFGWCFKL | RW8 (Nef 134–141) | A*2301, P = 6.8 × 10−12; q = 0 |
These data are taken from 59 HLA associations (q < 0.2) defined in a clade C South African cohort (unpublished data), in which analysis of gag sequences was performed using data from 672 study subjects and analysis of nef sequences was performed using data from 443 study subjects. The Los Alamos National Laboratory HIV Molecular Immunology Database (available at http://www.hiv.lanl.gov/content/index) was used to define known CTL epitopes.
HLA-associated mutations (bolded) shown in the context of the known CTL epitopes (underlined).
Defined CTL epitopes with amino acid residues based on the HXB2 sequences in parentheses.
Methods for calculating p- and q-values have been previously described (reference 16).