Table 2.
Longitudinal autologous epitope sequence data.
| Patient | Clade B consensus epitope sequence(s) | Autologous epitope sequence(s)1 | |||||
|---|---|---|---|---|---|---|---|
|
MM7 |
HLA-A3 RLRPGGKKK (Gag p17 20-28) |
d23 RLRPGGKKK |
d87 RLRPGGKKK |
d553 RLRPGGKKK |
d766 RLRPGGKKR |
d934 RLRPGGKKR |
|
| HLA-A3 QVPLRPMTYK (Nef 73-82) | QVPLRPMTYK | QVPLRPMT/NYK2 | QVPLRPMT/NYK | QVPL/VRPMT/NYK | QVPL/VGPMTYK | ||
|
MM9 |
HLA-B8 FLKEKGGL (Nef 90-97) |
d26 FLKEKGGL |
d54 FLKEKGGL |
d105 FLKEKGGL |
d273 FLKEKGGL |
d343 FLKEKGGL |
|
| HLA-Cw07 KRQDILDLWVY (Nef 105-115) | KRQDILDLWVY | KRQD/EILDLWVY | KRQD/EILDLWVY | RRQEILDLWVY | RRQEILDLWVY | ||
|
MM12 |
HLA-A3 QVPLRPMTYK (Nef 73-82) |
d16 QVPLRPMTYK |
d40 QVPLRPMTYK |
d139 QVPLRPMTYK |
d230 QVPLRPMTYK |
d321 QVPLRPMTYK |
d487 QVPLRPMTYK |
| HLA-A3 QIYAGIKVK (RT 269-277) | QIYAGIKVK | QIYAGIKVK | QIYAGIKVR | QIYAGIKVR | QIYAGIKVR | QIYAGIKVR | |
|
MM13 |
HLA-B8 FLKEKGGL (Nef 90-97) |
d16 FLKEKGGL |
d45 FLKEKGGL |
d96 FLKEK/EGGL |
d275 FLKEEGGL |
d544 FLKEEGGL |
|
| HLA-B57 KAFSPEVIPMF (Gag p24 30-40) | KAFSPEVIPMF | KAFSPEVIPMF | KAFSPEVIPMF | KAFSPEVIPMF | KAFSPEVIPMF | ||
| HLA-B57 HTQGYFPDWQ (Nef 116-125) | HTQGYFPDWQ | HTQGYFPDWQ | HTQGYFPDWQ | HTQGYFPDWQ | HTQGYFPDWQ | ||
|
MM26 |
HLA-B7 KPQVPLRPMTY (Nef 71-81) |
d55 KPQVPLRPMTY |
d169 RPQVPLRPMTY |
d253 RPQVPLRPMTY |
d415 RPQVPLRPMTY |
||
| HLA-A2 YTAFTIPSI (RT 127-135) | YTAFTIPSI | YTAFTIPSI/T | YTAFTIPST | YTAFTIPST | |||
|
MM27 |
HLA-A2 YTAFTIPSI (RT 127-135) |
d28 YTAFTIPSV |
d53 YTAFTIPSV |
d81 YTAFTIPSV |
d299 YTAFTIPSV/I |
d466 YTAFTIPSI |
|
|
MM28 |
HLA-A11 AAVDLSHFLK (Nef 83-92) |
d9 AAVDLSHFLK |
d34 AALDLSHFLK |
d198 AALDLSHFLK |
d405 GALDLSHFLK |
||
|
MM33 |
HLA-B44 EEMNLPGRW (Protease 34-42) |
d12 EEMNLPGRW |
d96 EDMNLPGRW |
d201 EDMNLPGRW |
d391 EDMNLPGRW |
||
|
MM34 |
HLA-B35 DPNPQEVVL (Gp160 78-86) |
d17 DPNPQEVVL |
d45 DPNPQEVVL |
d192 DPN/SPQEVVL |
d353 DPN/SPQEVVL |
||
| HLA-A24 RYPLTFGWCF (Nef 134-143) | RYPLTFGWCF | RYPLTFGWCF | RFPLTFGWCF | RFPLTFGWCF | |||
|
MM39 |
HLA-A3 RLRPGGKKK (Gag p17 20-28) |
d11 RLRPGGKKK |
d92 RLRPGGKKK |
d179 RLRPGGKKK |
d358 RLRPGGKKK |
||
| HLA-A3 QVPLRPMTYK (Nef 73-82) | QVPLRPMTYK | QVPLRPMTYK | QVPLRPMTYK | QVPLRPMTYK | |||
|
MM43 |
HLA-B40 KEKGGLEGL (Nef 92-100) |
d21 KEKGGLEGL |
d101 KEKGGLEGL |
d228 KEKGGLEGL |
d368 KEKGGLEGL |
||
| HLA-A2 ALQDSGLEV (RT 485-493) | ALQDSGLEV | ALQDSGLEV | ALQDSGLEV | ALQDSGLEV | |||
| HLA-A2 LEWRFDITL (Nef 181-189) | LEWRFDITL | LEWRFDITL | LE/Q/P/AWRFDITL | LAWRFDITL | |||
|
MM45 |
HLA-A3 RLRPGGKKK (Gag p17 20-28) |
d22 RLRPGGKKK |
d87 RLRPGGKKK |
d213 RLRPGGKKK |
|||
|
MM46 |
HLA-A2 LVWKFDSRL (Nef 181-189) |
d5 LVWKFDSRL |
d56 LVWKFDSRL |
d175 LVWKFDSRL |
d530 LVWKFDSRL |
||
| HLA-A11 RLAFHHVAR (Nef 188-196) | RLAFHHVAR | RLAFHHVAR | RLAFHHAAR | RLAFHHAAR | |||
|
MM47 |
HLA-B14 ERYLKDQQL (Gp160 584-592) |
d28 ERYLKDQQL |
d57 ERYLKDQQL |
d84 ERYLQDQQL |
d113 ERYLKDQQL |
d217 ERYLQDQQL |
d402 ERYLQDQQL |
| HLA-A24 RYPLTFGWCY (Nef 134-143) | RYPLTFGWCY | RFPLTFGWCY | RFPLTFGWCY | RFPLTFGWCY | RFPLTFGWCY | RFPLTFGWCY | |
|
MM48 |
HLA-B27 KRWIIMGLNK (Gag p24 131-140) |
d22 KRWIIMGLNK |
d50 KRWIIMGLNK |
d113 KRWIIMGLNK |
d204 KRWIIM/LGLNK |
||
| HLA-A24 RYPLTFGWCF (Nef 134-143) | RYPLTFGWCF | RYPLTFGWCF | RYPLTFGWCF | RYPLTFGWCF | |||
|
MM51 |
HLA-B13 RQANFLGKI (Gag p2p7p1p6 66-74) |
d18 RQANFLGKI |
d86 RQANFLGKI |
d207 RQANFLGKI |
d389 RQANFLGKI |
||
|
MM55 |
HLA-B14 DRFYKTLRAEQ (Gag p24 166-176) |
d31 DRFYKTLRAEQ |
d94 DRFYKTLRAEQ |
d227 DRFYKTLRAEQ |
d347 DRFYKTLRAEQ |
||
| HLA-B14 ERYLKDQQL (Gp160 584-592) | ERYLKDQQL | ERYLKDQQL | ERYLKDQQL | ERYLKDQQL | |||
| Unknown RDISGWILSTY (Rev 53-63) | RDISGWILSTY | RDISGWILSTY | RDISGWILSTY | RDISGWILST/AY | |||
|
MM56 |
HLA-B57 TSTLQEQIGW (Gag p24 108-117) |
d14 TSTLQEQIGW |
d75 TSTLQEQIGW |
d186 TSNLQEQIGW |
d375 TSNLQEQIGW |
||
1 The autologous virus sequence of the epitope at the indicated timepoint (day (d) FOSx is shown. Areas of amino acid variation within the epitope are indicated in bold italics and underlined.