Table 3.
Nef mutations with significant frequency changes across VE and VL and their associated epitopes
| Patient | Mutation | Frequency (%) | Epitope | ||||
|---|---|---|---|---|---|---|---|
| VE | VL | HLA | Position | Sequence | Location | ||
| EC11 | V133P | 70.7 | 99.4 | B49 | Nef (136–145) | PLTFGWCYKL | A |
| F191 V | 85.5 | 60.2 | B81 | Nef (183–192) | WRFDSRLAFH | I | |
| EC42 | V10R | 99.0 | 8.4 | B15 | Nef (13–20) | WPAIRERM | A |
| V10 K | 0.0 | 91.0 | B15 | Nef (13–20) | WPAIRERM | A | |
| G12R | 0.0 | 90.4 | B15 | Nef (13–20) | WPAIRERM | A | |
| M79I | 0.0 | 89.6 | B51/B15 | Nef (72–81)/Nef (75–82) | PQVPLRPMTY/PLRPMTYK | I | |
| N126S | 99.2 | 0.0 | B51 | Nef (120–128) | YFPDWQNYT | I | |
| Y135F | 99.2 | 10.4 | B15 | Nef (137–145) | LTFGWCFKL | A | |
| G140R | 0.0 | 88.5 | B15 | Nef (137–145) | LTFGWCFKL | I | |
| V148I | 99.2 | 0.7 | B15 | Nef (137–145) | LTFGWCFKL | A | |
| EC18 | K92R | 0.0 | 68.5 | B07 | Nef (83–91)/Nef (90–97) | AAVDLSHFL/FLKEKGGL | A/I |
| VC06 | V85I | Va | 45.2 | B15 | Nef (84–92) | AVDLSHFLK | I |
| V85L | Va | 28.3 | B15 | Nef (84–92) | AVDLSHFLK | I | |
| L87I | La | 56.9 | B15 | Nef (84–92) | AVDLSHFLK | I | |
| R105 K | Ra | 74.7 | B15 | Nef (106–114) | RQDILDLWI | A | |
| I114 V | Ia | 60.3 | B15 | Nef (106–114)/Nef (116–124) | RQDILDLWI/HTQGYFPDW | I/A | |
| VC10 | T15A | 59.2 | 98.5 | B15 | Nef (13–20) | WPTVRERM | I |
| E182Q | 99.9 | 17.8 | B15 | Nef (183–191) | WRFDSRLAF | A | |
| E182L | 0.0 | 81.8 | B15 | Nef (183–191) | WRFDSRLAF | A | |
| R188G | 99.8 | 90.9 | B15/B52 | Nef (183–191)/Nef (188–196) | WRFDSRLAF/RLAFHHVAR | I | |
| VC14 | T71R | 94.5 | 3.3 | B42 | Nef (71–79) | RPQVPLRPM | I |
| I101 V | 5.2 | 96.8 | B44 | Nef (92–100) | KEKGGLEGL | A | |
| H102Y | 4.9 | 97.1 | B44 | Nef (92–100)/Nef (105–115) | KEKGGLEGL/KRQEILDLWVY | A | |
| H102 N | 2.0 | 0.0 | B44 | Nef (92–100)/Nef (105–115) | KEKGGLEGL/KRQEILDLWVY | A | |
| H116 N | 94.5 | 2.4 | B44 | Nef (105–115) | KRQEILDLWVY | A | |
| P129Q | 5.7 | 96.5 | B42 | Nef (128–137) | TPGPGVRYPL | I | |
| V133I | 5.2 | 96.5 | B42 | Nef (128–137) | TPGPGVRYPL | I | |
| VC15 | V85L | 66.8 | 99.5 | B57 | Nef (82–90) | KAAFDLSFF | I |
| H102Y | 68.4 | 99.7 | B57 | Nef (105–115) | KRQEILDLWVY | A | |
| VC16 | Y81F | 54.3 | 47.6 | B57 | Nef (82–90) | KAAFDLSFF | A |
| H89Y | 0.0 | 29.3 | B57 | Nef (82–90)/Nef (90–97) | KAAFDLSFF/FLKEKGGL | I/A | |
| H102Y | 99.9 | 48.6 | B14/B57 | Nef (105–113)/Nef (105–115) | QRQDILDLW/KRQEILDLWVY | A | |
| H116 N | 63.4 | 63.1 | B57 | Nef (105–115)/Nef (116–124) | KRQEILDLWVY/HTQGYFPDW | A/I | |
| V133T | 99.4 | 13.3 | B57 | Nef (127–135) | YTPGPGIRY | I | |
| V133I | 0.0 | 74.3 | B57 | Nef (127–135) | YTPGPGIRY | I | |
aConsensus amino acid from the available bulk sequence shown instead of frequency; Location A—adjacent to epitope; Location I—within epitope