Table 1.
CD8+ T lymphocyte escape mutations engineered into three separate mutant SIVmac239 viruses
| MHC-I allele | Mutant virus | Epitope | SIVmac239 sequence | Mutant sequencea | Comment code(s)b |
|---|---|---|---|---|---|
| Mamu-A1*00101 | 14x-SIVmac239 | Gag372-379LF8 | LAPVPIPF | - - - G- - - - | 1 |
| Pol625-633SV9 | STPPLVRLV | - - - - - - - -A | 1 | ||
| Vif100-107VI8 | VTPNYADI | - - - - - - -T | 1 | ||
| Tat28-35SL8 | STPESANL | P- - - - - - P | 1 | ||
| Env233-241CL9 | CAPPGYALL | - - - - -FV- - | 1 | ||
| Env620-628TL9 | TVPWPNASL | - - - - - - - -I | 1 | ||
| Env726-735ST10 | SSPPSYFQQT | - - - - - - - - - I | 1 | ||
| Mamu-A1*00201 | 14x-SIVmac239 | Gag71-79GY9 | GSENLKSLY | S-D- - - - - - | 1 |
| Env788-795RY8 | RTLLSRVY | - - - -L- - - | 1 | ||
| Nef159-167YY9 | YTSGPGIRY | - - - - - - - -F | 1 | ||
| Nef221-229YY9 | YTYEAYVRY | H- - - - - - - - | 1 | ||
| Mamu-A1*01101 | 14x-SIVmac239 | Pol92-100AL9 | AERKQREAL | -G- - - - - - - | 1 |
| Env495-502GI8 | GDYKLVEI | - - - -V- - - | 1 | ||
| Nef124-132KI9 | KEKGGLEGI | -Q- - - - - - - | 1 | ||
| Mamu-B*00801 | 11x-SIVmac239 | Vif123-131RL9 | RRAIRGEQL | -K- - - - - - - | 2 |
| Vif172-179RL8 | RRDNRRGL | -G- - - - - - | 2 | ||
| Vpr62-70IF9 | IRILQRALF | -K- - - - - - - | 3 | ||
| Rev12-20KL9 | KRLRLIHLL | -K- - - - - - - | 3 | ||
| Rev44-51RL8 | RRRWQQLL | -K- - - -I- | 2, 3 | ||
| Env573-581KL9 | KRQQELLRL | - - - - - - - -M | 2 | ||
| Env868-876RL9 | RRIRQGLEL | - - - - - - - -R | 4 | ||
| Nef8-16RL9 | RRSRPSGDL | - - - -Q- - - - | 2 | ||
| Nef137-146RL10 | (A)RRHRILDIYL | (P)- - - - - - - - - - | 2, 5 | ||
| Nef245-253RL9 | RRRLTARGL | KK- - - - - - I | 2, 3 | ||
| Nef246-254RL9 | RRLTARGLL | K- - - - - - II | 2 | ||
| Mamu-B*01701 | 5x-SIVmac239 | Vif66-73HW8 | HLEVQGYW | Y- - - - - - - | 6 |
| cRW9 | RHLAFKCLW | - - - - - - - -R | 7 | ||
| Env830-838FW9 | FHEAVQAVW | -Y- - - - - - - | 6 | ||
| Nef165-173IW9 | IRYPKTFGW | T- - - -I- - - | 8 | ||
| Nef195-203MW9 | MHPAQTSQW | V- - - - - - - - | 6 |
Dashes indicate residues identical to the wild-type sequence.
Comments: 1, MHC-I allele-specific variation observed in sequences published in reference 36 and in sequences found in File S1 in the supplemental material; 2, variant published in reference 26; 3, previously unpublished variant discovered during chronic SIVmac239 infection in Mamu-B*00801-positive macaques; 4, variation in Mamu-B*00801 anchor residue observed in an HIV-2 sequence from the Los Alamos National Laboratory online HIV sequence database (www.hiv.lanl.gov); 5, putative processing mutation (extraepitopic variant published in references 22 and 24); 6, variant published in reference 29; 7, cryptic reading frame variant published in reference 28; 8, variant published in reference 16.