TABLE 2.
Unrecognized epitopes are predominantly consensus sequencea
| Protein | Epitope | Autologous sequence (no. of clones/total) | Predominant sequence type |
|---|---|---|---|
| Gag | SLYNTVATL | --F------(17/17) | Variant |
| ELRSLYNTV | --K------ (17/17) | Variant | |
| SPRTLNAWV | --------- (16/16) | Consensus | |
| TPQDLNTML | ---------(17/17) | Consensus | |
| GPGHKARVL | ---------(16/17) | Consensus | |
| GPGHKARVL | ----I---- (1/17) | ||
| HPVHAGPIA | ---------(17/17) | Consensus | |
| DCKTILKAL | ---------(17/17) | Consensus | |
| RFAVNPGLL | --------- (8/8) | Consensus | |
| RDYVDRFYKTL | --------- (8/8) | Consensus | |
| DYVDRFYKTL | --------- (8/8) | Consensus | |
| QASQEVKNW | ----D---- (7/7) | Variant | |
| FLGKIWPSYK | --------H- (5/6) | Variant | |
| FLGKIWPSYK | -----R--H- (1/6) | ||
| Nef | PLTFGWCYKL | -------F-- (4/5) | Variant |
| PLTFGWCYKL | ---------- (1/5) | ||
| VLEWRFDSRL | --V-K---M- (2/5) | Variant | |
| VLEWRFDSRL | --V-K---K- (2/5) | ||
| VLEWRFDSRL | ---------- (1/5) | ||
| Pol | ALVEICTEM | --------- (3/5) | Consensus |
| ALVEICTEM | ---G----- (1/5) | ||
| ALVEICTEM | --------L (1/5) | ||
| VIYQYMDDL | --------- (5/5) | Consensus | |
| ILKEPVHGV | --------- (5/5) | Consensus | |
| ITLWQRPLV | --------- (5/5) | Consensus | |
| DTVLEEMNL | --------- (3/5) | Consensus | |
| DTVLEEMNL | -----D--- (2/5) | ||
| Vpr | AIIRILQQL | -LV-----M (2/4) | Variant |
| AIIRILQQL | --L------ (1/4) |
a
In subjects TCH-017 and TCH-066, 20 previously described optimal HIV-1 epitopes were unrecognized despite having the appropriate HLA class I restriction. The viral sequencing of isolates from these subjects is shown. The predominant viral sequence within 14 of these 20 unrecognized epitopes was identical to that of the described optimal epitope used in the assay.