TABLE 1.
HIV-1-specific CTL targeting and epitope sequences in subjects 00015 and 00016a
| Protein | Location | Clade B consensus sequence | Subject 00015
|
Subject 00016
|
||
|---|---|---|---|---|---|---|
| CTL | Consensus sequence | CTL | Consensus sequence | |||
| Gag | 17-31 (p17) | EKIRLRPGGKKKYKL | Yes | -------------- (3) | Yes | -----------Q--- (2) |
| 25-39 (p17) | GKKKYKLKHIVWASR | Yes | --------------- (3) | ---Q----------- (2) | ||
| 213-222 (p24) | DRLHPVHAGP | --T------- (17) | --T------- (12) | |||
| 228-242 (p24) | MREPRGSDIAGTTST | --K-----------N (17) | --------------N (12) | |||
| 312-322 (p24) | EVKNWMTETLL | ----------- (17) | Yes | D---------- (12) | ||
| 397-411 (p7) | KEGHIAKNCRAPRKK | ----L-R-------- (3) | Yes | ----L-R-------- (2) | ||
| 425-435 (p7-p1) | DCTERQANFLG | ----------- (3) | Yes | ----------- (2) | ||
| 437-451 (p1-p6) | IWPSHKGRPGNFLQS | ND | Yes | ND | ||
| 461-475 (p6) | ESFRFGEETTTPSQK | ----L-----S--- (1) | Yes | ----------S--- (2) | ||
| 477-487 (p6) | EPIDKELYPLA | -T-G------- (1) | Yes | -A--------- (2) | ||
| Pol | 125-139 (protease) | HKAIGTVLVGPTPVN | Yes | Q-------------- (1) | Q-------------D (2) | |
| 141-155 (protease) | IGRNLLTQIGCTLNF | Yes | --------------- (18) | --------------- (12) | ||
| 421-435 (reverse transcriptase) | WASQIYAGIKVKQLC | Yes | --------------- (6) | --------------- (2) | ||
| 545-559 (reverse transcriptase) | KLPIQKETWEAWWTE | R------------M- (6) | Yes | R------------M- (1) | ||
| 625-639 (RNase) | TDTTNQKTELQAIHL | --------------- (6) | Yes | --------------- (3) | ||
| 933-947 (Int) | TKIQNFRVYYRDSRD | --------------- (3) | Yes | ------------H-- (2) | ||
| Env | 216-226 (gp120) | HYCAPAGFAIL | Yes | ND | ND | |
| 704-714 (gp41) | IVNRVRQGYSP | ND | Yes | ND | ||
| Vif | 121-135 | RNAILGHIVSPRCEY | Yes | -------V---I-D- (3) | ------R-------- (2) | |
| Nef | 81-91 | YKGALDLSHFL | Yes | ----V------ (23) | ----V------ (23) | |
| 105-115 | KRQDILDLWVY | ---E------- (23) | Yes | ---E------- (23) | ||
a
CTL responses (identified by IFN-γ ELISPOT with overlapping peptides) at the times shown in Fig. 2 are listed. The epitope region sequences correspond to isolated recognized 15-amino-acid peptides or the region of overlap between consecutive recognized peptides. Consensus sequences from each subject are given. The number of clonal sequences is given in parentheses. A dash indicates identity with the clade B consensus sequence. ND, not determined.