TABLE 3.
T-cell recognition of PTE peptide variants and the sequence of autologous viruses in subject 1188
| Epitope restricting HLA allelea | ELISPOT responses to 15-mer PTE peptides
|
Autologous sequences
|
|||||
|---|---|---|---|---|---|---|---|
| PTE peptide sequenceb | HXB2 aa position | Epitope sequencec | BLOSUM score(s)d | SFC/106 PBMC | Sequencee | Clonal frequency | |
| YPLTFGWCF | GPGIRYPLTFGWCF KLVPV | ||||||
| YF9/B35 | PGPGTRFPLTFGWCF | 129-143 | F........ | 3 | 1,046 | ...T. F........ ..... | 13/13 |
| PGPGIRYPLTFGWCF | 129-143 | ......... | NA | 523 | |||
| PGPGIRYPLCFGWCF | 129-143 | ....C.... | −1 | 87 | |||
| PGIRYPLTFGWCFKL | 131-145 | ......... | NA | 1,096 | |||
| GVRYPLTLGWCFKLV | 132-146 | ...L..... | 0 | 0 | |||
| GVRFPLCFGWCFKLV | 132-146 | F..C.... | 3, −1 | 9 | |||
| TRYPLTFGWCYKLVP | 133-147 | ........Y | 3 | 409 | |||
| WKFDSRLAF | REVLE WKFDSRLAF HHMAR | ||||||
| WF9/B15 | VLMWKFDSRLAFHHI | 180-194 | ......... | NA | 1,013 | ....M ......... ..... | 6/12 |
| EREVLEWKFDSRLAF | 177-191 | ......... | NA | 2,826 | ....I ......... ..L.. | 5/12 | |
| EVLQWKFDSRLALRH | 179-193 | ........L | 0 | 753 | ....M ...A..... ..... | 1/12 | |
| VLVWKFDSRLAFRHM | 180-194 | ......... | NA | 1,436 | |||
| LVWKFDSHLAFHHMA | 181-195 | .....H... | 0 | 123 | |||
| LVWKFDSSLAFHHRA | 181-195 | .....S... | −1 | 350 | |||
| VWRFDSHLAFRHMAR | 182-196 | .R...H... | 2, 0 | 106 | |||
| WRFDSRLAFHHMARE | 183-197 | .R....... | 2, 0 | 949 | |||
| KRQDILDLWVY | IYSQ KRQDILDLWVY HTQG | ||||||
| KY11/Cw07 | IYSQKRQDILDLWIY | 101-115 | .........I. | 3 | 1,256 | .... .........I. .... | 9/13 |
| KRQDILDLWVYHTQG | 105-119 | ........... | NA | 1,453 | .... ........... .... | 4/13 | |
| IYSRKRQEILDLWIY | 101-115 | R..E.....I. | 2, 2, 1 | 773 | |||
| SQRRQDILDLWVYHT | 103-117 | R.......... | 2 | 1,516 | |||
| RQEILDLWVYHTQGY | 106-120 | ..E....... | 2 | 647 | |||
Epitope WF9 was previously mapped, and HLA restriction was performed (9). Epitopes YF9 and KY11 are presumed based on the subject having the appropriate HLA allele and publication in the Los Alamos database (23).
Amino acid differences from the CON sequence are underlined. The optimal epitope sequence is in bold type.
The CON B sequence for each epitope is indicated on the top. Identity to amino acid in the CON sequence is indicated by a dot.
Conservative amino acid substitutions are denoted by positive scores and nonconservative substitutions by negative scores. The scoring is on a scale of −4 to +3. NA, not applicable.
The CON B sequence for the domain is indicated on the top. Identity to amino acid in the CON sequence is indicated by a dot. Numbers at the end of the sequences indicate the percentage of clones encoding the given variant. The compartment sampled was PBMC.