Table 1.
A total of 120 CD8+ T cell epitopes of SARS-CoV-2 were validated by in vitro DC-peptide-PBL costimulation experiments
| Epitope | In silico predicted HLA-A restriction | Healthy donor 1 | Healthy donor 2 | Healthy donor 3 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| A allele | Method | Enhancement (fold) | A allele | Method | Enhancement (fold) | A allele | Method | Enhancement (fold) | ||
| A1 | 0201, 0207, 0206, 2402 | 0201/6843 | CFSE | 1.244 | 3101/0207 | IFN-γ | 2.300 | 1101/0201 | IFN-γ | 2.207 |
| A3 | 0201, 0203, 1101, 1102 | 0201/2402 | IFN-γ | 4.142 | ||||||
| A4 | 0201, 0207, 0203 | 0201/3303 | IFN-γ | 2.162 | 6801/3303 | IFN-γ | 5.366 | 2402/0207 | IFN-γ | 2.373 |
| A5 | 0201, 0203 | 0201/3303 | IFN-γ | 6.892 | 0201/3001 | IFN-γ | 7.502 | 6801/3303 | IFN-γ | 8.288 |
| A6 | 0207, 0206 | 0206/0207 | IFN-γ | 2.985 | 1101/0206 | IFN-γ | 3.630 | |||
| A7 | 0207 | 0206/0207 | IFN-γ | 3.538 | ||||||
| A9 | 0206 | 0206/1101 | IFN-γ | 2.632 | 0206/0203 | IFN-γ | 2.317 | 1101/0206 | IFN-γ | 7.660 |
| A10 | 0203 | 0203/3101 | IFN-γ | 2.091 | ||||||
| A12 | 1101, 1102, 3303 | 1101/3001 | CFSE | 1.221 | 0201/1101 | IFN-γ | 2.585 | 3303/1101 | IFN-γ | 3.630 |
| A16 | 1101, 3303 | 0201/1101 | CFSE | 1.408 | ||||||
| A18 | 1102, 3303, 3001 | 1101/3101 | IFN-γ | 2.191 | ||||||
| A19 | 1102 | 1101/3101 | IFN-γ | 2.029 | 1101/2402 | CFSE | 1.223 | |||
| A20 | 2402 | 2402/2601 | IFN-γ | 6.439 | 2402/2402 | IFN-γ | 2.461 | |||
| A21 | 2402 | 2402/2601 | IFN-γ | 12.544 | 2402/2402 | IFN-γ | 2.532 | |||
| A22 | 2402 | 2402/2601 | IFN-γ | 4.789 | ||||||
| A23 | 2402 | 2402/2601 | IFN-γ | 4.035 | 2402/2402 | IFN-γ | 2.355 | |||
| A25 | 3001 | 1101/3001 | CFSE | 2.292 | ||||||
| A26 | 3001 | 1101/3001 | CFSE | 1.395 | 1101/3001 | IFN-γ | 3.910 | |||
| B1 | 0201, 0206, 0203 | 0201/3303 | IFN-γ | 2.108 | 0201/3001 | IFN-γ | 3.229 | 6801/3303 | IFN-γ | 4.980 |
| B2 | 0201, 0206, 0203, 0207 | 0201/0101 | IFN-γ | 2.281 | ||||||
| B3 | 0201, 0207, 0206 | 0201/3001 | IFN-γ | 5.073 | ||||||
| B4 | 0201, 0206 | 0201/3001 | IFN-γ | 3.166 | ||||||
| B6 | 0201, 0207, 0203 | 0203/0207 | IFN-γ | 3.421 | 0201/1101 | CFSE | 1.357 | 2402/0207 | IFN-γ | 2.648 |
| B10 | 0207 | 0207/0206 | IFN-γ | 9.887 | 3101/0207 | IFN-γ | 2.200 | 2402/0207 | IFN-γ | 2.238 |
| B11 | 0206 | 0206/1101 | IFN-γ | 2.545 | 0206/3201 | CFSE | 1.258 | 1101/0206 | IFN-γ | 4.070 |
| B12 | 0206 | 1101/0206 | CFSE | 1.225 | 1101/0206 | IFN-γ | 2.040 | |||
| B15 | 0203 | 0203/3101 | IFN-γ | 5.165 | ||||||
| B16 | 0203 | 0203/3001 | CFSE | 1.247 | ||||||
| B17 | 0203 | 0203/3101 | IFN-γ | 2.227 | ||||||
| B18 | 1101, 1102 | 1101/3001 | CFSE | 1.790 | ||||||
| B20 | 1101, 1102, 3303 | 0201/1101 | CFSE | 1.334 | ||||||
| B21 | 1101, 1102 | 0201/1101 | CFSE | 1.554 | ||||||
| B23 | 1101, 1102, 3303 | 3303/1101 | IFN-γ | 5.315 | ||||||
| B26 | 2402 | 2402/2402 | IFN-γ | 3.145 | 2402/2601 | IFN-γ | 3.772 | |||
| B28 | 2402 | 2402/3303 | IFN-γ | 3.145 | ||||||
| B29 | 2402 | 2402/3303 | IFN-γ | 6.000 | 2402/2402 | IFN-γ | 4.418 | 6801/3303 | IFN-γ | 2.425 |
| B30 | 2402 | 2402/3303 | IFN-γ | 4.627 | ||||||
| B31 | 2402 | 2402/2402 | IFN-γ | 2.290 | 2402/2402 | IFN-γ | 2.390 | |||
| B34 | 3303 | 3303/3001 | IFN-γ | 2.021 | ||||||
| B35 | 3303 | 3303/1101 | IFN-γ | 2.482 | ||||||
| B36 | 3001 | 1101/3001 | CFSE | 1.549 | 1101/3001 | IFN-γ | 4.740 | |||
| B37 | 3001 | 1101/3001 | CFSE | 1.349 | 3001/2402 | IFN-γ | 2.105 | 1101/3001 | IFN-γ | 2.910 |
| B38 | 3001 | 2402/3001 | IFN-γ | 2.868 | ||||||
| B40 | 3001 | 1101/3001 | IFN-γ | 2.400 | ||||||
| B41 | 3001 | 1101/3001 | IFN-γ | 5.250 | ||||||
| C1 | 0201, 0206, 0203 | 0201/1101 | CFSE | 1.300 | ||||||
| C3 | 0201, 0206, 0203 | 0201/2402 | IFN-γ | 3.709 | ||||||
| C10 | 0206 | 0206/1101 | CFSE | 1.259 | ||||||
| C12 | 0206 | 0206/3201 | CFSE | 1.208 | ||||||
| C16 | 0206 | 0206/1101 | IFN-γ | 2.877 | ||||||
| C17 | 0203 | 0203/3101 | IFN-γ | 2.574 | ||||||
| C27 | 1101 | 1101/1101 | CFSE | 1.401 | ||||||
| C35 | 2402 | 2402/2601 | IFN-γ | 2.440 | ||||||
| C45 | 3303 | 1101/3303 | IFN-γ | 2.811 | ||||||
| C46 | 3303 | 1101/3303 | IFN-γ | 2.000 | ||||||
| C47 | 3303 | 1101/0101 | IFN-γ | 3.238 | ||||||
| C49 | 1102 | 0201/1101 | IFN-γ | 17.633 | ||||||
| D2 | 0201, 0206, 0203 | 0201/1101 | IFN-γ | 2.223 | ||||||
| D5 | 0207, 0206, 1102 | 0206/1102 | IFN-γ | 5.792 | ||||||
| D6 | 0201, 0207 | 0201/2402 | CFSE | 2.055 | 0201/0101 | IFN-γ | 2.069 | |||
| D12 | 0201, 0207, 0206 | 0201/0201 | CFSE | 1.234 | ||||||
| D13 | 0201, 0203 | 0201/2402 | IFN-γ | 11.013 | ||||||
| D17 | 0207, 0203 | 0206/0207 | IFN-γ | 2.123 | ||||||
| D26 | 0206 | 0201/0207 | CFSE | 1.299 | ||||||
| D30 | 0203 | 0203/0206 | CFSE | 1.346 | 0203/0207 | IFN-γ | 2.453 | |||
| D31 | 0203 | 0203/0206 | CFSE | 1.335 | ||||||
| D32 | 0203 | 0203/0206 | CFSE | 1.333 | ||||||
| D33 | 0203, 0206 | 0203/0206 | CFSE | 1.280 | ||||||
| D34 | 1101/1102 | 1101/0101 | IFN-γ | 2.172 | ||||||
| D38 | 1101, 1102 | 1101/0101 | IFN-γ | 2.059 | ||||||
| D40 | 1101, 1102, 3001 | 1101/3303 | IFN-γ | 2.000 | ||||||
| D41 | 1101 | 1101/0101 | IFN-γ | 3.680 | ||||||
| D42 | 1101, 0206, 0201 | 1101/0101 | IFN-γ | 2.284 | 1101/1101 | CFSE | 1.476 | |||
| D46 | 1102 | 0201/1101 | IFN-γ | 5.586 | ||||||
| D47 | 1102 | 0201/1101 | IFN-γ | 2.799 | ||||||
| D48 | 1102, 3303 | 0201/1101 | IFN-γ | 2.669 | 3303/1101 | IFN-γ | 2.178 | |||
| D50 | 1102 | 0201/1101 | IFN-γ | 3.420 | ||||||
| D52 | 2402 | 2402/3001 | IFN-γ | 3.417 | ||||||
| D53 | 2402, 3303 | 2402/3001 | IFN-γ | 5.608 | 3303/1101 | IFN-γ | 3.755 | |||
| D55 | 2402 | 2402/0207 | IFN-γ | 2.102 | ||||||
| D56 | 2402 | 2402/2601 | IFN-γ | 3.669 | ||||||
| D62 | 2402 | 2402/3001 | IFN-γ | 2.824 | ||||||
| D64 | 2402 | 0201/2402 | IFN-γ | 2.449 | ||||||
| D65 | 3001 | 0101/3001 | CFSE | 1.208 | ||||||
| D71 | 3001 | 0301/3001 | IFN-γ | 2.329 | ||||||
| D72 | 3001, 1102, 0201, 0207 | 3303/1101 | IFN-γ | 2.577 | ||||||
| D76 | 3303 | 1101/0101 | IFN-γ | 4.467 | ||||||
| D77 | 3303, 1102 | 3303/1101 | IFN-γ | 2.095 | 3303/0203 | IFN-γ | 2.029 | |||
| D78 | 3303, 0203, 0206 | 3303/1101 | IFN-γ | 2.014 | ||||||
| D79 | 3303, 1101, 0207, 2402 | 3303/1101 | IFN-γ | 2.758 | ||||||
| D80 | 3303, 1102, 0201, 0207 | 3303/1101 | IFN-γ | 2.482 | ||||||
| D81 | 3303, 1102, 0203 | 3303/1101 | IFN-γ | 2.496 | ||||||
| D82 | 3303, 1102 | 3303/1101 | IFN-γ | 2.017 | ||||||
| R4 | 0201 | 0201/1101 | IFN-γ | 2.078 | 0201/3201 | CFSE | 1.473 | |||
| R5 | 0201, 0203 | 0201/3201 | CFSE | 2.078 | 0201/0101 | IFN-γ | 2.175 | |||
| R6 | 0201, 0207, 0206, 0203 | 0201/3201 | CFSE | 1.493 | ||||||
| R8 | 0201 | 0201/0101 | IFN-γ | 2.132 | ||||||
| R9 | 0201, 0206, 0203 | 0201/0101 | IFN-γ | 2.070 | ||||||
| R10 | 0201 | 0201/2402 | IFN-γ | 2.043 | ||||||
| R11 | 0201 | 0201/3001 | IFN-γ | 3.036 | 0201/1101 | IFN-γ | 2.044 | |||
| R12 | 0201 | 0201/3001 | IFN-γ | 2.470 | 0201/0101 | IFN-γ | 2.886 | |||
| R13 | 0201 | 0201/3001 | IFN-γ | 2.470 | 0201/1101 | IFN-γ | 2.269 | |||
| R14 | 0201, 0203 | 0201/0101 | IFN-γ | 2.333 | ||||||
| R15 | 0201 | 0201/2402 | IFN-γ | 3.184 | ||||||
| R17 | 0207 | 0207/0206 | IFN-γ | 2.030 | ||||||
| R23 | 0206 | 2402/0207 | IFN-γ | 2.094 | ||||||
| R24 | 0203 | 0203/0206 | CFSE | 1.608 | ||||||
| R30 | 1101 | 1101/3001 | CFSE | 2.102 | 0201/1101 | CFSE | 1.387 | |||
| R32 | 1101/1102 | 0201/1101 | CFSE | 1.293 | ||||||
| R34 | 1101, 3001 | 0201/1101 | CFSE | 1.200 | 1101/3101 | IFN-γ | 2.221 | |||
| R35 | 1101, 1102 | 1101/3101 | CFSE | 1.249 | ||||||
| R38 | 1101, 3303 | 0201/1101 | CFSE | 1.502 | ||||||
| R39 | 1101, 1102, 3001 | 0201/1101 | CFSE | 1.543 | ||||||
| R40 | 1101, 3001 | 0201/1101 | CFSE | 1.397 | 0201/1101 | CFSE | 1.195 | |||
| R41 | 1101, 3303 | 0201/1101 | CFSE | 1.533 | ||||||
| R42 | 1101 | 0201/1101 | CFSE | 1.210 | ||||||
| R43 | 1101, 3303 | 1101/3001 | CFSE | 1.419 | 0201/1101 | CFSE | 1.345 | |||
| R44 | 1101, 1102 | 0201/1101 | CFSE | 1.376 | 0201/1101 | CFSE | 1.248 | |||
| R47 | 2402 | 2402/3303 | IFN-γ | 4.398 | ||||||
| R48 | 2402 | 2402/3303 | IFN-γ | 4.096 | ||||||
CFSE: after DC-peptide-CFSE-prelabeled PBL cocultures, the percent of proliferating CD8+ T cells in the CD3+/CD8+ population was analyzed according to the reduction in CFSE staining intensity. IFN-γ: after DC-peptide-PBL cocultures, the frequency of IFN-γ+/CD8+ T cells in the CD3+/CD8+ population was analyzed by IFN-γ ICS. Enhancement (fold): the fold change in the frequency of IFN-γ+/CD8+ T cells or percent of proliferating CD8+ T cells in the DC-peptide-PBL coculture wells compared with that in the DC-PBL coculture wells without peptide