Table 2.
Characteristics of the shortlisted high-scoring SARS-CoV-2 HTL epitopes and their respective HLA allele binders.
| SARS-CoV-2a protein | Peptide | Conservancy (%) | Toxicity | Alleles | Methods usedb | Percentile rank |
| E proteinc | LLFLAFVVFLLVTLA | 480/482 (99.59) | Nontoxic | DPA1-03:01/DPB1-04:02 | Consensus (comb.lib./smm/nn) | 0.02 |
| E protein | VLLFLAFVVFLLVTL | 480/482 (99.59) | Nontoxic | DPA1-03:01/DPB1-04:02 | Consensus (comb.lib./smm/nn) | 0.02 |
| M proteind | GLMWLSYFIASFRLF | 465/477 (97.48) | Nontoxic | DPA1-01:03/DPB1-02:01 | Consensus (comb.lib./smm/nn) | 0.05 |
| M Protein | LMWLSYFIASFRLFA | 466/477 (97.69) | Nontoxic | DPA1-01:03/DPB1-02:01 | Consensus (comb.lib./smm/nn) | 0.05 |
| M protein | LSYYKLGASQRVAGDe | 472/477 (98.95) | Nontoxic | DRB1-09:01 | Consensus (comb.lib./smm/nn) | 0.06 |
| N proteinf | AQFAPSASAFFGMSR | 486/498 (97.59) | Nontoxic | DRB1-09:01 | Consensus (comb.lib./smm/nn) | 0.01 |
| N protein | IAQFAPSASAFFGMS | 485/498 (97.39) | Nontoxic | DRB1-09:01 | Consensus (comb.lib./smm/nn) | 0.01 |
| N protein | PQIAQFAPSASAFFG | 485/498 (97.39) | Nontoxic | DRB1-09:01 | Consensus (comb.lib./smm/nn) | 0.01 |
| ORF1ab | AIILASFSASTSAFV | 456/456 (100.00) | Nontoxic | DRB1-09:01 | Consensus (comb.lib./smm/nn) | 0.01 |
| ORF1ab | ESPFVMMSAPPAQYEe | 456/456 (100.00) | Nontoxic | DRB1-01:01 | Consensus (comb.lib./smm/nn) | 0.01 |
| ORF1ab | IILASFSASTSAFVE | 456/456 (100.00) | Nontoxic | DRB1-09:01 | Consensus (comb.lib./smm/nn) | 0.01 |
| ORF1ab | QESPFVMMSAPPAQY | 456/456 (100.00) | Nontoxic | DRB1-01:01 | Consensus (comb.lib./smm/nn) | 0.01 |
| ORF1ab | SPFVMMSAPPAQYEL | 456/456 (100.00) | Nontoxic | DRB1-01:01 | Consensus (comb.lib./smm/nn) | 0.01 |
| ORF3a | FVRATATIPIQASLP | 478/481 (99.37) | Nontoxic | DPA1-02:01/DPB1-14:01 | NetMHCIIpan | 0.12 |
| ORF3a | LLFVTVYSHLLLVAA | 467/481 (97.08) | Nontoxic | DRB1-01:01 | Consensus (comb.lib./smm/nn) | 0.1 |
| ORF6 | FKVSIWNLDYIINLI | 478/481 (99.38) | Nontoxic | DQA1-01:01/DQB1-05:01 | Consensus (comb.lib./smm/nn) | 0.02 |
| ORF6 | KVSIWNLDYIINLII | 478/481 (99.38) | Nontoxic | DQA1-01:01/DQB1-05:01 | Consensus (comb.lib./smm/nn) | 0.02 |
| ORF6 | TFKVSIWNLDYIINLe | 478/481 (99.38) | Nontoxic | DQA1-01:01/DQB1-05:01 | Consensus (comb.lib./smm/nn) | 0.02 |
| ORF7a | IILFLALITLATCEL | 479/480 (99.79) | Nontoxic | DRB1-01:01 | Consensus (comb.lib./smm/nn) | 0.16 |
| ORF7a | ILFLALITLATCELY | 479/480 (99.79) | Nontoxic | DRB1-01:01 | Consensus (comb.lib./smm/nn) | 0.16 |
| ORF7b | CFLAFLLFLVLIMLI | 231/236 (97.88) | Nontoxic | DPA1-03:01/DPB1-04:02 | Consensus (comb.lib./smm/nn) | 0.03 |
| ORF7b | LCFLAFLLFLVLIML | 231/236 (97.88) | Nontoxic | DPA1-03:01/DPB1-04:02 | Consensus (comb.lib./smm/nn) | 0.02 |
| ORF7b | YLCFLAFLLFLVLIM | 231/236 (97.88) | Nontoxic | DPA1-03:01/DPB1-04:02 | Consensus (comb.lib./smm/nn) | 0.02 |
| ORF8 | CTQHQPYVVDDPCPI | 476/480 (99.17) | Nontoxic | DRB3-01:01 | Consensus (comb.lib./smm/nn) | 0.08 |
| ORF8 | HQPYVVDDPCPIHFY | 476/480 (99.17) | Nontoxic | DRB3-01:01 | Consensus (comb.lib./smm/nn) | 0.08 |
| ORF8 | QPYVVDDPCPIHFYS | 476/480 (99.17) | Nontoxic | DRB3-01:01 | Consensus (comb.lib./smm/nn) | 0.07 |
| ORF10 | INVFAFPFTIYSLLL | 476/480 (99.17) | Nontoxic | HLA-DPA1-01:03/DPB1-02:01 | Consensus (comb.lib./smm/nn) | 0.29 |
| ORF10 | YINVFAFPFTIYSLL | 476/479 (99.37) | Nontoxic | DPA1-01:03/DPB1-02:01 | Consensus (comb.lib./smm/nn) | 0.29 |
| S proteing | KTQSLLIVNNATNVV | 472/472 (100.00) | Nontoxic | DRB1-13:02 | Consensus (smm/nn/sturniolo) | 0.01 |
| S protein | LLIVNNATNVVIKVC | 469/472 (99.36) | Nontoxic | DRB1-13:02 | Consensus (smm/nn/sturniolo) | 0.01 |
| S protein | QSLLIVNNATNVVIK | 471/472 (99.79) | Nontoxic | DRB1-13:02 | Consensus (smm/nn/sturniolo) | 0.01 |
| S protein | SLLIVNNATNVVIKVe | 471/472 (99.79) | Nontoxic | DRB1-13:02 | Consensus (smm/nn/sturniolo) | 0.01 |
| S protein | TQSLLIVNNATNVVI | 471/472 (99.79) | Nontoxic | DRB1-13:02 | Consensus (smm/nn/sturniolo) | 0.01 |
aSARS-CoV-2: severe acute resipiratory syndrome coronavirus 2.
bMethods: comb.lib.: combinatorial library. nn: neural network. smm: stabilized matrix method.
cE protein: envelope protein.
dM protein: membrane protein.
eMatches a recently published epitope, indicating consensus with results [58].
fN protein: nucleocapsid protein
gS protein: surface protein.