Table 1.
Characteristics of the shortlisted high-percentile-ranking SARS-CoV-2 CTL epitopes and their respective HLA allele binders.
| SARS-CoV-2a protein |
Peptide length, amino acids | Peptide sequence | Conservancy (%) | Immunogenicity | Toxicity | Allele | Methods usedb | Percentile rank |
| E proteinc | 9 | LLFLAFVVF | 480/482 (99.59) | 0.2341 | Nontoxic | B15:01 | Consensus (ann/smm/comblib_sidney 2008) |
0.1 |
| E protein | 9 | LTALRLCAY | 478/482 (99.17) | 0.01886 | Nontoxic | A01:01 | Consensus (ann/smm) | 0.12 |
| M proteind | 11 | YFIASFRLFAR | 474/477 (99.37) | 0.19709 | Nontoxic | A33:01 | ann | 0.03 |
| M protein | 10 | ATSRTLSYYKe | 472/477 (98.95) | –0.13563 | Nontoxic | A11:01 | Consensus (ann/smm) | 0.06 |
| N proteinf | 9 | MEVTPSGTW | 485/498 (97.39) | –0.06279 | Nontoxic | B44:02 | Consensus (ann/smm) | 0.06 |
| N protein | 9 | KPRQKRTAT | 487/498 (97.79) | –0.20542 | Nontoxic | B07:02 | Consensus (ann/smm/comblib_sidney 2008) |
0.1 |
| orf10 | 9 | MGYINVFAF | 477/480 (99.38) | –0.09452 | Nontoxic | B35:01 | Consensus (ann/smm/comblib_sidney 2008) |
0.1 |
| orf10 | 10 | GYINVFAFPFe | 232/236 (98.31) | 0.20158 | Nontoxic | A23:01 | Consensus (ann/smm) | 0.11 |
| orf-1ab | 11 | SEMVMCGGSLY | 452/456 (99.12) | 0.32633 | Nontoxic | B44:02 | ann | 0.03 |
| orf-1ab | 11 | FYWFFSNYLKR | 455/456 (99.78) | 0.37766 | Nontoxic | A33:01 | ann | 0.04 |
| orf-1ab | 8 | ISNSWLMW | 454/456 (99.56) | –0.24791 | Nontoxic | B58:01 | ann | 0.05 |
| orf-1ab | 10 | ETISLAGSYK | 455/456 (99.78) | 0.08174 | Nontoxic | A68:01 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 9 | QEILGTVSW | 455/456 (99.78) | 0.27341 | Nontoxic | B44:02 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 9 | STFNVPMEK | 456/456 (100.00) | –0.32016 | Nontoxic | A11:01 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 10 | RMYIFFASFY | 456/456 (100.00) | 0.21107 | Nontoxic | A30:02 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 10 | FLFVAAIFYL | 454/456 (99.56) | –0.19814 | Nontoxic | A02:01 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 10 | RYFRLTLGVY | 456/456 (100.00) | 0.03976 | Nontoxic | A30:02 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 9 | FLNGSCGSV | 456/456 (100.00) | –0.20585 | Nontoxic | A02:03 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 9 | CTDDNALAY | 476/479 (99.37) | 0.32004 | Nontoxic | A01:01 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 10 | CTDDNALAYYe | 476/479( 99.37) | 0.28694 | Nontoxic | A01:01 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 11 | MYKGLPWNVVR | 456/456 (100.00) | –0.11151 | Nontoxic | A33:01 | ann | 0.06 |
| orf-1ab | 10 | SIINNTVYTKe | 456/456 (100.00) | 0.15936 | Nontoxic | A11:01 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 10 | LPVNVAFELW | 450/456 (98.68) | –0.00254 | Nontoxic | B53:01 | Consensus (ann/smm) | 0.06 |
| orf-1ab | 9 | DEWSMATYYe | 455/456 (99.78) | 0.07355 | Nontoxic | B44:03 | Consensus (ann/smm) | 0.07 |
| orf-1ab | 10 | YILFTRFFYV | 454/456 (99.56) | –0.02845 | Nontoxic | A02:06 | Consensus (ann/smm) | 0.07 |
| orf-1ab | 10 | YIFFASFYYV | 456/456 (100.00) | 0.12661 | Nontoxic | A02:06 | Consensus (ann/smm) | 0.07 |
| ORF3a | 9 | YLYALVYFLe | 456/456 (100.00) | 0.40924 | Nontoxic | A02:01 | Consensus (ann/smm/comblib_sidney 2008) |
0.1 |
| ORF3a | 10 | IPYNSVTSSI | 454/456 (99.56) | 0.13772 | Nontoxic | B51:01 | Consensus (ann/smm) | 0.11 |
| Orf6 | 8 | RTFKVSIW | 466/481 (96.88) | 0.13151 | Nontoxic | B57:01 | ann | 0.05 |
| Orf6 | 11 | AEILLIIMRTF | 471/481 (97.92) | –0.32835 | Nontoxic | B44:02 | ann | 0.06 |
| ORF7a | 8 | RARSVSPK | 480/481 (99.79) | –0.18221 | Nontoxic | A30:01 | ann | 0.11 |
| ORF7a | 10 | QLRARSVSPK | 479/481 (99.58) | 0.1815 | Nontoxic | A03:01 | Consensus (ann/smm) | 0.16 |
| orf7b | 9 | FLAFLLFLV | 472/480 (98.33) | –0.16177 | Nontoxic | A02:03 | Consensus (ann/smm) | 0.07 |
| orf8 | 9 | HFYSKWYIR | 472/480 (98.33) | –0.27456 | Nontoxic | A31:01 | Consensus (ann/smm) | 0.11 |
| S proteing | 10 | WTAGAAAYYV | 470/472 (99.58) | 0.15455 | Nontoxic | A68:02 | Consensus (ann/smm) | 0.06 |
| S protein | 10 | FPNITNLCPF | 472/472 (100.00) | 0.1009 | Nontoxic | B53:01 | Consensus (ann/smm) | 0.06 |
| S protein | 10 | NYNYLYRLFR | 465/472 (98.52) | 0.08754 | Nontoxic | A33:01 | Consensus (ann/smm) | 0.07 |
| S protein | 8 | NYLYRLFR | 465/472 (98.52) | 0.13144 | Nontoxic | A33:01 | ann | 0.07 |
aSARS-CoV-2: severe acute resipiratory syndrome coronavirus 2.
bMethods: ann: artificial neural network. Comblib_sidney2008: combinatorial peptide libraries [19]. 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.