Table 6. List of predicted SARS-CoV-2-derived T-cell epitopes with high-affinity binding to MHC I molecules.
| SARS-CoV-2 protein | Sl. No. | Peptide | Position | Alleles | Number of Alleles | Servers | Probable Antigenicity by VexiJen (Threshold = 0.4) | Probable Allergenicity by AllerTop | Conservancy analysis by IEDB tool | Conservancy analysis by IEDB tool | IFN gamma epitope | Experimentally verified epitopes / ViPR reference |
|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SARS-CoV-2 | SARS-CoV | ||||||||||||
| Spike (S) | 1 | FSNVTWFHA | 59–67 | HLA-A*02:06, HLA-A*68:02 | 2 | 1 & 3 | Antigen (0.8156) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1074888 [59] | 1 |
| 2 | VTWFHAIHV | 62–70 | HLA-A*02:06, HLA-A*68:02, HLA-A*02:01, HLA-A*32:01, HLA-A*02:03 | 5 | 1, 2 & 3 | Antigen (0.5426) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | - | 2 | |
| 3 | GVYFASTEK | 89–97 | HLA-A*11:01, HLA-A*03:01, HLA-A*68:01, HLA-A*30:01 | 4 | 1, 2 & 3 | Antigen (0.7112) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1075093 [59] [In silico predicted, 24, 26] | 3 | |
| 4 | TFEYVSQPF | 167–175 | HLA-A*23:01, HLA-A*24:02 | 2 | 1, 2 & 3 | Antigen (0.6641) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1074869 [59] [In silico predicted, 22, 29] | 4 | |
| 5 | WTAGAAAYY | 258–266 | HLA-A*26:01, HLA-A*68:01, HLA-A*01:01, HLA-A*30:02, HLA-B*35:01, HLA-B*15:01, HLA-B*58:01 | 7 | 1, 2 & 3 | Antigen (0.6306) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1075117 [59] [In silico predicted, 21, 22, 26] | 5 | |
| 6 | GAAAYYVGY | 261–269 | HLA-A*30:02, HLA-B*15:01, HLA-B*35:01, HLA-A*26:01, HLA-B*58:01, HLA-A*11:01, HLA-A*01:01 | 7 | 1, 2 & 3 | Antigen (0.6604) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1075117 1075077 [59] [In silico predicted, 22] |
6 | |
| 7 | YYVGYLQPR | 265–273 | HLA-A*33:01, HLA-A*31:01, HLA-A*68:01 | 3 | 1, 2 & 3 | Antigen (1.4692) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1075077 [59] | 7 | |
| 8 | GYLQPRTFL | 268–276 | HLA-A*23:01, HLA-A*24:02 | 2 | 2 | Antigen (0.6082) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | [17, 76] | 8 | |
| 9 | AVDCALDPL | 288–296 | HLA-A*02:06 | 1 | 1 & 3 | Antigen (0.6604) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | - | 9 | |
| 10 | QIAPGQTGK | 409–417 | HLA-A*68:01, HLA-A*11:01, HLA-A*03:01 | 3 | 1, 2 & 3 | Antigen (1.8297) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1075039 [59] | 10 | |
| 11 | TGKIADYNY | 415–423 | HLA-A*30:02 | 1 | 2 | Antigen (1.5305) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1075039 [59] | 11 | |
| 12 | LDSKVGGNY | 441–449 | HLA-A*01:01 | 1 | 2 | Antigen (0.7814) | Non-allergen | 100.00% (175/175) | 0.00% (0/326) | Positive | IEDB ID: 1075002 [59] | 12 | |
| 13 | SKVGGNYNY | 443–451 | HLA-A*30:02, HLA-B*15:01 | 2 | 2 | Antigen (0.9111) | Non-allergen | Spike (S) | 0.00% (0/326) | Positive | IEDB ID: 1074979 [59] | 13 | |
| 14 | YQPYRVVVL | 505–513 | HLA-A*02:06, HLA-B*08:01, HLA-A*02:03 | 3 | 1, 2 & 3 | Antigen (0.5964) | Non-allergen | 100.00% (175/175) | 84.97% (277/326) | Positive | [In silico predicted, 21, 22] [17] |
14 | |
| 15 | VVVLSFELL | 510–518 | HLA-A*02:06 | 1 | 1 & 3 | Antigen (1.0909) | Non-allergen | 100.00% (175/175) | 85.89% (280/326) | Positive | - | 15 | |
| 16 | GVLTESNKK | 550–558 | HLA-A*11:01, HLA-A*03:01 | 2 | 1, 2 & 3 | Antigen (0.8797) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | - | 16 | |
| 17 | CSFGGVSVI | 590–598 | HLA-A*68:02, HLA-A*32:01, HLA-A*02:06, HLA-A*02:03, HLA-B*58:01 | 5 | 1 & 3 | Antigen (1.2630) | Non-allergen | 100.00% (175/175) | 83.44% (272/326) | Positive | - | 17 | |
| 18 | SIAIPTNFT | 711–719 | HLA-A*68:02 | 1 | 1 | Antigen (0.5808) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1074855 [59] | 18 | |
| 19 | GSFCTQLNR | 757–765 | HLA-A*11:01, HLA-A*31:01, HLA-A*68:01, HLA-A*03:01 | 4 | 1, 2 & 3 | Antigen (0.9306) | Non-allergen | 100.00% (175/175) | 76.07% (248/326) | Positive | [17] | 19 | |
| 20 | TLADAGFIK | 827–835 | HLA-A*11:01, HLA-A*68:01, HLA-A*03:01 | 3 | 1, 2 & 3 | Antigen (0.5781) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | IEDB ID: 1074948 [59] | 20 | |
| 21 | YTSALLAGT | 873–881 | HLA-A*68:02, HLA-A*02:06, HLA-A*02:03 | 3 | 1 & 3 | Antigen (0.5487) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | [17] | 21 | |
| 22 | WTFGAGAAL | 886–894 | HLA-A*68:02, HLA-A*02:06, HLA-B*35:01, HLA-B*15:01, HLA-A*02:03, HLA-A*26:01 | 6 | 1, 2 & 3 | Antigen (0.4918) | Non-allergen | 100.00% (175/175) | 85.28% (278/326) | Positive | IEDB ID: 1074998 [59] [In silico predicted, 20] |
22 | |
| 23 | FAMQMAYRF | 898–906 | HLA-B*35:01, HLA-B*53:01, HLA-B*58:01, HLA-A*23:01, HLA-B*15:01, HLA-A*24:02, HLA-A*32:01, HLA-B*57:01, HLA-A*02:06 | 9 | 1, 2 & 3 | Antigen (1.0278) | Non-allergen | 100.00% (175/175) | 86.20% (281/326) | Positive | [In silico predicted, 20, 22] | 23 | |
| 24 | SALGKLQDV | 943–951 | HLA-A*02:06 | 1 | 1 & 3 | Antigen (0.8291) | Non-allergen | 100.00% (175/175) | 0.31% (1/326) | Positive | - | 24 | |
| 25 | YIKWPWYIW | 1209–1217 | HLA-A*32:01, HLA-A*23:01, HLA-B*58:01, HLA-B*57:01 | 4 | 1 & 3 | Antigen (0.9673) | Non-allergen | 94.86% (166/175) | 0.92% (3/326) | Positive | [17] | 25 | |
| 26 | GLIAIVMVT | 1223–1231 | HLA-A*02:03, HLA-A*02:01 | 2 | 1, 2 & 3 | Antigen (1.0885) | Non-allergen | 94.86% (166/175) | 79.14% (258/326) | Positive | - | 26 | |
| Nucleocapsid (N) | 1 | RSGARSKQR | 32–40 | HLA-A*31:01 | 1 | 1,2&3 | Antigen (0.9734) | Non-allergen | 99.46% (184/185) | 0.00% (0/301) | Positive | IEDB ID: 1075022 [59] | 1 |
| 2 | FPRGQGVPI | 66–74 | HLA-B*07:02, HLA-B*35:01, HLA-B*51:01, HLA-B*08:01, HLA-B*53:01 | 5 | 1,2&3 | Antigen (1.2832) | Non-allergen | 100.00% (185/185) | 83.39% (251/301) | Positive | [61] | 2 | |
| 3 | SPDDQIGYY | 79–87 | HLA-B*35:01, HLA-B*53:01, HLA-A*01:01, HLA-A*30:02 | 4 | 1,2&3 | Antigen (0.864) | Non-allergen | 100.00% (185/185) | 0.00% (0/301) | Positive | IEDB ID: 1074917 [59] | 3 | |
| 4 | KDLSPRWYF | 102–110 | HLA-B*44:02, HLA-B*44:03 | 2 | 2 | Antigen (0.8611) | Non-allergen | 99.46% (184/185) | 0.00% (0/301) | Positive | [17], [In silico predicted, 23] | 4 | |
| 5 | KGFYAEGSR | 169–177 | HLA-A*31:01 | 1 | 1,2&3 | Antigen (0.4353) | Non-allergen | 100.00% (185/185) | 85.71% (258/301) | Positive | - | 5 | |
| 6 | RGGSQASSR | 177–185 | HLA-A*31:01 | 1 | 1,2&3 | Antigen (0.7468) | Non-allergen | 100.00% (185/185) | 79.73% (240/301) | Positive | - | 6 | |
| 7 | QASSRSSSR | 181–189 | HLA-A*68:01, HLA-A*31:01 | 2 | 1,2&3 | Antigen (0.5495) | Non-allergen | 100.00% (185/185) | 81.40% (245/301) | Positive | - | 7 | |
| 8 | SSRNSTPGS | 193–201 | HLA-A*30:01 | 1 | 1,2&3 | Antigen (0.6287) | Non-allergen | 100.00% (185/185) | 0.66% (2/301) | Positive | - | 8 | |
| 9 | SSRGTSPAR | 201–209 | HLA-A*31:01, HLA-A*30:01, HLA-A*68:01 | 3 | 1,2&3 | Antigen (0.4548) | Non-allergen | 100.00% (185/185) | 1.33% (4/301) | Positive | IEDB ID: 1075062 [59] | 9 | |
| 10 | KSAAEASKK | 249–257 | HLA-A*11:01, HLA-A*03:01, HLA-A*30:01 | 3 | 1,2&3 | Antigen (0.5547) | Non-allergen | 100.00% (185/185) | 83.39% (251/301) | Positive | - | 10 | |
| 11 | KAYNVTQAF | 266–274 | HLA-A*32:01, HLA-B*58:01, HLA-B*15:01, HLA-B*57:01, HLA-B*35:01, HLA-A*30:02, HLA-B*53:01, HLA-A*23:01, HLA-A*30:01, HLA-B*07:02, HLA-A*24:02 | 11 | 1,2&3 | Antigen (1.7645) | Non-allergen | 100.00% (185/185) | 0.66% (2/301) | Positive | IEDB ID: 1074947 [59] | 11 | |
| 12 | QFAPSASAF | 306–314 | HLA-A*24:02, HLA-A*23:01, HLA-B*15:01, HLA-B*35:01 | 4 | 1&2 | Antigen (0.55) | Non-allergen | 100.00% (185/185) | 85.71% (258/301) | Positive | [In silico predicted, 23] | 12 | |
| 13 | ASAFFGMSR | 311–319 | HLA-A*11:01, HLA-A*68:01, HLA-A*31:01, HLA-A*03:01, HLA-A*30:01, HLA-A*33:01 | 6 | 1,2&3 | Antigen (0.4529) | Non-allergen | 100.00% (185/185) | 85.71% (258/301) | Positive | IEDB ID: 56979 [59] | 13 | |
| 14 | DPNFKDQVI | 343–351 | HLA-B*51:01, HLA-B*08:01, HLA-B*53:01 | 3 | 2 | Antigen (0.5439) | Non-allergen | 100.00% (185/185) | 0.33% (1/301) | Positive | [17] | 14 | |
| 15 | LNKHIDAYK | 353–361 | HLA-A*68:01, HLA-A*31:01, HLA-A*30:01 | 3 | 3 | Antigen (1.7367) | Non-allergen | 98.38% (182/185) | 85.71% (258/301) | Positive | - | 15 | |
| 16 | KTFPPTEPK | 361–369 | HLA-A*11:01, HLA-A*30:01, HLA-A*03:01, HLA-A*31:01, HLA-A*68:01 | 5 | 1,2&3 | Antigen (1.1677) | Non-allergen | 100.00% (185/185) | 84.05% (253/301) | Positive | - | 16 | |
| Membrane (M) | 1 | GTITVEELK | 6–14 | HLA-A*11:01, HLA-A*68:01 | 2 | 2&3 | Antigen (1.0976) | Non-allergen | 98.82% (168/170) | 50.00% (134/268) | Positive | IEDB ID: 107499 [59] | 1 |
| 2 | WICLLQFAY | 31–39 | HLA-A*02:06, HLA-A*30:01 | 2 | 3 | Antigen (1.4562) | Non-allergen | 98.82% (168/170) | 0.75% (2/268) | Positive | IEDB ID: 10749920 [59] | 2 | |
| 3 | AYANRNRFL | 38–46 | HLA-A*02:06, HLA-A*02:01, HLA-A*68:02, HLA-A*02:03, HLA-A*32:01 | 5 | 1,2&3 | Antigen (0.5136) | Non-allergen | 98.24% (167/170) | 0.75% (2/268) | Positive | IEDB ID: 1074985 [59] | 3 | |
| 4 | LWLLWPVTL | 54–62 | HLA-B*40:01, HLA-B*44:03, HLA-B*44:02 | 3 | 2&3 | Antigen (0.6409) | Non-allergen | 98.82% (168/170) | 82.46% (221/268) | Positive | [76] | 4 | |
| 5 | CFVLAAVYR | 64–72 | HLA-A*33:01, HLA-A*31:01 | 2 | 1,2&3 | Antigen (0.9181) | Non-allergen | 98.82% (168/170) | 78.73% (211/268) | Positive | - | 5 | |
| 6 | WITGGIAIA | 75–83 | HLA-A*02:01, HLA-A*02:06 | 2 | 1&3 | Antigen (1.4835) | Non-allergen | 98.82% (168/170) | 0.75% (2/268) | Positive | IEDB ID: 1075124 [59] | 6 | |
| 7 | MACLVGLMW | 84–92 | HLA-A*33:01, HLA-A*31:01, HLA-A*68:01 | 3 | 1,2&3 | Antigen (1.1961) | Non-allergen | 98.82% (168/170) | 0.75% (2/268) | Positive | IEDB ID: 1075124) [59] | 7 | |
| 8 | FIASFRLFA | 96–104 | HLA-A*32:01, HLA-B*58:01, HLA-A*23:01, HLA-B*57:01 | 4 | 1&3 | Antigen (0.4968) | Non-allergen | 98.24% (167/170) | 3.36% (9/268) | Positive | IEDB ID: 1075069 [59] | 8 | |
| 9 | RSMWSFNPE | 107–115 | HLA-A*02:06, HLA-A*68:02, HLA-B*58:01, HLA-A*02:03, HLA-B*51:01 | 5 | 3 | Antigen (1.1704) | Non-allergen | 98.82% (168/170) | 82.46% (221/268) | Positive | IEDB ID: 1075081 [59] | 9 | |
| 10 | TSRTLSYYK | 172–180 | HLA-A*68:01, HLA-A*31:01, HLA-A*11:01, HLA-A*33:01 | 4 | 1,2&3 | Antigen (1.1027) | Non-allergen | 98.82% (168/170) | 80.97% (217/268) | Positive | [17] | 10 | |
| Envelope (E) | 1 | VLLFLAFVV | 17–25 | HLA-A*02:01, HLA-A*02:06, HLA-A*02:03, HLA-A*32:01 | 4 | 1 & 3 | Antigen (0.5677) | Non-allergen | 100.00% (177/177) | 83.27% (204/245) | Positive | IEDB ID: 62215 [59] | 1 |
| 2 | FLLVTLAIL | 26–34 | HLA-A*02:01, HLA-A*02:03, HLA-A*02:06 | 3 | 1 & 3 | Antigen (0.9645) | Non-allergen | 100.00% (177/177) | 86.12% (211/245) | Positive | - | 2 | |
| 3 | RLCAYCCNI | 38–46 | HLA-A*02:03, HLA-A*02:01, HLA-A*02:06 | 3 | 3 | Antigen (1.1243) | Non-allergen | 100.00% (177/177) | 84.90% (208/245) | Positive | IEDB ID: 154490 [59] | 3 | |
List of top-ranked CD8+ T-cell epitopes predicted using at least two servers, with the corresponding prediction servers numbered as (1) for IEDB Proteasomal cleavage/TAP transport/MHC class I combined predictor, (2) for MHC-NP, and (3) for TepiTool. Epitopes of 9-mer length with IC50 value < 500 nM were considered good binders towards specific alleles.