Table 9. T-cell epitopes predicted with high affinity to MHC II molecules common to SARS-CoV-2 and SARS-CoV.
| SARS-CoV-2 protein | Sl. No. | Peptide | SARS-CoV-2 | SARS-CoV | Probable Antigenicity by VexiJen (Threshold = 0.4) |
Probable Allergenicity by AllerTop | IFN gamma epitope |
Experimentally verified epitopes / ViPR reference |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Core | Position | Alleles | Number of Alleles | Conservancy | Servers | Core | Position | Alleles | Number of Alleles | Conservancy | Servers | |||||||
| Spike (S) | 1 | LLQYGSFCTQLNRAL | - | 753–767 | HLA-DRB1*04:05, HLA-DRB1*04:01, HLA-DRB1*09:01, HLA-DPA1*01:03/DPB1*02:01, HLA-DPA1*01:03/DPB1*04:01, HLA-DRB1*01:01, HLA-DRB1*15:01, HLA-DPA1*02:01/DPB1*01:01, HLA-DRB1*07:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DRB5*01:01, HLA-DRB1*11:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB1*08:02, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB4*01:01 | 16 | 100.00% (175/175) | 2 | - | 735–749 | HLA-DRB1*04:05, HLA-DRB1*04:01, HLA-DRB1*09:01, HLA-DPA1*01:03/DPB1*02:01, HLA-DPA1*01:03/DPB1*04:01, HLA-DRB1*01:01, HLA-DRB1*15:01, HLA-DPA1*02:01/DPB1*01:01, HLA-DRB1*07:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DRB5*01:01, HLA-DRB1*11:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB1*08:02, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB4*01:01 | 16 | 76.07% (248/326) | 2 | Antigen (0.722) | Non-allergen | Positive | - |
| 2 | RAAEIRASANLAATK |
IRASANLAA | 1014–1028 | HLA-DRB1*04:01, HLA-DRB1*08:02, HLA-DRB1*13:02, HLA-DRB1*15:01, HLA-DRB4*01:01, HLA-DPA1*02:01/DPB1*14:01 | 6 | 100.00% (175/175) | 1 | IRASANLAA | 996–1010 | HLA-DRB1*04:01, HLA-DRB1*13:02, HLA-DRB1*08:02, HLA-DRB1*15:01, HLA-DRB3*02:02, HLA-DRB4*01:01, HLA-DPA10201/DPB11401 | 7 | 85.58% (279/326) | 1 | Antigen (0.5709) | Non-allergen | Positive | IEDB-ID: 100428 [59] | |
| 3 | VNFNFNGLTGTGVLT | FNGLTGTGV | 539–553 | HLA-DRB1*09:01, HLA-DRB1*01:01, HLA-DRB1*07:01, HLA-DRB3*02:02, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DRB1*13:02, HLA-DRB5*01:01, HLA-DRB1*15:01, HLA-DRB1*11:01 | 11 | 100.00% (175/175) | 1 & 2 | FNGLTGTGV | 525–539 | HLA-DRB1*09:01, HLA-DRB1*01:01, HLA-DRB1*07:01, HLA-DRB3*02:02, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DRB1*13:02, HLA-DRB5*01:01, HLA-DRB1*15:01, HLA-DRB1*11:01 | 11 | 86.20% (281/326) | 1 & 2 | Antigen (1.2439) | Allergen | Negative | [59] | |
| 4 | AMQMAYRFNGIGVTQ | YRFNGIGVT | 899–913 | HLA-DRB3*02:02 | 1 | 100.00% (175/175) | 1 | YRFNGIGVT | 881–895 | HLA-DRB3*02:02 | 1 | 86.20% (281/326) | 1 | Antigen (1.2934) | Non-allergen | Negative | [43] | |
| Nucleocapsid (N) | 1 | RGGSQASSRSSSRSR | 177–191 | HLA-DQA1*05:01/DQB1*03:01 | 1 | 99.46% (184/185) | 2 | 178–192 | HLA-DQA1*05:01/DQB1*03:01 | 1 | 79.73% (240/301) | 2 | Antigen (1.0041) | Non-allergen | Positive | |||
| 2 | LALLLLDRLNQLESK | - | 219–233 | HLA-DRB1*03:01, HLA-DRB3*01:01, HLA-DRB4*01:01, HLA-DRB1*12:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DQA1*01:01/DQB1*05:01, HLA-DRB1*13:02, HLA-DPA1*02:01/DPB1*01:01, HLA-DPA1*02:01/DPB1*05:01, HLA-DPA1*01:03/DPB1*04:01, HLA-DRB1*04:05, HLA-DPA1*01:03/DPB1*02:01, HLA-DRB1*04:01, HLA-DRB1*11:01, HLA-DRB3*02:02, HLA-DRB1*08:02, HLA-DRB1*15:01, HLA-DRB1*01:01, HLA-DRB5*01:01 | 19 | 100.00% (185/185) | 2 | - | 220–234 | HLA-DRB1*03:01, HLA-DRB3*01:01, HLA-DRB4*01:01, HLA-DRB1*12:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DQA1*01:01/DQB1*05:01, HLA-DRB1*13:02, HLA-DPA1*02:01/DPB1*01:01, HLA-DPA1*02:01/DPB1*05:01, HLA-DPA1*01:03/DPB1*04:01, HLA-DRB1*04:05, HLA-DPA1*01:03/DPB1*02:01, HLA-DRB1*04:01, HLA-DRB1*11:01, HLA-DRB3*02:02, HLA-DRB1*08:02, HLA-DRB1*15:01, HLA-DRB1*01:01, HLA-DRB5*01:01 | 19 | 84.72% (255/301) | 2 | Antigen (0.7357) | Non-allergen | Positive | [77] | |
| 3 | YKHWPQIAQFAPSAS | - | 298–312 | HLA-DQA1*05:01/DQB1*03:01, H,LA-DQA1*01:02/DQB1*06:02, HLA-DRB1*09:01, HLA-DRB1*01:01, HLA-DRB1*04:01, HLA-DRB1*04:05 | 6 | 100.00% (185/185) | 2 | - | 299–313 | HLA-DQA1*05:01/DQB1*03:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB1*09:01, HLA-DRB1*01:01, HLA-DRB1*04:01, HLA-DRB1*04:05 | 6 | 82.72% (249/301) | 2 | Antigen (0.434) | Non-allergen | Positive | [77] | |
| 4 | ASAFFGMSRIGMEVT | FFGMSRIGM | 311–325 | HLA-DRB1*11:01, HLA-DRB1*04:05, HLA-DRB1*01:01, HLA-DRB1*08:02, HLA-DRB1*09:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB5*01:01, HLA-DPA1*01:03/DPB1*04:01, HLA-DRB1*07:01, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*04:01, HLA-DPA1*01:03/DPB1*02:01, HLA-DRB1*15:01, HLA-DPA1*02:01/DPB1*01:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DRB1*12:01, HLA-DRB4*01:01, HLA-DRB1*13:02 | 18 | 100.00% (185/185) | 1 & 2 | FFGMSRIGM | 312–326 | HLA-DRB1*11:01, HLA-DRB1*04:05, HLA-DRB1*01:01, HLA-DRB1*08:02, HLA-DRB1*09:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB5*01:01, HLA-DPA1*01:03/DPB1*04:01, HLA-DRB1*07:01, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*04:01, HLA-DPA1*01:03/DPB1*02:01, HLA-DRB1*15:01, HLA-DPA1*02:01/DPB1*01:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DRB1*12:01, HLA-DRB4*01:01, HLA-DRB1*13:02 | 18 | 84.72% (255/301) | 1 & 2 | Antigen (0.8620) | Non-allergen | Negative | [77] | |
| 5 | MSRIGMEVTPSGTWL | - | 317–331 | HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*08:02, HLA-DRB4*01:01, HLA-DRB1*01:01, HLA-DRB1*09:01 | 7 | 100.00% (185/185) | 2 | - | 318–332 | HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*08:02, HLA-DRB4*01:01, HLA-DRB1*01:01, HLA-DRB1*09:01 | 7 | 83.06% (250/301) | 2 | Antigen (0.7397) | Non-allergen | Negative | [59] | |
| Membrane (M) | 1 | PVTLACFVLAAVYRI | - | 59–73 | HLA-DPA1*01:03/DPB1*02:01, HLA-DPA1*01:03/DPB1*04:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DQA1*01:02/DQB1*06:02, HLA-DQA1*01:01/DQB1*05:01, HLA-DRB1*09:01, HLA-DRB1*01:01, HLA-DRB1*15:01, HLA-DPA1*02:01/DPB1*01:01, HLA-DRB1*12:01, HLA-DRB3*01:01, HLA-DRB5*01:01, HLA-DRB1*04:05, HLA-DRB1*13:02, HLA-DRB1*11:01, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*08:02, HLA-DRB1*04:01, HLA-DRB4*01:01, HLA-DRB1*07:01 | 20 | 98.24% (167/170) | 2 | - | 58–72 | HLA-DRB1*07:01, HLA-DPA1*01:03/DPB1*02:01, HLA-DPA1*01:03/DPB1*04:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DQA1*01:01/DQB1*05:01, HLA-DRB1*09:01, HLA-DRB1*01:01, HLA-DRB1*15:01, HLA-DPA1*02:01/DPB1*01:01, HLA-DRB1*12:01, HLA-DRB3*01:01, HLA-DRB5*01:01, HLA-DRB1*04:05, HLA-DRB1*13:02, HLA-DRB1*11:01, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*08:02, HLA-DRB1*04:01, HLA-DRB4*01:01 | 20 | 78.73% (211/268) | 2 | Antigen (0.8548) | Non-allergen | Positive | - |
| 2 | PKEITVATSRTLSYY | ITVATSRTL | 165–179 | HLA-DRB1*01:02, HLA-DRB1*09:01, HLA-DRB1*07:01, HLA-DRB1*09:01, HLA-DRB1*08:02, HLA-DRB1*13:02, HLA-DRB1*03:01, HLA-DRB1*01:01, HLA-DRB1*15:01, HLA-DRB3*02:02, HLA-DRB1*12:01, HLA-DRB5*01:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB1*04:01, HLA-DRB1*11:01, HLA-DRB4*01:01, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*04:05 | 18 | 98.24% (167/170) | 1 & 2 | ITVATSRTL | 164–178 | HLA-DRB1*07:01, HLA-DRB1*09:01, HLA-DRB1*08:02, HLA-DRB1*13:02, HLA-DRB1*03:01, HLA-DRB1*01:01, HLA-DRB1*15:01, HLA-DRB3*02:02, HLA-DRB1*12:01, HLA-DRB5*01:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB1*04:01, HLA-DRB1*11:01, HLA-DRB4*01:01, HLA-DQA1*05:01/DQB1*03:01, HLA-DRB1*04:05 | 16 | 79.48% (213/268) | 1 & 2 | Antigen (0.5800) | Non-allergen | Negative | ||
| Envelope (E) | 1 | VLLFLAFVVFLLVTL | - | 17–31 | HLA-DPA1*01:03/DPB1*04:01, HLA-DPA1*01:03/DPB1*02:01 | 2 | 100.00% (177/177) | 2 | - | 17–31 | HLA-DPA1*01:03/DPB1*04:01, HLA-DPA1*01:03/DPB1*02:01 | 2 | 82.86% (203/245) | 2 | Antigen (0.6386) | Non-allergen | Positive | [59] |
| 2 | AFVVFLLVTLAILTA | - | 22–36 | HLA-DPA1*01:03/DPB1*02:01, HLA-DRB1*01:01 | 2 | 100.00% (177/177) | 2 | - | 22–36 | HLA-DPA1*01:03/DPB1*02:01,HLA-DRB1*01:01 | 2 | 86.12% (211/245) | 2 | Antigen (0.6229) | Non-allergen | Positive | [59] | |
| 3 | LVTLAILTALRLCAY | - | 28–42 | HLA-DRB1*12:01, HLA-DRB1*15:01, HLA-DRB4*01:01, HLA-DRB1*01:01, HLA-DRB1*08:02, HLA-DRB1*11:01, HLA-DPA1*02:01/DPB1*05:01, HLA-DRB5*01:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DRB1*04:05, HLA-DPA1*01:03/DPB1*04:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB1*07:01, HLA-DPA1*01:03/DPB1*02:01, HLA-DPA1*02:01/DPB1*01:01, HLA-DRB1*03:01, HLA-DRB1*04:01, HLA-DRB1*13:02, HLA-DRB1*09:01 | 19 | 99.44% (176/177) | 2 | - | 28–42 | HLA-DRB1*12:01, HLA-DRB1*15:01, HLA-DRB4*01:01, HLA-DRB1*01:01, HLA-DRB1*08:02, HLA-DRB1*11:01, HLA-DPA1*02:01/DPB1*05:01, HLA-DRB5*01:01, HLA-DPA1*03:01/DPB1*04:02, HLA-DRB1*04:05, HLA-DPA1*01:03/DPB1*04:01, HLA-DQA1*01:02/DQB1*06:02, HLA-DRB1*07:01, HLA-DPA1*01:03/DPB1*02:01, HLA-DPA1*02:01/DPB1*01:01, HLA-DRB1*03:01, HLA-DRB1*04:01, HLA-DRB1*13:02, HLA-DRB1*09:01 | 19 | 82.45% (202/245) | 2 | Antigen (0.407) | Non-allergen | Negative | [59] | |
| 4 | LCAYCCNIVNVSLVK | - | 39–53 | HLA-DRB3*02:02, HLA-DRB1*13:02, HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DRB1*07:01, HLA-DRB1*01:01, HLA-DRB1*08:02, HLA-DRB1*09:01, HLA-DRB1*15:01, HLA-DRB4*01:01 | 10 | 100.00% (177/177) | 2 | - | 39–53 | HLA-DRB3*02:02, HLA-DRB1*13:02, HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DRB1*07:01, HLA-DRB1*01:01, HLA-DRB1*08:02, HLA-DRB1*09:01, HLA-DRB1*15:01, HLA-DRB4*01:01 | 10 | 84.08% (206/245) | 2 | Antigen (0.8552) | Non-allergen | Negative | - | |
CD4+ T-cell epitopes were identified using two independent prediction algorithms and servers, which are numbered as (1) for NetMHCpan4 and (2) for TepiTool.