Table 3.
Predicted HTL epitopes from SARS-CoV-2 proteins to design multi-epitope vaccine construct with their corresponding MHC Class II alleles and their immunogenic properties.
| Proteins | MHC II Epitope | High affinity HLA Alleles binding to predicted epitopes as analyzed using the NetMHCIIpan-4.0 server | Pos | IC50 value | NetMHCIIpan-4.0 Score | Conservancy | Toxicity | Hydrophobicity | Hydropathicity | Hydrophilicity | Charge | Mol wt. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Spike Protein (P59594) | VVLSFELLNAPATVC | DRB1*01:12, DRB1*01:15, DRB1*01:17, DRB1*01:24, DRB1*01:25, DRB1*01:27, DRB1*03:31, DRB1*03:46, DRB1*03:48, DRB1*04:27, DRB1*04:41, DRB1*07:01, DRB1*09:02, DRB1*11:35, DRB1*11:65, DRB1*11:78, DRB1*12:03, DRB1*12:18, DRB1*13:10, DRB1*13:12, DRB1*14:52, DRB1*14:53, DRB1*15:26, DRB1*15:44, DRB1*16:14, DRB3*01:08, DRB3*01:14, DRB3*02:04, DRB3*02:23, DRB3*02:25, DRB4*01:04, DRB4*01:07, DRB4*01:08, DRB5*01:02, DRB5*01:03, DRB5*02:05, DPA1*02:04 DPB1*48:01, DPA1*02:02 DPB1*118:01, DPA1*04:01DPB1*69:01, DQA1*01:04DQB1*03:07, DQA1*03:03 DQB1*06:35, DQA1*04:04DQB1*05:01 | 497–511 | 4 | 0.50 | 93.33% | Nontoxin | 0.17 | 1.52 | −0.75 | −1 | 1576.1 |
| Small Envelope Protein (P59637) | LLFLAFVVFLLVTLA | DRB1*01:03, DRB1*01:15, DRB1*01:19, DRB1*01:24, DRB1*01:27, DRB1*01:35, DRB1*03:38, DRB1*03:46, DRB1*03:48, DRB1*04:29, DRB1*04:41, DRB1*07:05, DRB1*09:02, DRB1*11:35, DRB1*11:65, DRB1*11:78, DRB1*12:07, DRB1*12:12, DRB1*13:10, DRB1*13:12, DRB1*14:52, DRB1*14:53, DRB1*15:21, DRB1*15:44, DRB1*16:16, DRB3*01:05, DRB3*01:12, DRB3*02:04, DRB3*02:12, DRB3*02:23, DRB3*02:25, DRB3*03:03, DRB4*01:01, DRB4*01:03, DRB4*01:06, DRB4*01:07, DRB4*01:08, DRB5*01:02, DRB5*01:08 N, DRB5*02:02, DRB5*02:03, DPA1*02:04 DPB1*48:01, DPA1*02:02 DPB1*118:01, DPA1*04:01DPB1*69:01, DQA1*01:04DQB1*03:07, DQA1*03:03 DQB1*06:35, DQA1*04:04DQB1*05:01 | 18–32 | 7 | 0.40 | 100.00% | Nontoxin | 0.46 | 3.11 | −1.61 | 0 | 1679.4 |
| Membrane Protein (P59596) | IGFLFLAWIMLLQFA | DRB1*01:07, DRB1*01:13, DRB1*01:19, DRB1*01:26, DRB1*01:32, DRB1*01:35, DRB1*03:43, DRB1*03:46, DRB1*03:54, DRB1*04:03, DRB1*04:04, DRB1*04:16, DRB1*04:39, DRB1*04:47, DRB1*07:03, DRB1*08:06, DRB1*08:07, DRB1*08:34, DRB1*09:07, DRB1*10:02, DRB1*11:45, DRB1*11:59, DRB1*11:74, DRB1*12:07, DRB1*12:16, DRB1*13:13, DRB1*13:33, DRB1*14:42, DRB1*14:53, DRB1*15:21, DRB1*15:44, DRB1*16:16, DRB3*01:05, DRB3*01:12, DRB3*02:04, DRB3*02:12, DRB3*02:23, DRB3*02:24, DRB3*03:01, DRB3*03:03, DRB4*01:01, DRB4*01:03, DRB4*01:06, DRB4*01:07, DRB4*01:08, DRB5*01:02, DRB5*01:08 N, DRB5*01:14, DRB5*02:03, DRB5*02:04, DPA1*02:04 DPB1*48:01, DPA1*02:02 DPB1*118:01, DPA1*04:01DPB1*69:01, DQA1*01:04DQB1*03:07, DQA1*03:03 DQB1*06:35, DQA1*04:04DQB1*05:01 | 23–37 | 17 | 0.50 | 86.67% | Nontoxin | 0.4 | 2.22 | −1.59 | 0 | 1783.49 |
| Nucleocapsid Protein (P59595) |
PRWYFYYLGTGPEAS | DRB1*01:06, DRB1*01:11, DRB1*01:24, DRB1*01:29, DRB1*01:30, DRB1*01:36, DRB1*03:38, DRB1*03:40, DRB1*03:49, DRB1*040, DRB1*04:16, DRB1*04:34, DRB1*07:03, DRB1*07:11, DRB1*08:05, DRB1*08:21, DRB1*09:03, DRB1*09:09, DRB1*10:01, DRB1*10:02, DRB1*11:70, DRB1*11:83, DRB1*12:03, DRB1*12:18, DRB1*13:10, DRB1*13:12, DRB1*14:52, DRB1*14:53, DRB1*15:26, DRB1*15:44, DRB1*16:14, DRB3*01:13, DRB3*01:14, DRB3*02:07, DRB3*02:16, DRB3*02:23, DRB3*03:03, DRB4*01:04, DRB4*01:06, DRB4*01:07, DRB5*01:02, DRB5*01:01, DRB5*01:05, DRB5*01:11, DRB5*02:04, DPA1*03:02 DPB1*46:01, DPA1*02:02 DPB1*118:01, DPA1*04:01DPB1*69:01, DQA1*01:04DQB1*03:07, DQA1*03:03 DQB1*06:35, DQA1*04:04DQB1*05:01 | 107–121 | 44 | 0.50 | 93.33% | Nontoxin | −0.05 | −0.66 | −0.61 | 0 | 1807.2 |