Summary
This strain contains 15 protein-level mutations:
- 2 mutations in Spike protein: M153T, D614G
- 3 mutations in N protein: 203-204 RG->KR, G214C, P383L
- 2 mutations in NS9c protein: G50N, M60I
- 4 mutations in NSP3 protein: T428I, T725I, P1469S, F1569V
- 1 mutation in NSP4 protein: L438P
- 1 mutation in NSP6 protein: SGF 106-108 deletion
- 1 mutation in NSP12 protein: P323L
- 1 mutation in NSP16 protein: G213N
We identified all possible linear viral peptides affected by these mutations. Whenever it was possible, we matched the reference peptide with the mutated one. For example, D -> L mutation transformed SDNGPQNQR to SLNGPQNQR. Cases when it was not meaningful included deletions and insertions at the flanks of the peptide, e.g., HV deletion in NVTWFHAIHV peptide.
Then, we predicted binding affinities between the selected peptides and frequent HLA alleles. Predictions were made with NetMHCpan-4.1 and NetMHCIIpan-4.0. The binding affinities were classifies into three groups:
- Tight binding (IC50 affinity ≤ 50 nM)
- Moderate binding (50 nM < IC50 affinity ≤ 500 nM)
- Weak/no binding (IC50 affinity > 500 nM)
Here we report HLA-peptide interactions whose affinity was altered by at least two folds. Note that mutations with empty set of altered interactions are not showed.
The total number of interactions between HLA-DRB1*01:02 and peptides affected by the mutations
Weaker binding was found for 26 epitopes, while stronger binding was found for 101 entries. There are 408 tight binders for the HLA-DRB1*01:02 in the reference immunopeptidome (IC50 affinity ≤ 50 nM); 0 of them became non-tight binders (0.0%) and 0 novel tight binders appeared (0.0%). To avoid possible divisions by zero, we used + 1 regularization term in denominators when calculating percentages.
NSP3 protein
T428I
Reference SVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLV
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Mutated SVEQRKQDDKKIKACVEEVTTTLEEIKFLTENLLLYIDINGNLHPDSATLV
| Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
|---|---|---|---|---|
| HLA-DRB1*01:02 | TTLEETKFLTENLLL | TTLEEIKFLTENLLL | 1002 | 181 |
| HLA-DRB1*01:02 | TTTLEETKFLTENLL | TTTLEEIKFLTENLL | 1713 | 360 |
| HLA-DRB1*01:02 | TLEETKFLTENLLLY | TLEEIKFLTENLLLY | 586 | 128 |
| HLA-DRB1*01:02 | TTTLEETKFLTENLLLY | TTTLEEIKFLTENLLLY | 1560 | 374 |
| HLA-DRB1*01:02 | TTLEETKFLTENLLLY | TTLEEIKFLTENLLLY | 1536 | 418 |
| HLA-DRB1*01:02 | EETKFLTENLLLYID | EEIKFLTENLLLYID | 455 | 128 |
| HLA-DRB1*01:02 | LEETKFLTENLLLYI | LEEIKFLTENLLLYI | 438 | 133 |
| HLA-DRB1*01:02 | TTLEETKFLTENLLLYI | TTLEEIKFLTENLLLYI | 1183 | 369 |
| HLA-DRB1*01:02 | TLEETKFLTENLLLYID | TLEEIKFLTENLLLYID | 1118 | 370 |
| HLA-DRB1*01:02 | EETKFLTENLLLYIDIN | EEIKFLTENLLLYIDIN | 1156 | 388 |
| HLA-DRB1*01:02 | EETKFLTENLLLYIDI | EEIKFLTENLLLYIDI | 1256 | 433 |
| HLA-DRB1*01:02 | TLEETKFLTENLLLYI | TLEEIKFLTENLLLYI | 1251 | 433 |
| HLA-DRB1*01:02 | LEETKFLTENLLLYIDI | LEEIKFLTENLLLYIDI | 1092 | 384 |
| HLA-DRB1*01:02 | LEETKFLTENLLLYID | LEEIKFLTENLLLYID | 1207 | 455 |
| HLA-DRB1*01:02 | ETKFLTENLLLYIDI | EIKFLTENLLLYIDI | 507 | 217 |
T725I
Reference GQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTI
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Mutated GQSTQLGIEFLKRGDKSVYYTSNPTIFHLDGEVITFDNLKTLLSLREVRTI
| Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
|---|---|---|---|---|
| HLA-DRB1*01:02 | TSNPTTFHLDGEVIT | TSNPTIFHLDGEVIT | 1878 | 88 |
| HLA-DRB1*01:02 | SNPTTFHLDGEVITF | SNPTIFHLDGEVITF | 1026 | 58 |
| HLA-DRB1*01:02 | NPTTFHLDGEVITFD | NPTIFHLDGEVITFD | 1075 | 62 |
| HLA-DRB1*01:02 | PTTFHLDGEVITFDN | PTIFHLDGEVITFDN | 1320 | 77 |
| HLA-DRB1*01:02 | TSNPTTFHLDGEVITFD | TSNPTIFHLDGEVITFD | 2501 | 150 |
| HLA-DRB1*01:02 | SNPTTFHLDGEVITFD | SNPTIFHLDGEVITFD | 2244 | 135 |
| HLA-DRB1*01:02 | NPTTFHLDGEVITFDN | NPTIFHLDGEVITFDN | 2297 | 141 |
| HLA-DRB1*01:02 | SNPTTFHLDGEVITFDN | SNPTIFHLDGEVITFDN | 2420 | 149 |
| HLA-DRB1*01:02 | TSNPTTFHLDGEVITF | TSNPTIFHLDGEVITF | 2448 | 153 |
| HLA-DRB1*01:02 | NPTTFHLDGEVITFDNL | NPTIFHLDGEVITFDNL | 2576 | 161 |
| HLA-DRB1*01:02 | YTSNPTTFHLDGEVIT | YTSNPTIFHLDGEVIT | 3911 | 246 |
| HLA-DRB1*01:02 | YTSNPTTFHLDGEVITF | YTSNPTIFHLDGEVITF | 2728 | 177 |
| HLA-DRB1*01:02 | YTSNPTTFHLDGEVI | YTSNPTIFHLDGEVI | 3646 | 251 |
| HLA-DRB1*01:02 | PTTFHLDGEVITFDNL | PTIFHLDGEVITFDNL | 2816 | 208 |
| HLA-DRB1*01:02 | YYTSNPTTFHLDGEVIT | YYTSNPTIFHLDGEVIT | 3789 | 286 |
| HLA-DRB1*01:02 | YTSNPTTFHLDGEVITFDNL | YTSNPTIFHLDGEVITFDNL | 2511 | 192 |
| HLA-DRB1*01:02 | TTFHLDGEVITFDNL | TIFHLDGEVITFDNL | 1817 | 139 |
| HLA-DRB1*01:02 | TSNPTTFHLDGEVITFDNLK | TSNPTIFHLDGEVITFDNLK | 2561 | 197 |
| HLA-DRB1*01:02 | TSNPTTFHLDGEVITFDNL | TSNPTIFHLDGEVITFDNL | 3252 | 252 |
| HLA-DRB1*01:02 | YTSNPTTFHLDGEVITFDN | YTSNPTIFHLDGEVITFDN | 3225 | 252 |
| HLA-DRB1*01:02 | YTSNPTTFHLDGEVITFD | YTSNPTIFHLDGEVITFD | 5876 | 473 |
| HLA-DRB1*01:02 | TSNPTTFHLDGEVITFDN | TSNPTIFHLDGEVITFDN | 5747 | 464 |
| HLA-DRB1*01:02 | YYTSNPTTFHLDGEVITFDN | YYTSNPTIFHLDGEVITFDN | 2345 | 190 |
| HLA-DRB1*01:02 | PTTFHLDGEVITFDNLK | PTIFHLDGEVITFDNLK | 3034 | 246 |
| HLA-DRB1*01:02 | SNPTTFHLDGEVITFDNLK | SNPTIFHLDGEVITFDNLK | 3238 | 264 |
| HLA-DRB1*01:02 | YYTSNPTTFHLDGEVITFD | YYTSNPTIFHLDGEVITFD | 3127 | 259 |
| HLA-DRB1*01:02 | SNPTTFHLDGEVITFDNL | SNPTIFHLDGEVITFDNL | 5737 | 478 |
| HLA-DRB1*01:02 | SNPTTFHLDGEVITFDNLKT | SNPTIFHLDGEVITFDNLKT | 2266 | 207 |
| HLA-DRB1*01:02 | NPTTFHLDGEVITFDNLKT | NPTIFHLDGEVITFDNLKT | 3110 | 294 |
| HLA-DRB1*01:02 | VYYTSNPTTFHLDGEVITFD | VYYTSNPTIFHLDGEVITFD | 2041 | 196 |
| HLA-DRB1*01:02 | VYYTSNPTTFHLDGEVITF | VYYTSNPTIFHLDGEVITF | 2749 | 321 |
| HLA-DRB1*01:02 | NPTTFHLDGEVITFDNLKTL | NPTIFHLDGEVITFDNLKTL | 1967 | 234 |
| HLA-DRB1*01:02 | SVYYTSNPTTFHLDGEVITF | SVYYTSNPTIFHLDGEVITF | 1790 | 233 |
| HLA-DRB1*01:02 | PTTFHLDGEVITFDNLKTL | PTIFHLDGEVITFDNLKTL | 2688 | 485 |
| HLA-DRB1*01:02 | PTTFHLDGEVITFDNLKTLL | PTIFHLDGEVITFDNLKTLL | 1796 | 389 |
| HLA-DRB1*01:02 | KSVYYTSNPTTFHLDGEVIT | KSVYYTSNPTIFHLDGEVIT | 1301 | 312 |
NSP4 protein
L438P
Reference EEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSY
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Mutated EEAALCTFLLNKEMYLKLRSDVLLPPTQYNRYLALYNKYKYFSGAMDTTSY
| Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
|---|---|---|---|---|
| HLA-DRB1*01:02 | VLLPLTQYNRYLALY | VLLPPTQYNRYLALY | 359 | 1603 |
| HLA-DRB1*01:02 | DVLLPLTQYNRYLAL | DVLLPPTQYNRYLAL | 367 | 1596 |
| HLA-DRB1*01:02 | SDVLLPLTQYNRYLA | SDVLLPPTQYNRYLA | 422 | 1470 |
| HLA-DRB1*01:02 | LLPLTQYNRYLALYN | LLPPTQYNRYLALYN | 468 | 1336 |
| HLA-DRB1*01:02 | RSDVLLPLTQYNRYL | RSDVLLPPTQYNRYL | 425 | 947 |
| HLA-DRB1*01:02 | LKLRSDVLLPLTQYN | LKLRSDVLLPPTQYN | 414 | 855 |
NSP6 protein
SGF 106-108 deletion
Reference FNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYD
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Mutated FNMVYMPASWVMRIMTWLDMVDTSL‑‑‑KLKDCVMYASAVVLLILMTARTVYD
| Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
|---|---|---|---|---|
| HLA-DRB1*01:02 | FKLKDCVMYASAVVL | KLKDCVMYASAVVL | 156 | - |
| HLA-DRB1*01:02 | FKLKDCVMYASAVVLLI | - | 266 | - |
| HLA-DRB1*01:02 | WLDMVDTSLSGFKLK | WLDMVDTSLKLK | 269 | - |
| HLA-DRB1*01:02 | GFKLKDCVMYASAVVLL | - | 275 | - |
| HLA-DRB1*01:02 | GFKLKDCVMYASAVV | KLKDCVMYASAVV | 287 | - |
| HLA-DRB1*01:02 | MTWLDMVDTSLSGFK | MTWLDMVDTSLK | 303 | - |
| HLA-DRB1*01:02 | FKLKDCVMYASAVVLL | - | 306 | - |
| HLA-DRB1*01:02 | TWLDMVDTSLSGFKL | TWLDMVDTSLKL | 339 | - |
| HLA-DRB1*01:02 | TSLSGFKLKDCVMYASAVVLLIL | TSLKLKDCVMYASAVVLLIL | - | 349 |
| HLA-DRB1*01:02 | SGFKLKDCVMYASAVVLLIL | - | 349 | - |
| HLA-DRB1*01:02 | DTSLSGFKLKDCVMYASAVVLLI | DTSLKLKDCVMYASAVVLLI | - | 352 |
| HLA-DRB1*01:02 | LDMVDTSLSGFKLKD | LDMVDTSLKLKD | 360 | - |
| HLA-DRB1*01:02 | GFKLKDCVMYASAVVLLILM | - | 361 | - |
| HLA-DRB1*01:02 | SLSGFKLKDCVMYASAVVLLILM | SLKLKDCVMYASAVVLLILM | - | 362 |
| HLA-DRB1*01:02 | VDTSLSGFKLKDCVMYASAVVLL | VDTSLKLKDCVMYASAVVLL | - | 370 |
| HLA-DRB1*01:02 | MRIMTWLDMVDTSLS | MRIMTWLDMVDTSL | 375 | - |
| HLA-DRB1*01:02 | SGFKLKDCVMYASAVVL | KLKDCVMYASAVVL | 381 | - |
| HLA-DRB1*01:02 | IMTWLDMVDTSLSGF | IMTWLDMVDTSL | 390 | - |
| HLA-DRB1*01:02 | FKLKDCVMYASAVVLLILMT | - | 402 | - |
| HLA-DRB1*01:02 | LSGFKLKDCVMYASAVVLLILMT | LKLKDCVMYASAVVLLILMT | - | 404 |
| HLA-DRB1*01:02 | GFKLKDCVMYASAVVL | KLKDCVMYASAVVL | 413 | - |
| HLA-DRB1*01:02 | RIMTWLDMVDTSLSG | RIMTWLDMVDTSL | 431 | - |
| HLA-DRB1*01:02 | MVDTSLSGFKLKDCV | MVDTSLKLKDCV | 454 | - |
| HLA-DRB1*01:02 | MVDTSLSGFKLKDCVMYASAVVL | MVDTSLKLKDCVMYASAVVL | - | 473 |
| HLA-DRB1*01:02 | DMVDTSLSGFKLKDC | DMVDTSLKLKDC | 476 | - |
| HLA-DRB1*01:02 | TSLSGFKLKDCVMYASAVVLLI | TSLKLKDCVMYASAVVLLI | - | 480 |
| HLA-DRB1*01:02 | SGFKLKDCVMYASAVVLLI | - | 487 | - |
| HLA-DRB1*01:02 | DTSLSGFKLKDCVMYASAVVLL | DTSLKLKDCVMYASAVVLL | - | 494 |
| HLA-DRB1*01:02 | LSGFKLKDCVMYASAVVL | LKLKDCVMYASAVVL | 1376 | 159 |
| HLA-DRB1*01:02 | SLSGFKLKDCVMYASAVV | SLKLKDCVMYASAVV | 2151 | 301 |
| HLA-DRB1*01:02 | MRIMTWLDMVDTSLSGFK | MRIMTWLDMVDTSLK | 2049 | 308 |
| HLA-DRB1*01:02 | RIMTWLDMVDTSLSGFKL | RIMTWLDMVDTSLKL | 2054 | 330 |
| HLA-DRB1*01:02 | IMTWLDMVDTSLSGFKLK | IMTWLDMVDTSLKLK | 1818 | 308 |
| HLA-DRB1*01:02 | MTWLDMVDTSLSGFKLKD | MTWLDMVDTSLKLKD | 1961 | 440 |
NSP12 protein
P323L
Reference CVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF
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Mutated CVNCLDDRCILHCANFNVLFSTVFPLTSFGPLVRKIFVDGVPFVVSTGYHF
| Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
|---|---|---|---|---|
| HLA-DRB1*01:02 | FSTVFPPTSFGPLVR | FSTVFPLTSFGPLVR | 1639 | 141 |
| HLA-DRB1*01:02 | STVFPPTSFGPLVRK | STVFPLTSFGPLVRK | 1541 | 150 |
| HLA-DRB1*01:02 | FSTVFPPTSFGPLVRK | FSTVFPLTSFGPLVRK | 2677 | 348 |
| HLA-DRB1*01:02 | STVFPPTSFGPLVRKI | STVFPLTSFGPLVRKI | 2454 | 354 |
| HLA-DRB1*01:02 | FSTVFPPTSFGPLVRKI | FSTVFPLTSFGPLVRKI | 1981 | 295 |
| HLA-DRB1*01:02 | TVFPPTSFGPLVRKI | TVFPLTSFGPLVRKI | 1055 | 159 |
| HLA-DRB1*01:02 | LFSTVFPPTSFGPLVRK | LFSTVFPLTSFGPLVRK | 1898 | 341 |
| HLA-DRB1*01:02 | STVFPPTSFGPLVRKIF | STVFPLTSFGPLVRKIF | 1594 | 288 |
| HLA-DRB1*01:02 | LFSTVFPPTSFGPLVR | LFSTVFPLTSFGPLVR | 2446 | 448 |
| HLA-DRB1*01:02 | TVFPPTSFGPLVRKIF | TVFPLTSFGPLVRKIF | 1718 | 338 |
| HLA-DRB1*01:02 | VFPPTSFGPLVRKIF | VFPLTSFGPLVRKIF | 712 | 152 |
| HLA-DRB1*01:02 | TVFPPTSFGPLVRKIFV | TVFPLTSFGPLVRKIFV | 1308 | 312 |
| HLA-DRB1*01:02 | FSTVFPPTSFGPLVRKIFVD | FSTVFPLTSFGPLVRKIFVD | 1348 | 324 |
| HLA-DRB1*01:02 | STVFPPTSFGPLVRKIFVDG | STVFPLTSFGPLVRKIFVDG | 1445 | 356 |
| HLA-DRB1*01:02 | LFSTVFPPTSFGPLVRKIF | LFSTVFPLTSFGPLVRKIF | 1760 | 437 |
| HLA-DRB1*01:02 | FSTVFPPTSFGPLVRKIFV | FSTVFPLTSFGPLVRKIFV | 1725 | 438 |
| HLA-DRB1*01:02 | VFPPTSFGPLVRKIFV | VFPLTSFGPLVRKIFV | 1437 | 375 |
| HLA-DRB1*01:02 | STVFPPTSFGPLVRKIFVD | STVFPLTSFGPLVRKIFVD | 1866 | 493 |
| HLA-DRB1*01:02 | VFPPTSFGPLVRKIFVD | VFPLTSFGPLVRKIFVD | 1364 | 366 |
| HLA-DRB1*01:02 | LFSTVFPPTSFGPLVRKIFV | LFSTVFPLTSFGPLVRKIFV | 1128 | 306 |
| HLA-DRB1*01:02 | LFSTVFPPTSFGPLV | LFSTVFPLTSFGPLV | 1104 | 304 |
| HLA-DRB1*01:02 | VLFSTVFPPTSFGPLVR | VLFSTVFPLTSFGPLVR | 1537 | 431 |
| HLA-DRB1*01:02 | FPPTSFGPLVRKIFV | FPLTSFGPLVRKIFV | 653 | 185 |
| HLA-DRB1*01:02 | VLFSTVFPPTSFGPLVRKI | VLFSTVFPLTSFGPLVRKI | 1741 | 495 |
| HLA-DRB1*01:02 | TVFPPTSFGPLVRKIFVDGV | TVFPLTSFGPLVRKIFVDGV | 1223 | 374 |
| HLA-DRB1*01:02 | VLFSTVFPPTSFGPLVRKIF | VLFSTVFPLTSFGPLVRKIF | 1018 | 315 |
| HLA-DRB1*01:02 | VFPPTSFGPLVRKIFVDGVP | VFPLTSFGPLVRKIFVDGVP | 1151 | 398 |
| HLA-DRB1*01:02 | PPTSFGPLVRKIFVD | PLTSFGPLVRKIFVD | 951 | 335 |
| HLA-DRB1*01:02 | NVLFSTVFPPTSFGPLVRKI | NVLFSTVFPLTSFGPLVRKI | 990 | 349 |
| HLA-DRB1*01:02 | ANFNVLFSTVFPPTS | ANFNVLFSTVFPLTS | 332 | 133 |
| HLA-DRB1*01:02 | CANFNVLFSTVFPPT | CANFNVLFSTVFPLT | 527 | 228 |
| HLA-DRB1*01:02 | FNVLFSTVFPPTSFGPLVRK | FNVLFSTVFPLTSFGPLVRK | 899 | 399 |
| HLA-DRB1*01:02 | FPPTSFGPLVRKIFVDGVPF | FPLTSFGPLVRKIFVDGVPF | 1025 | 482 |
| HLA-DRB1*01:02 | NVLFSTVFPPTSFGP | NVLFSTVFPLTSFGP | 490 | 238 |
| HLA-DRB1*01:02 | VLFSTVFPPTSFGPL | VLFSTVFPLTSFGPL | 658 | 321 |
| HLA-DRB1*01:02 | HCANFNVLFSTVFPP | HCANFNVLFSTVFPL | 745 | 368 |