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:

  1. Tight binding (IC50 affinity ≤ 50 nM)
  2. Moderate binding (50 nM < IC50 affinity ≤ 500 nM)
  3. 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.

HLA-DRB1*01:02

NSP3 protein

T428I

Reference  SVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLV
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Mutated    SVEQRKQDDKKIKACVEEVTTTLEEIKFLTENLLLYIDINGNLHPDSATLV

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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

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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

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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

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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

Export table to csv 
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