Summary

This strain contains 20 protein-level mutations:

  • 6 mutations in Spike protein: L5F, HV 69-70 deletion, T95I, D614G, T859N, D950H
  • 2 mutations in N protein: T205I, M234I
  • 2 mutations in NS3 protein: P42L, Q57H
  • 2 mutations in NS8 protein: T11I, A51S
  • 1 mutation in NS9c protein: L52F
  • 1 mutation in NSP2 protein: T85I
  • 3 mutations in NSP4 protein: K399E, L438P, A446V
  • 2 mutations in NSP6 protein: SGF 106-108 deletion, V278I
  • 1 mutation in NSP12 protein: P323L

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 HLA-peptide interactions affected by the mutations

For each allele we calculated the number of peptides with increased and decreased affinitiy (two or more times). The absolute number of such peptides is showed on the left side of the figure (blue bars — weaker binding, orange bars — stronger).

While absolute numbers are of interest, they do not reflect the initial number of tighly binding peptides for the specific allele. Roughly speaking, if an allele had high number of tight binders, then vanished affinity of several peptides will not affect much the integral ability of peptide presentation. To the contrary, low number of vanished peptides could be important if the particular allele initially had narrow epitope repertoire. To account for this effect, we normalized the absolute numbers of new/vanished tight binders (IC50 affinity ≤ 50 nM) by the total number of tight binders for each allele. To avoid possible divisions by zero, we used + 1 regularization term in all denominators. For example, if some allele had no tight binders in the reference genome, and three new tight binders appeared as a result of the mutation, the relative increase will be 300%. The results are showed in the right part of the figure. Protein-specific plots are listed below.

Summary

Spike protein

Spike

L5F

Reference  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTN
           |||| |||||||||||||||||||||||||
Mutated    MFVFFVLLPLVSSQCVNLTTRTQLPPAYTN

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 FLVLLPLV FFVLLPLV 34 5226
HLA-A*02:01 FLVLLPLV FFVLLPLV 83 8821
HLA-A*02:02 FLVLLPLV FFVLLPLV 139 7441
HLA-A*02:06 FLVLLPLV FFVLLPLV 144 4618
HLA-A*02:02 FLVLLPLVSS FFVLLPLVSS 379 5854
HLA-A*02:11 FLVLLPLVSS FFVLLPLVSS 340 5067
HLA-A*02:01 FLVLLPLVSS FFVLLPLVSS 500 6333
HLA-A*02:11 FLVLLPLVSSQCV FFVLLPLVSSQCV 134 1444
HLA-A*02:02 FLVLLPLVSSQCV FFVLLPLVSSQCV 484 4599
HLA-A*02:01 FLVLLPLVSSQCV FFVLLPLVSSQCV 462 4095
HLA-A*02:06 LVLLPLVSS FVLLPLVSS 1562 285
HLA-A*68:02 FVFLVLLPL FVFFVLLPL 212 40
HLA-A*68:02 MFVFLVLLPL MFVFFVLLPL 354 78
HLA-A*68:02 FVFLVLLPLV FVFFVLLPLV 128 32
HLA-A*02:06 LVLLPLVSSQCV FVLLPLVSSQCV 656 174
HLA-A*02:02 FVFLVLLPL FVFFVLLPL 132 44
HLA-A*02:01 FVFLVLLPL FVFFVLLPL 125 46
HLA-C*14:02 VFLVLLPL VFFVLLPL 782 313
HLA-A*02:11 FVFLVLLPL FVFFVLLPL 17 7
HLA-A*02:11 MFVFLVLLPL MFVFFVLLPL 269 116
HLA-A*02:06 FVFLVLLPL FVFFVLLPL 67 30
HLA-A*02:02 FVFLVLLPLV FVFFVLLPLV 104 48
HLA-A*02:11 LVLLPLVSSQCV FVLLPLVSSQCV 290 135
HLA-C*12:03 FVFLVLLPL FVFFVLLPL 215 102
HLA-C*12:02 FVFLVLLPL FVFFVLLPL 609 292
HLA-A*02:02 MFVFLVLLPL MFVFFVLLPL 395 193

HV 69-70 deletion

Reference  RSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFAST
           |||||||||||||||||||||||||  |||||||||||||||||||||||||
Mutated    RSSVLHSTQDLFLPFFSNVTWFHAI‑‑SGTNGTKRFDNPVLPFNDGVYFASI

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:02 NVTWFHAIHV - 16 -
HLA-A*68:01 HVSGTNGTKR - 42 -
HLA-A*02:11 NVTWFHAIHV - 125 -
HLA-A*02:11 FFSNVTWFHAIHV - 219 -
HLA-A*02:11 FSNVTWFHAIHV - 250 -
HLA-A*02:06 NVTWFHAIHV - 263 -
HLA-A*68:02 FSNVTWFHAIHV - 311 -
HLA-A*02:06 FSNVTWFHAIHV - 449 -
HLA-A*02:02 NVTWFHAIHV - 468 -
HLA-A*68:02 FFSNVTWFHAIHV - 492 -
HLA-A*11:01 HAIHVSGTNGTK HAISGTNGTK 2998 438
HLA-A*03:02 AIHVSGTNGTK AISGTNGTK 1179 271
HLA-A*68:01 HAIHVSGTNGTK HAISGTNGTK 174 43
HLA-A*11:01 AIHVSGTNGTK AISGTNGTK 742 223
HLA-A*03:01 AIHVSGTNGTK AISGTNGTK 534 196
HLA-A*33:03 HAIHVSGTNGTKR HAISGTNGTKR 374 755

T95I

Reference  VSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    ‑SGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIV

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*57:01 STEKSNIIRGW SIEKSNIIRGW 135 2014
HLA-B*58:01 STEKSNIIRGW SIEKSNIIRGW 183 2582
HLA-B*42:01 LPFNDGVYFAST LPFNDGVYFASI 4329 325
HLA-B*53:01 LPFNDGVYFAST LPFNDGVYFASI 6125 497
HLA-C*12:03 ASTEKSNII ASIEKSNII 2443 439
HLA-A*31:01 ASTEKSNIIR ASIEKSNIIR 1324 354
HLA-C*03:03 FASTEKSNII FASIEKSNII 1633 453
HLA-C*03:04 FASTEKSNII FASIEKSNII 1633 453
HLA-A*68:01 ASTEKSNIIR ASIEKSNIIR 1387 410
HLA-C*12:03 FASTEKSNII FASIEKSNII 902 268
HLA-A*11:01 ASTEKSNIIR ASIEKSNIIR 1555 495
HLA-C*15:02 ASTEKSNII ASIEKSNII 729 264
HLA-B*44:02 TEKSNIIRGW IEKSNIIRGW 20 55
HLA-B*44:03 TEKSNIIRGW IEKSNIIRGW 33 84
HLA-C*16:01 ASTEKSNII ASIEKSNII 603 239
HLA-A*68:01 STEKSNIIR SIEKSNIIR 186 458
HLA-A*33:03 YFASTEKSNIIR YFASIEKSNIIR 337 148
HLA-A*11:01 GVYFASTEKS GVYFASIEKS 648 298
HLA-A*11:01 DGVYFASTEK DGVYFASIEK 205 96
HLA-B*58:01 ASTEKSNIIRGW ASIEKSNIIRGW 245 122

D614G

Reference  PCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTG
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    PCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTG

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*05:01 YQDVNCTEV YQGVNCTEV 82 8597
HLA-C*08:02 YQDVNCTEV YQGVNCTEV 89 8066
HLA-A*02:11 DVNCTEVPV GVNCTEVPV 2140 72
HLA-A*02:02 DVNCTEVPV GVNCTEVPV 4099 213
HLA-A*68:02 DVNCTEVPV GVNCTEVPV 36 659
HLA-A*02:06 DVNCTEVPV GVNCTEVPV 3807 208
HLA-A*68:02 QVAVLYQDV QVAVLYQGV 183 13
HLA-A*68:02 NQVAVLYQDV NQVAVLYQGV 650 52
HLA-A*02:06 QVAVLYQDV QVAVLYQGV 1312 148
HLA-A*02:11 QVAVLYQDV QVAVLYQGV 2169 268
HLA-A*68:02 NTSNQVAVLYQDV NTSNQVAVLYQGV 1858 231
HLA-A*68:02 TSNQVAVLYQDV TSNQVAVLYQGV 3281 457
HLA-A*02:02 QVAVLYQDV QVAVLYQGV 1107 188
HLA-A*02:01 YQDVNCTEV YQGVNCTEV 75 315
HLA-A*02:06 YQDVNCTEV YQGVNCTEV 17 57
HLA-A*02:11 VLYQDVNCT VLYQGVNCT 224 74
HLA-A*02:11 YQDVNCTEV YQGVNCTEV 31 93
HLA-A*02:11 VLYQDVNCTEVP VLYQGVNCTEVP 1000 402
HLA-A*02:02 NQVAVLYQDV NQVAVLYQGV 269 116
HLA-A*02:11 AVLYQDVNCTEV AVLYQGVNCTEV 500 238
HLA-A*02:01 NQVAVLYQDV NQVAVLYQGV 558 267
HLA-A*02:06 NQVAVLYQDV NQVAVLYQGV 36 18

T859N

Reference  IKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITS
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    IKQYGDCLGDIAARDLICAQKFNGLNVLPPLLTDEMIAQYTSALLAGTITS

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*15:03 AQKFNGLTV AQKFNGLNV 65 252
HLA-B*15:01 AQKFNGLTV AQKFNGLNV 210 628
HLA-A*02:11 FNGLTVLPPLL FNGLNVLPPLL 171 68
HLA-A*02:11 GLTVLPPLL GLNVLPPLL 29 14

D950H

Reference  NQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISS
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    NQFNSAIGKIQDSLSSTASALGKLQHVVNQNAQALNTLVKQLSSNFGAISS

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 ALGKLQDVV ALGKLQHVV 103 12
HLA-A*02:11 ALGKLQDV ALGKLQHV 2627 370
HLA-A*02:02 KLQDVVNQNAQAL KLQHVVNQNAQAL 81 495
HLA-A*02:11 KLQDVVNQNAQAL KLQHVVNQNAQAL 71 341
HLA-A*02:11 KLQDVVNQNAQA KLQHVVNQNAQA 95 455
HLA-A*02:02 KLQDVVNQNAQA KLQHVVNQNAQA 318 1510
HLA-A*02:11 SALGKLQDVV SALGKLQHVV 1227 264
HLA-A*02:01 KLQDVVNQNAQAL KLQHVVNQNAQAL 435 2021
HLA-A*02:11 SALGKLQDV SALGKLQHV 475 104
HLA-A*02:06 SALGKLQDV SALGKLQHV 258 60
HLA-A*02:01 ALGKLQDVV ALGKLQHVV 852 203
HLA-A*02:11 KLQDVVNQNA KLQHVVNQNA 56 228
HLA-A*02:02 KLQDVVNQNA KLQHVVNQNA 129 519
HLA-C*12:03 SALGKLQDV SALGKLQHV 197 54
HLA-C*15:02 SALGKLQDV SALGKLQHV 566 182
HLA-A*02:02 ALGKLQDVV ALGKLQHVV 129 48
HLA-A*68:02 STASALGKLQDV STASALGKLQHV 442 168
HLA-B*15:03 LQDVVNQNAQAL LQHVVNQNAQAL 1044 416
HLA-C*16:01 SALGKLQDV SALGKLQHV 160 70
HLA-A*68:02 STASALGKLQDVV STASALGKLQHVV 414 202

N protein

N

T205I

Reference  SQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQL
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    SQASSRSSSRSRNSSRNSTPGSSRGISPARMAGNGGDAALALLLLDRLNQL

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*01:02 STPGSSRGT STPGSSRGI 10810 468
HLA-A*30:01 GTSPARMAG GISPARMAG 493 1901
HLA-A*68:01 SSRGTSPAR SSRGISPAR 186 61
HLA-A*68:01 STPGSSRGTSPAR STPGSSRGISPAR 860 288
HLA-A*30:01 RGTSPARMA RGISPARMA 1160 422
HLA-A*68:01 GSSRGTSPAR GSSRGISPAR 615 248
HLA-A*31:01 GSSRGTSPAR GSSRGISPAR 262 111
HLA-A*33:03 SSRGTSPAR SSRGISPAR 106 46
HLA-A*33:03 STPGSSRGTSPAR STPGSSRGISPAR 968 473

M234I

Reference  RMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPR
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    RMAGNGGDAALALLLLDRLNQLESKISGKGQQQQGQTVTKKSAAEASKKPR

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*15:03 RLNQLESKM RLNQLESKI 210 3572
HLA-B*15:01 RLNQLESKM RLNQLESKI 434 5192
HLA-A*02:11 LLLDRLNQLESKM LLLDRLNQLESKI 1721 220
HLA-A*32:01 RLNQLESKM RLNQLESKI 1285 261
HLA-A*02:11 RLNQLESKM RLNQLESKI 584 173

NS3 protein

NS3

P42L

Reference  QGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSASKIITLKK
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    QGEIKDATPSDFVRATATIPIQASLLFGWLIVGVALLAVFHSASKIITLKK

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:01 LPFGWLIVGV LLFGWLIVGV 4732 8
HLA-A*02:11 LPFGWLIVGV LLFGWLIVGV 1743 3
HLA-A*02:11 LPFGWLIVGVAL LLFGWLIVGVAL 14245 29
HLA-A*02:02 LPFGWLIVGV LLFGWLIVGV 3442 11
HLA-A*02:11 LPFGWLIVGVA LLFGWLIVGVA 18600 65
HLA-C*01:02 TIPIQASLP TIPIQASLL 25201 102
HLA-B*42:01 LPFGWLIVGVAL LLFGWLIVGVAL 62 14834
HLA-A*02:11 LPFGWLIV LLFGWLIV 9504 41
HLA-B*35:01 LPFGWLIVG LLFGWLIVG 247 27950
HLA-B*35:01 LPFGWLIVGVAL LLFGWLIVGVAL 286 31951
HLA-B*51:01 LPFGWLIV LLFGWLIV 245 26530
HLA-A*02:06 LPFGWLIVGV LLFGWLIVGV 2421 23
HLA-A*02:11 LPFGWLIVG LLFGWLIVG 23342 241
HLA-A*02:02 LPFGWLIVGVAL LLFGWLIVGVAL 19947 226
HLA-A*02:01 LPFGWLIVGVAL LLFGWLIVGVAL 18634 236
HLA-A*02:01 LPFGWLIVGVA LLFGWLIVGVA 23543 342
HLA-B*07:02 LPFGWLIVGVAL LLFGWLIVGVAL 411 27790
HLA-A*02:11 LPFGWLIVGVALLA LLFGWLIVGVALLA 12056 210
HLA-A*02:01 LPFGWLIV LLFGWLIV 15645 295
HLA-A*02:11 LPFGWLIVGVALL LLFGWLIVGVALL 980 20
HLA-A*02:01 LPFGWLIVGVALL LLFGWLIVGVALL 2106 68
HLA-B*42:01 IPIQASLP IPIQASLL 6612 226
HLA-A*02:02 LPFGWLIVGVALL LLFGWLIVGVALL 762 31
HLA-A*02:11 PFGWLIVGV LFGWLIVGV 7794 398
HLA-C*15:02 ASLPFGWLI ASLLFGWLI 110 2004
HLA-A*68:02 ATIPIQASLP ATIPIQASLL 3074 222
HLA-B*58:01 ASLPFGWLI ASLLFGWLI 37 471
HLA-B*57:01 ASLPFGWLI ASLLFGWLI 116 1279
HLA-B*07:02 ATIPIQASLPF ATIPIQASLLF 308 3348
HLA-B*07:02 IPIQASLPF IPIQASLLF 24 259
HLA-B*07:02 TIPIQASLPF TIPIQASLLF 121 1294
HLA-A*02:06 ASLPFGWLI ASLLFGWLI 44 447
HLA-B*07:02 RATATIPIQASLPF RATATIPIQASLLF 206 2014
HLA-C*15:02 ASLPFGWLIV ASLLFGWLIV 460 4426
HLA-B*07:02 IPIQASLPFGWL IPIQASLLFGWL 157 1493
HLA-B*58:01 IQASLPFGWLI IQASLLFGWLI 310 2878
HLA-A*32:01 ASLPFGWLI ASLLFGWLI 63 550
HLA-A*02:11 ASLPFGWLI ASLLFGWLI 73 626
HLA-B*42:01 TIPIQASLPF TIPIQASLLF 121 888
HLA-B*35:01 TATIPIQASLPF TATIPIQASLLF 153 1104
HLA-A*23:01 ASLPFGWLI ASLLFGWLI 330 2218
HLA-B*35:01 TIPIQASLPF TIPIQASLLF 27 179
HLA-B*42:01 IPIQASLPF IPIQASLLF 20 121
HLA-A*02:06 ASLPFGWLIVGV ASLLFGWLIVGV 156 941
HLA-A*02:01 SLPFGWLIV SLLFGWLIV 221 38
HLA-A*02:11 SLPFGWLIVGVAL SLLFGWLIVGVAL 1004 174
HLA-A*02:06 IQASLPFGWLIV IQASLLFGWLIV 239 43
HLA-B*35:01 ATIPIQASLPF ATIPIQASLLF 488 2676
HLA-A*02:01 ASLPFGWLI ASLLFGWLI 500 2741
HLA-B*58:01 ASLPFGWLIV ASLLFGWLIV 475 2567
HLA-B*35:01 IPIQASLPFG IPIQASLLFG 290 1566
HLA-B*58:01 RATATIPIQASLPF RATATIPIQASLLF 890 176
HLA-B*15:01 TIPIQASLPF TIPIQASLLF 32 158
HLA-A*02:06 ASLPFGWLIV ASLLFGWLIV 88 426
HLA-B*15:01 ATATIPIQASLPF ATATIPIQASLLF 419 1991
HLA-B*35:03 IPIQASLPF IPIQASLLF 52 242
HLA-B*42:01 IPIQASLPFGWL IPIQASLLFGWL 106 491
HLA-A*02:06 IQASLPFGWL IQASLLFGWL 138 31
HLA-B*58:01 QASLPFGWLI QASLLFGWLI 81 349
HLA-C*03:03 IPIQASLPF IPIQASLLF 406 1653
HLA-C*03:04 IPIQASLPF IPIQASLLF 406 1653
HLA-B*57:01 QASLPFGWLI QASLLFGWLI 222 889
HLA-C*03:02 TATIPIQASLPF TATIPIQASLLF 461 1837
HLA-A*02:01 SLPFGWLIVGV SLLFGWLIVGV 170 44
HLA-B*15:03 TIPIQASLPF TIPIQASLLF 165 618
HLA-A*02:11 SLPFGWLIVGVALL SLLFGWLIVGVALL 622 168
HLA-B*15:01 ATIPIQASLPF ATIPIQASLLF 150 555
HLA-B*15:03 TATIPIQASLPF TATIPIQASLLF 412 1462
HLA-C*14:02 IPIQASLPF IPIQASLLF 425 1465
HLA-B*15:03 ATIPIQASLPF ATIPIQASLLF 307 1003
HLA-B*15:01 RATATIPIQASLPF RATATIPIQASLLF 429 1366
HLA-A*02:01 IQASLPFGWLIV IQASLLFGWLIV 1078 359
HLA-A*02:11 SLPFGWLIV SLLFGWLIV 21 7
HLA-A*02:11 IQASLPFGWLIV IQASLLFGWLIV 544 186
HLA-A*02:11 SLPFGWLIVGVA SLLFGWLIVGVA 663 228
HLA-B*15:03 RATATIPIQASLPF RATATIPIQASLLF 159 454
HLA-B*58:01 ATIPIQASLPF ATIPIQASLLF 250 91
HLA-A*02:06 SLPFGWLIV SLLFGWLIV 200 74
HLA-C*03:02 IPIQASLPF IPIQASLLF 140 373
HLA-A*02:01 IQASLPFGWL IQASLLFGWL 550 208
HLA-A*02:11 IQASLPFGWL IQASLLFGWL 342 132
HLA-A*02:11 ASLPFGWLIVGV ASLLFGWLIVGV 276 111
HLA-B*15:03 IPIQASLPF IPIQASLLF 39 93
HLA-A*02:06 IQASLPFGWLIVGV IQASLLFGWLIVGV 387 163
HLA-A*02:11 SLPFGWLIVGV SLLFGWLIVGV 26 11
HLA-B*53:01 IPIQASLPFG IPIQASLLFG 1146 491
HLA-B*53:01 TIPIQASLPF TIPIQASLLF 218 98
HLA-B*53:01 TATIPIQASLPF TATIPIQASLLF 937 423
HLA-B*57:01 ATIPIQASLPF ATIPIQASLLF 369 169
HLA-B*35:01 IPIQASLPF IPIQASLLF 3 6

Q57H

Reference  TATIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCN
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    TATIPIQASLLFGWLIVGVALLAVFHSASKIITLKKRWQLALSKGVHFVCN

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*15:01 FQSASKIITL FHSASKIITL 156 6196
HLA-A*02:06 FQSASKIITL FHSASKIITL 43 1441
HLA-A*02:01 FQSASKIITL FHSASKIITL 205 5629
HLA-A*02:11 FQSASKIITL FHSASKIITL 79 2010
HLA-A*02:02 FQSASKIITL FHSASKIITL 38 957
HLA-B*38:01 FQSASKIITL FHSASKIITL 2071 94
HLA-B*15:03 FQSASKIITL FHSASKIITL 88 851
HLA-C*03:03 QSASKIITL HSASKIITL 285 37
HLA-C*03:04 QSASKIITL HSASKIITL 285 37
HLA-C*03:02 QSASKIITL HSASKIITL 724 94
HLA-C*12:03 QSASKIITL HSASKIITL 250 34
HLA-C*12:02 QSASKIITL HSASKIITL 1730 284
HLA-C*02:02 QSASKIITL HSASKIITL 2653 440
HLA-C*02:10 QSASKIITL HSASKIITL 2653 440
HLA-A*68:02 QSASKIITL HSASKIITL 1085 232
HLA-C*17:01 QSASKIITL HSASKIITL 453 102
HLA-A*30:01 QSASKIITLK HSASKIITLK 727 164
HLA-A*30:01 LAVFQSASK LAVFHSASK 1169 264
HLA-C*15:02 QSASKIITL HSASKIITL 222 51
HLA-C*16:01 QSASKIITL HSASKIITL 52 12
HLA-A*68:01 QSASKIITLKK HSASKIITLKK 1356 322
HLA-A*30:01 QSASKIITLKK HSASKIITLKK 1813 486
HLA-A*68:01 QSASKIITLKKR HSASKIITLKKR 683 195
HLA-A*68:01 QSASKIITLK HSASKIITLK 35 10
HLA-A*02:11 LLAVFQSA LLAVFHSA 1121 356
HLA-A*31:01 QSASKIITLKKR HSASKIITLKKR 968 344
HLA-A*03:01 QSASKIITLK HSASKIITLK 214 83
HLA-A*03:01 AVFQSASKIITLKK AVFHSASKIITLKK 227 90
HLA-A*02:02 LLAVFQSASKII LLAVFHSASKII 298 727
HLA-A*03:01 AVFQSASK AVFHSASK 795 335
HLA-A*03:01 AVFQSASKIITLK AVFHSASKIITLK 74 32
HLA-A*03:02 AVFQSASKIITLKK AVFHSASKIITLKK 619 272
HLA-A*02:11 GVALLAVFQSA GVALLAVFHSA 895 401
HLA-A*68:01 AVFQSASKIITLK AVFHSASKIITLK 808 368
HLA-A*03:02 AVFQSASKIITLK AVFHSASKIITLK 170 82
HLA-A*02:11 VALLAVFQSA VALLAVFHSA 173 85
HLA-A*02:11 ALLAVFQSAS ALLAVFHSAS 691 340
HLA-A*02:01 ALLAVFQSA ALLAVFHSA 42 21
HLA-B*58:01 QSASKIITLKKRW HSASKIITLKKRW 142 71

NS8 protein

NS8

T11I

Reference  MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDP
           |||||||||| |||||||||||||||||||||||||
Mutated    MKFLVFLGIIITVAAFHQECSLQSCTQHQPYVVDDP

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:02 TTVAAFHQECSL ITVAAFHQECSL 288 2832
HLA-A*02:11 FLVFLGIIT FLVFLGIII 1125 153
HLA-A*02:01 FLVFLGIITT FLVFLGIIIT 83 564
HLA-B*15:01 FLGIITTVAAF FLGIIITVAAF 131 835
HLA-A*02:06 FLVFLGIITT FLVFLGIIIT 234 1444
HLA-A*02:11 FLVFLGIITT FLVFLGIIIT 45 273
HLA-A*02:06 LVFLGIITT LVFLGIIIT 366 2114
HLA-A*02:02 FLVFLGIITT FLVFLGIIIT 83 468
HLA-C*14:02 VFLGIITTV VFLGIIITV 189 1058
HLA-A*02:02 KFLVFLGIITTV KFLVFLGIIITV 215 1039
HLA-A*02:02 FLVFLGIITTV FLVFLGIIITV 57 257
HLA-B*15:01 VFLGIITTVAAF VFLGIIITVAAF 439 1864
HLA-B*15:03 FLGIITTVAAF FLGIIITVAAF 484 2052
HLA-B*15:01 LGIITTVAAF LGIIITVAAF 18 73
HLA-B*15:01 FLVFLGIITTVAAF FLVFLGIIITVAAF 485 1933
HLA-B*15:01 LVFLGIITTVAAF LVFLGIIITVAAF 219 851
HLA-A*02:06 KFLVFLGIITTV KFLVFLGIIITV 382 1347
HLA-C*03:02 GIITTVAAF GIIITVAAF 338 1191
HLA-A*02:01 KFLVFLGIITTV KFLVFLGIIITV 138 436
HLA-B*15:03 GIITTVAAF GIIITVAAF 40 123
HLA-A*02:06 FLVFLGIITTV FLVFLGIIITV 64 189
HLA-B*15:03 LGIITTVAAF LGIIITVAAF 123 360
HLA-A*02:11 KFLVFLGIITTV KFLVFLGIIITV 36 101
HLA-A*02:02 FLVFLGIITTVA FLVFLGIIITVA 263 730
HLA-A*02:01 FLVFLGIITTVA FLVFLGIIITVA 184 506
HLA-B*15:01 GIITTVAAF GIIITVAAF 18 48
HLA-A*02:11 FLVFLGIITTVA FLVFLGIIITVA 56 147
HLA-A*02:01 FLVFLGIITTV FLVFLGIIITV 25 64
HLA-A*02:11 MKFLVFLGIITTV MKFLVFLGIIITV 205 516
HLA-A*02:02 LVFLGIITTV LVFLGIIITV 94 217
HLA-A*02:02 FLGIITTV FLGIIITV 29 66
HLA-A*02:11 FLVFLGIITTVAA FLVFLGIIITVAA 248 557
HLA-A*02:06 FLGIITTVAA FLGIIITVAA 282 603
HLA-A*02:11 FLVFLGIITTV FLVFLGIIITV 7 14

A51S

Reference  TQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIELCVDEAGSKSPIQYIDI
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    TQHQPYVVDDPCPIHFYSKWYIRVGSRKSAPLIELCVDEAGSKSPIQYIDI

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:02 YSKWYIRVGA YSKWYIRVGS 262 3511
HLA-A*30:01 YSKWYIRVGA YSKWYIRVGS 229 894
HLA-A*30:01 GARKSAPLI GSRKSAPLI 55 19
HLA-A*30:01 VGARKSAPLI VGSRKSAPLI 599 249

NS9c protein

NS9c

L52F

Reference  VKPLLVPHHVVATVQEIQLQAAVGELLLLEWLAMAVMLLLLCCCLTD
           ||||||||||||||||||||||||| |||||||||||||||||||||
Mutated    VKPLLVPHHVVATVQEIQLQAAVGEFLLLEWLAMAVMLLLLCCCLTD

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 QLQAAVGEL QLQAAVGEF 120 5031
HLA-A*02:11 GELLLLEWLA GEFLLLEWLA 267 9767
HLA-B*15:01 QLQAAVGEL QLQAAVGEF 2048 65
HLA-A*02:01 GELLLLEWLA GEFLLLEWLA 409 12481
HLA-A*02:02 QLQAAVGEL QLQAAVGEF 92 2789
HLA-B*15:03 QLQAAVGEL QLQAAVGEF 2231 81
HLA-A*02:02 IQLQAAVGEL IQLQAAVGEF 170 4413
HLA-A*02:11 ELLLLEWLA EFLLLEWLA 345 8719
HLA-A*02:11 IQLQAAVGEL IQLQAAVGEF 338 7506
HLA-B*15:01 IQLQAAVGEL IQLQAAVGEF 467 24
HLA-B*15:03 IQLQAAVGEL IQLQAAVGEF 168 10
HLA-B*15:03 LQAAVGEL LQAAVGEF 295 18
HLA-B*15:03 VQEIQLQAAVGEL VQEIQLQAAVGEF 6575 430
HLA-A*02:11 LLLLEWLAM FLLLEWLAM 283 20
HLA-B*40:01 QEIQLQAAVGEL QEIQLQAAVGEF 201 2708
HLA-B*15:01 LQAAVGEL LQAAVGEF 1712 138
HLA-A*02:01 LLLLEWLAM FLLLEWLAM 573 54
HLA-A*02:11 LLLLEWLA FLLLEWLA 844 82
HLA-A*02:02 LLLLEWLAM FLLLEWLAM 1379 150
HLA-B*44:03 QEIQLQAAVGEL QEIQLQAAVGEF 1386 164
HLA-A*02:06 LLLLEWLAM FLLLEWLAM 763 94
HLA-A*02:01 LLLLEWLA FLLLEWLA 1287 163
HLA-B*44:02 QEIQLQAAVGEL QEIQLQAAVGEF 1403 179
HLA-A*02:02 LLLLEWLA FLLLEWLA 2866 389
HLA-C*03:02 LLLLEWLAM FLLLEWLAM 2566 358
HLA-A*02:06 IQLQAAVGEL IQLQAAVGEF 280 1893
HLA-A*02:06 LLLLEWLA FLLLEWLA 2803 489
HLA-A*02:02 LLLLEWLAMA FLLLEWLAMA 67 13
HLA-A*02:01 ELLLLEWLAMA EFLLLEWLAMA 1276 266
HLA-A*02:11 QLQAAVGELLL QLQAAVGEFLL 733 157
HLA-B*40:02 QEIQLQAAVGEL QEIQLQAAVGEF 334 1488
HLA-A*02:06 LLLLEWLAMA FLLLEWLAMA 49 11
HLA-A*02:11 LLLLEWLAMAVM FLLLEWLAMAVM 926 212
HLA-A*02:02 LLLLEWLAMAVMLL FLLLEWLAMAVMLL 714 164
HLA-A*02:01 LLLLEWLAMAVML FLLLEWLAMAVML 1353 320
HLA-A*02:11 LLLLEWLAMAVML FLLLEWLAMAVML 385 97
HLA-A*02:11 LQAAVGELLL LQAAVGEFLL 1331 346
HLA-A*02:01 LLLLEWLAMA FLLLEWLAMA 23 6
HLA-A*02:11 ELLLLEWLAMA EFLLLEWLAMA 299 79
HLA-A*02:11 LLLLEWLAMAVMLL FLLLEWLAMAVMLL 544 146
HLA-A*02:01 LLLLEWLAMAVMLL FLLLEWLAMAVMLL 1361 373
HLA-B*40:01 GELLLLEWLAM GEFLLLEWLAM 791 222
HLA-B*15:03 AAVGELLLL AAVGEFLLL 1475 426
HLA-A*02:01 QLQAAVGELLL QLQAAVGEFLL 1401 441
HLA-A*02:02 LLLLEWLAMAV FLLLEWLAMAV 453 147
HLA-C*03:03 QAAVGELLL QAAVGEFLL 283 829
HLA-C*03:04 QAAVGELLL QAAVGEFLL 283 829
HLA-A*02:02 QLQAAVGELLL QLQAAVGEFLL 530 186
HLA-B*50:01 GELLLLEWLA GEFLLLEWLA 1298 484
HLA-A*02:11 LLLLEWLAMA FLLLEWLAMA 8 3
HLA-A*02:01 LQAAVGELLL LQAAVGEFLL 917 347
HLA-C*03:03 AAVGELLLL AAVGEFLLL 107 41
HLA-C*03:04 AAVGELLLL AAVGEFLLL 107 41
HLA-A*02:06 LQAAVGELLL LQAAVGEFLL 162 63
HLA-B*40:06 GELLLLEWLA GEFLLLEWLA 268 106
HLA-B*40:02 GELLLLEWLAM GEFLLLEWLAM 201 83
HLA-A*02:02 LQAAVGELLL LQAAVGEFLL 100 42
HLA-C*03:02 AAVGELLLL AAVGEFLLL 269 116
HLA-A*02:01 LLLLEWLAMAV FLLLEWLAMAV 97 44
HLA-A*02:11 QLQAAVGELL QLQAAVGEFL 303 139
HLA-B*15:01 LQAAVGELLL LQAAVGEFLL 109 237
HLA-B*15:03 LQAAVGELLL LQAAVGEFLL 98 210
HLA-A*02:11 LQAAVGELL LQAAVGEFL 386 183
HLA-B*40:02 GELLLLEWLAMAV GEFLLLEWLAMAV 815 391
HLA-B*40:02 GELLLLEWLA GEFLLLEWLA 475 231
HLA-A*02:06 IQLQAAVGELLL IQLQAAVGEFLL 626 310
HLA-C*16:01 AAVGELLLL AAVGEFLLL 205 102

NSP2 protein

NSP2

T85I

Reference  WYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEK
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    WYTERSEKSYELQTPFEIKLAKKFDIFNGECPNFVFPLNSIIKTIQPRVEK

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:02 DTFNGECPNFVFPL DIFNGECPNFVFPL 203 1683
HLA-A*68:02 DTFNGECPNFV DIFNGECPNFV 60 311
HLA-A*32:01 KLAKKFDTF KLAKKFDIF 44 159
HLA-A*24:02 KLAKKFDTF KLAKKFDIF 237 578
HLA-B*15:03 KKFDTFNGECPNF KKFDIFNGECPNF 226 542
HLA-A*23:01 TFNGECPNF IFNGECPNF 517 219
HLA-A*23:01 TFNGECPNFVF IFNGECPNFVF 425 191
HLA-A*23:01 KLAKKFDTF KLAKKFDIF 284 624

NSP4 protein

NSP4

K399E

Reference  PFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNK
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    PFWITIAYIICISTKHFYWFFSNYLERRVVFNGVSFSTFEEAALCTFLLNK

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*11:01 STKHFYWFFSNYLK STKHFYWFFSNYLE 23 19000
HLA-A*03:02 STKHFYWFFSNYLK STKHFYWFFSNYLE 99 19924
HLA-A*68:01 STKHFYWFFSNYLK STKHFYWFFSNYLE 44 7593
HLA-A*31:01 FYWFFSNYLK FYWFFSNYLE 36 3176
HLA-A*31:01 HFYWFFSNYLK HFYWFFSNYLE 59 5103
HLA-A*68:01 FYWFFSNYLK FYWFFSNYLE 38 3279
HLA-A*11:01 YWFFSNYLK YWFFSNYLE 183 14582
HLA-A*68:01 HFYWFFSNYLK HFYWFFSNYLE 108 8458
HLA-A*31:01 YWFFSNYLK YWFFSNYLE 40 2756
HLA-A*03:01 STKHFYWFFSNYLK STKHFYWFFSNYLE 312 21449
HLA-A*11:01 FYWFFSNYLK FYWFFSNYLE 290 19830
HLA-A*03:02 FYWFFSNYLK FYWFFSNYLE 184 12494
HLA-A*03:02 YWFFSNYLK YWFFSNYLE 150 9439
HLA-A*03:02 HFYWFFSNYLK HFYWFFSNYLE 259 15089
HLA-A*68:01 YWFFSNYLK YWFFSNYLE 50 2894
HLA-A*11:01 HFYWFFSNYLK HFYWFFSNYLE 455 24513
HLA-A*31:01 STKHFYWFFSNYLK STKHFYWFFSNYLE 169 8198
HLA-A*33:03 FYWFFSNYLK FYWFFSNYLE 45 2158
HLA-B*08:01 YLKRRVVFNGVSF YLERRVVFNGVSF 53 2200
HLA-A*33:03 HFYWFFSNYLK HFYWFFSNYLE 105 4130
HLA-A*31:01 KHFYWFFSNYLK KHFYWFFSNYLE 101 3884
HLA-A*33:03 YWFFSNYLK YWFFSNYLE 53 1783
HLA-B*08:01 SNYLKRRVV SNYLERRVV 131 3344
HLA-B*08:01 YLKRRVVFNGV YLERRVVFNGV 218 5504
HLA-A*30:01 YWFFSNYLK YWFFSNYLE 318 7629
HLA-A*30:01 HFYWFFSNYLK HFYWFFSNYLE 463 10847
HLA-A*30:01 STKHFYWFFSNYLK STKHFYWFFSNYLE 356 7660
HLA-B*27:05 KRRVVFNGV ERRVVFNGV 284 4785
HLA-B*08:01 YLKRRVVF YLERRVVF 10 122
HLA-A*30:01 KRRVVFNGV ERRVVFNGV 486 5351
HLA-A*29:02 FYWFFSNYLK FYWFFSNYLE 292 2013
HLA-A*29:02 YWFFSNYLK YWFFSNYLE 219 1202
HLA-A*68:01 FFSNYLKRR FFSNYLERR 1541 310
HLA-B*15:01 YLKRRVVFNGVSF YLERRVVFNGVSF 210 1013
HLA-B*15:03 LKRRVVFNGVSF LERRVVFNGVSF 74 324
HLA-B*15:03 KRRVVFNGVSF ERRVVFNGVSF 328 1183
HLA-C*14:02 SNYLKRRVVF SNYLERRVVF 202 61
HLA-A*68:02 FSNYLKRRV FSNYLERRV 1253 416
HLA-C*14:02 FSNYLKRRVVF FSNYLERRVVF 434 147
HLA-B*27:05 KRRVVFNGVSF ERRVVFNGVSF 387 1030
HLA-C*07:02 NYLKRRVVF NYLERRVVF 167 66
HLA-A*02:11 YLKRRVVFNGV YLERRVVFNGV 194 82
HLA-C*14:02 YWFFSNYLKRRVVF YWFFSNYLERRVVF 575 264
HLA-A*68:01 WFFSNYLKRR WFFSNYLERR 315 155

L438P

Reference  EEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSY
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    EEAALCTFLLNKEMYLKLRSDVLLPPTQYNRYLVLYNKYKYFSGAMDTTSY

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 KLRSDVLLPL KLRSDVLLPP 5 1146
HLA-C*06:02 LRSDVLLPL LRSDVLLPP 103 17926
HLA-A*02:11 YLKLRSDVLLPL YLKLRSDVLLPP 5 788
HLA-A*02:11 LKLRSDVLLPL LKLRSDVLLPP 93 14621
HLA-C*07:02 LRSDVLLPL LRSDVLLPP 104 15467
HLA-C*07:01 LRSDVLLPL LRSDVLLPP 104 15210
HLA-A*02:01 KLRSDVLLPL KLRSDVLLPP 10 1434
HLA-A*02:02 KLRSDVLLPL KLRSDVLLPP 6 686
HLA-A*02:11 MYLKLRSDVLLPL MYLKLRSDVLLPP 82 9276
HLA-A*02:02 LKLRSDVLLPL LKLRSDVLLPP 120 12620
HLA-A*02:01 LKLRSDVLLPL LKLRSDVLLPP 161 15657
HLA-A*02:02 MYLKLRSDVLLPL MYLKLRSDVLLPP 49 4677
HLA-A*02:02 LPLTQYNRYL LPPTQYNRYL 241 20700
HLA-B*08:01 YLKLRSDVLLPL YLKLRSDVLLPP 13 1103
HLA-A*02:01 YLKLRSDVLLPL YLKLRSDVLLPP 11 889
HLA-A*02:02 YLKLRSDVLLPL YLKLRSDVLLPP 6 417
HLA-A*02:06 KLRSDVLLPL KLRSDVLLPP 29 1825
HLA-A*02:01 MYLKLRSDVLLPL MYLKLRSDVLLPP 161 9143
HLA-C*14:02 MYLKLRSDVLLPL MYLKLRSDVLLPP 313 17335
HLA-C*08:02 RSDVLLPL RSDVLLPP 400 21753
HLA-B*27:05 LRSDVLLPL LRSDVLLPP 81 4120
HLA-B*15:03 LRSDVLLPL LRSDVLLPP 149 6800
HLA-B*27:05 KLRSDVLLPL KLRSDVLLPP 94 4082
HLA-A*02:06 YLKLRSDVLLPL YLKLRSDVLLPP 35 1507
HLA-A*02:01 KLRSDVLLPLT KLRSDVLLPPT 144 5473
HLA-A*02:02 KLRSDVLLPLT KLRSDVLLPPT 183 6897
HLA-B*08:01 EMYLKLRSDVLLPL EMYLKLRSDVLLPP 231 8566
HLA-B*38:01 LRSDVLLPL LRSDVLLPP 499 18496
HLA-A*02:11 EMYLKLRSDVLLPL EMYLKLRSDVLLPP 400 14119
HLA-B*08:01 MYLKLRSDVLLPL MYLKLRSDVLLPP 151 5303
HLA-B*27:05 YLKLRSDVLLPL YLKLRSDVLLPP 270 9416
HLA-A*32:01 KLRSDVLLPL KLRSDVLLPP 418 14267
HLA-A*30:01 LTQYNRYLA PTQYNRYLV 171 5507
HLA-A*02:02 YLKLRSDVLLPLT YLKLRSDVLLPPT 82 2621
HLA-C*16:01 LTQYNRYLAL PTQYNRYLVL 285 9019
HLA-A*02:02 EMYLKLRSDVLLPL EMYLKLRSDVLLPP 322 9290
HLA-B*27:05 MYLKLRSDVLLPL MYLKLRSDVLLPP 378 10377
HLA-A*02:11 LLPLTQYNRYLA LLPPTQYNRYLV 1450 57
HLA-B*15:01 LTQYNRYLAL PTQYNRYLVL 125 3068
HLA-A*02:11 KLRSDVLLPLT KLRSDVLLPPT 114 2763
HLA-A*23:01 MYLKLRSDVLLPL MYLKLRSDVLLPP 466 10083
HLA-B*15:01 KLRSDVLLPL KLRSDVLLPP 335 6450
HLA-A*02:06 LTQYNRYLAL PTQYNRYLVL 483 7006
HLA-B*15:03 LTQYNRYLAL PTQYNRYLVL 15 197
HLA-A*02:01 YLKLRSDVLLPLT YLKLRSDVLLPPT 177 2183
HLA-A*02:11 VLLPLTQYNRYLA VLLPPTQYNRYLV 229 19
HLA-B*08:01 LTQYNRYLAL PTQYNRYLVL 126 1517
HLA-A*68:02 LTQYNRYLA PTQYNRYLV 349 3473
HLA-A*11:01 LTQYNRYLALYNK PTQYNRYLVLYNK 388 3729
HLA-B*53:01 LPLTQYNRY LPPTQYNRY 497 4773
HLA-A*02:11 YLKLRSDVLLPLT YLKLRSDVLLPPT 115 1005
HLA-B*35:01 LPLTQYNRY LPPTQYNRY 66 540
HLA-A*02:02 LLPLTQYNRYLA LLPPTQYNRYLV 1272 178
HLA-B*08:01 YLKLRSDVLLPLT YLKLRSDVLLPPT 258 1470
HLA-A*01:01 LTQYNRYLALY PTQYNRYLVLY 400 1908
HLA-A*02:01 VLLPLTQYNRYLA VLLPPTQYNRYLV 545 117
HLA-A*02:06 VLLPLTQYNRYLA VLLPPTQYNRYLV 1552 412
HLA-A*02:11 LLPLTQYNRYL LLPPTQYNRYL 389 105
HLA-A*30:01 KLRSDVLLPL KLRSDVLLPP 108 390
HLA-A*30:02 LTQYNRYLALY PTQYNRYLVLY 92 330
HLA-A*02:02 VLLPLTQYNRYLA VLLPPTQYNRYLV 980 284
HLA-B*07:02 LPLTQYNRYLAL LPPTQYNRYLVL 100 333
HLA-A*02:01 VLLPLTQYNRYLAL VLLPPTQYNRYLVL 343 1088
HLA-A*29:02 LTQYNRYLALY PTQYNRYLVLY 212 636
HLA-B*08:01 LPLTQYNRYLAL LPPTQYNRYLVL 58 163
HLA-A*02:02 LLPLTQYNRYL LLPPTQYNRYL 400 145
HLA-B*08:01 LLPLTQYNRYLAL LLPPTQYNRYLVL 190 517
HLA-A*02:01 VLLPLTQYNRYL VLLPPTQYNRYL 170 445
HLA-B*42:01 LPLTQYNRYLAL LPPTQYNRYLVL 29 74
HLA-A*02:02 VLLPLTQYNRYLAL VLLPPTQYNRYLVL 381 940
HLA-A*02:02 VLLPLTQYNRYL VLLPPTQYNRYL 147 335
HLA-B*42:01 LPLTQYNRYL LPPTQYNRYL 72 154
HLA-A*29:02 VLLPLTQYNRY VLLPPTQYNRY 143 302
HLA-A*30:02 PLTQYNRYLALY PPTQYNRYLVLY 379 778

A446V

Reference  LLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHL
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    LLNKEMYLKLRSDVLLPPTQYNRYLVLYNKYKYFSGAMDTTSYREAACCHL

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*30:01 LTQYNRYLA PTQYNRYLV 171 5507
HLA-C*16:01 LTQYNRYLAL PTQYNRYLVL 285 9019
HLA-A*02:11 LLPLTQYNRYLA LLPPTQYNRYLV 1450 57
HLA-B*15:01 LTQYNRYLAL PTQYNRYLVL 125 3068
HLA-C*16:01 LALYNKYKY LVLYNKYKY 76 1859
HLA-A*02:06 LTQYNRYLAL PTQYNRYLVL 483 7006
HLA-C*16:01 LALYNKYKYF LVLYNKYKYF 347 4564
HLA-B*15:03 LTQYNRYLAL PTQYNRYLVL 15 197
HLA-A*02:11 VLLPLTQYNRYLA VLLPPTQYNRYLV 229 19
HLA-B*08:01 LTQYNRYLAL PTQYNRYLVL 126 1517
HLA-A*68:02 LTQYNRYLA PTQYNRYLV 349 3473
HLA-C*03:02 LALYNKYKY LVLYNKYKY 124 1202
HLA-A*11:01 LTQYNRYLALYNK PTQYNRYLVLYNK 388 3729
HLA-C*12:03 LALYNKYKY LVLYNKYKY 461 4287
HLA-B*35:01 LALYNKYKY LVLYNKYKY 142 1049
HLA-A*02:02 LLPLTQYNRYLA LLPPTQYNRYLV 1272 178
HLA-B*58:01 LALYNKYKYF LVLYNKYKYF 280 1881
HLA-C*03:02 LALYNKYKYF LVLYNKYKYF 356 2340
HLA-B*58:01 LALYNKYKY LVLYNKYKY 474 2939
HLA-A*01:01 LTQYNRYLALY PTQYNRYLVLY 400 1908
HLA-C*03:02 YLALYNKYKY YLVLYNKYKY 500 2355
HLA-A*02:01 VLLPLTQYNRYLA VLLPPTQYNRYLV 545 117
HLA-A*29:02 LALYNKYKY LVLYNKYKY 146 35
HLA-A*23:01 ALYNKYKYF VLYNKYKYF 963 250
HLA-A*02:06 VLLPLTQYNRYLA VLLPPTQYNRYLV 1552 412
HLA-A*30:02 LTQYNRYLALY PTQYNRYLVLY 92 330
HLA-A*02:02 VLLPLTQYNRYLA VLLPPTQYNRYLV 980 284
HLA-B*07:02 LPLTQYNRYLAL LPPTQYNRYLVL 100 333
HLA-A*03:02 YLALYNKYK YLVLYNKYK 47 151
HLA-A*02:01 VLLPLTQYNRYLAL VLLPPTQYNRYLVL 343 1088
HLA-A*24:02 RYLALYNKYKYF RYLVLYNKYKYF 49 151
HLA-B*15:03 LALYNKYKY LVLYNKYKY 250 768
HLA-A*29:02 LTQYNRYLALY PTQYNRYLVLY 212 636
HLA-A*03:01 YLALYNKYK YLVLYNKYK 102 305
HLA-C*14:02 RYLALYNKY RYLVLYNKY 82 235
HLA-A*23:01 RYLALYNKYKYF RYLVLYNKYKYF 21 60
HLA-B*08:01 LPLTQYNRYLAL LPPTQYNRYLVL 58 163
HLA-A*02:11 TQYNRYLAL TQYNRYLVL 144 395
HLA-B*08:01 LLPLTQYNRYLAL LLPPTQYNRYLVL 190 517
HLA-A*29:02 YNRYLALYNKY YNRYLVLYNKY 226 604
HLA-A*03:02 RYLALYNKYK RYLVLYNKYK 35 91
HLA-B*42:01 TQYNRYLAL TQYNRYLVL 478 1233
HLA-B*42:01 LPLTQYNRYLAL LPPTQYNRYLVL 29 74
HLA-A*02:06 TQYNRYLAL TQYNRYLVL 57 144
HLA-A*02:02 YLALYNKYKYFSGA YLVLYNKYKYFSGA 247 614
HLA-A*02:02 VLLPLTQYNRYLAL VLLPPTQYNRYLVL 381 940
HLA-A*29:02 YLALYNKY YLVLYNKY 383 916
HLA-A*02:02 TQYNRYLAL TQYNRYLVL 349 828
HLA-A*11:01 YLALYNKYK YLVLYNKYK 197 445
HLA-A*30:02 QYNRYLALY QYNRYLVLY 109 246
HLA-A*03:01 RYLALYNKYK RYLVLYNKYK 27 58
HLA-A*24:02 RYLALYNKY RYLVLYNKY 333 709
HLA-A*29:02 RYLALYNKY RYLVLYNKY 219 465
HLA-A*30:02 PLTQYNRYLALY PPTQYNRYLVLY 379 778
HLA-A*23:01 RYLALYNKY RYLVLYNKY 156 314
HLA-B*08:01 TQYNRYLAL TQYNRYLVL 33 66

NSP6 protein

NSP6

SGF 106-108 deletion

Reference  FNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYD
           |||||||||||||||||||||||||   |||||||||||||||||||||||||
Mutated    FNMVYMPASWVMRIMTWLDMVDTSL‑‑‑KLKDCVMYASAVVLLILMTARTVYD

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:02 FKLKDCVMYA - 8 -
HLA-A*02:11 FKLKDCVMYA - 12 -
HLA-B*15:03 FKLKDCVMY - 15 -
HLA-A*02:01 FKLKDCVMYA - 27 -
HLA-A*02:06 FKLKDCVMYA - 90 -
HLA-A*02:02 SGFKLKDCVMYA - 126 -
HLA-A*02:11 SGFKLKDCVMYA - 200 -
HLA-A*02:02 GFKLKDCVMYA - 239 -
HLA-A*23:01 TWLDMVDTSLSGF - 387 -
HLA-A*02:11 GFKLKDCVMYA - 394 -
HLA-A*02:02 WLDMVDTSLS - 441 -
HLA-A*02:11 FKLKDCVMYASAVV - 481 -
HLA-B*15:03 LSGFKLKDCVMY LKLKDCVMY 3466 22
HLA-A*02:11 LDMVDTSLSGFKL LDMVDTSLKL 16396 166
HLA-A*02:02 LDMVDTSLSGFKL LDMVDTSLKL 9971 106
HLA-A*02:11 SLSGFKLKDCV SLKLKDCV 122 9934
HLA-A*02:01 LDMVDTSLSGFKL LDMVDTSLKL 20579 311
HLA-B*08:01 SLSGFKLKDCVM SLKLKDCVM 929 36
HLA-A*02:02 SLSGFKLKDCV SLKLKDCV 408 10216
HLA-C*05:01 WLDMVDTSLSGFKL WLDMVDTSLKL 8375 417
HLA-B*15:01 SLSGFKLKDCVMY SLKLKDCVMY 2952 158
HLA-B*08:01 TSLSGFKLKDCVM TSLKLKDCVM 4628 289
HLA-B*15:01 SLSGFKLKDCVM SLKLKDCVM 2654 197
HLA-A*68:01 DMVDTSLSGFK DMVDTSLK 366 4919
HLA-A*02:11 WLDMVDTSLSGFKL WLDMVDTSLKL 1342 108
HLA-C*08:02 MVDTSLSGFKL MVDTSLKL 2134 174
HLA-B*15:03 SLSGFKLKDCVM SLKLKDCVM 3634 297
HLA-A*02:01 WLDMVDTSLSGFKL WLDMVDTSLKL 2214 195
HLA-A*03:02 WLDMVDTSLSGFK WLDMVDTSLK 1756 156
HLA-A*02:02 LSGFKLKDCVMYA LKLKDCVMYA 305 28
HLA-A*02:01 LSGFKLKDCVMYA LKLKDCVMYA 1788 165
HLA-A*02:11 LSGFKLKDCVMYA LKLKDCVMYA 578 54
HLA-B*15:03 SLSGFKLKDCVMY SLKLKDCVMY 3626 349
HLA-A*03:01 WLDMVDTSLSGFK WLDMVDTSLK 2900 287
HLA-C*05:01 MVDTSLSGFKL MVDTSLKL 1125 124
HLA-A*11:01 WLDMVDTSLSGFK WLDMVDTSLK 4020 492
HLA-A*02:02 WLDMVDTSLSGFKL WLDMVDTSLKL 788 116
HLA-A*68:01 DMVDTSLSGFKLK DMVDTSLKLK 1679 251
HLA-A*02:01 SLSGFKLKDCVMYA SLKLKDCVMYA 203 853
HLA-A*02:11 SLSGFKLKDCVMYA SLKLKDCVMYA 64 223
HLA-A*02:02 SLSGFKLKDCVMYA SLKLKDCVMYA 55 171
HLA-A*29:02 SLSGFKLKDCVMY SLKLKDCVMY 404 1192
HLA-A*11:01 MVDTSLSGFKLK MVDTSLKLK 143 50
HLA-A*03:02 MVDTSLSGFKLK MVDTSLKLK 312 127
HLA-A*68:01 MVDTSLSGFKLK MVDTSLKLK 602 246
HLA-A*03:01 MVDTSLSGFKLK MVDTSLKLK 441 190

V278I

Reference  YMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQ
           ||||||||||||||||||||||||| ||||||||||||
Mutated    YMNSQGLLPPKNSIDAFKLNIKLLGIGGKPCIKVATVQ

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*32:01 KLNIKLLGV KLNIKLLGI 1672 277
HLA-A*02:01 KLNIKLLGV KLNIKLLGI 35 211
HLA-A*02:06 KLNIKLLGV KLNIKLLGI 116 682
HLA-A*02:11 AFKLNIKLLGV AFKLNIKLLGI 356 1832
HLA-A*02:01 FKLNIKLLGV FKLNIKLLGI 41 191
HLA-A*02:02 KLNIKLLGV KLNIKLLGI 26 114
HLA-A*02:06 FKLNIKLLGV FKLNIKLLGI 161 667
HLA-A*02:11 FKLNIKLLGV FKLNIKLLGI 9 31
HLA-A*02:11 KLNIKLLGV KLNIKLLGI 5 17
HLA-A*02:02 FKLNIKLLGV FKLNIKLLGI 20 66
HLA-A*02:11 LLGVGGKPCI LLGIGGKPCI 998 404

NSP12 protein

NSP12

P323L

Reference  CVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    CVNCLDDRCILHCANFNVLFSTVFPLTSFGPLVRKIFVDGVPFVVSTGYHF

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:01 FPPTSFGPLV FPLTSFGPLV 8999 21
HLA-A*02:02 FPPTSFGPLV FPLTSFGPLV 7237 18
HLA-A*02:11 FPPTSFGPLV FPLTSFGPLV 3405 9
HLA-A*32:01 VLFSTVFPP VLFSTVFPL 5415 27
HLA-A*02:11 LFSTVFPP LFSTVFPL 6706 35
HLA-A*02:11 ANFNVLFSTVFPP ANFNVLFSTVFPL 1827 12
HLA-A*02:11 NFNVLFSTVFPP NFNVLFSTVFPL 1779 13
HLA-A*02:11 NVLFSTVFPP NVLFSTVFPL 739 6
HLA-C*03:03 VLFSTVFPP VLFSTVFPL 28468 265
HLA-C*03:04 VLFSTVFPP VLFSTVFPL 28468 265
HLA-A*02:11 FNVLFSTVFPP FNVLFSTVFPL 413 4
HLA-C*14:02 VLFSTVFPP VLFSTVFPL 21407 220
HLA-A*02:11 FNVLFSTVFPPT FNVLFSTVFPLT 2618 27
HLA-A*02:01 LFSTVFPP LFSTVFPL 7475 81
HLA-C*14:02 LFSTVFPP LFSTVFPL 11979 138
HLA-B*15:03 VLFSTVFPP VLFSTVFPL 3115 36
HLA-A*02:11 VLFSTVFPP VLFSTVFPL 78 1
HLA-C*03:02 VLFSTVFPP VLFSTVFPL 20533 273
HLA-A*02:01 FNVLFSTVFPP FNVLFSTVFPL 656 9
HLA-A*02:01 ANFNVLFSTVFPP ANFNVLFSTVFPL 2569 37
HLA-A*02:11 FNVLFSTVFPPTS FNVLFSTVFPLTS 9448 142
HLA-A*02:02 NVLFSTVFPP NVLFSTVFPL 1088 17
HLA-A*02:11 CANFNVLFSTVFPP CANFNVLFSTVFPL 6143 96
HLA-A*02:02 FNVLFSTVFPP FNVLFSTVFPL 1014 16
HLA-A*68:02 NVLFSTVFPP NVLFSTVFPL 2213 37
HLA-A*02:02 ANFNVLFSTVFPP ANFNVLFSTVFPL 3126 53
HLA-A*02:11 PPTSFGPLV PLTSFGPLV 28329 483
HLA-C*16:01 VLFSTVFPP VLFSTVFPL 24733 432
HLA-C*17:01 VLFSTVFPP VLFSTVFPL 25087 439
HLA-A*02:01 FNVLFSTVFPPT FNVLFSTVFPLT 3765 66
HLA-A*02:02 LFSTVFPP LFSTVFPL 9311 167
HLA-A*02:01 NVLFSTVFPP NVLFSTVFPL 928 17
HLA-A*02:02 NFNVLFSTVFPP NFNVLFSTVFPL 2542 47
HLA-A*02:02 VLFSTVFPP VLFSTVFPL 269 5
HLA-A*02:01 NFNVLFSTVFPP NFNVLFSTVFPL 2286 44
HLA-A*02:06 FPPTSFGPLV FPLTSFGPLV 3379 73
HLA-A*02:01 VLFSTVFPP VLFSTVFPL 179 4
HLA-A*02:06 FNVLFSTVFPP FNVLFSTVFPL 1609 37
HLA-A*02:02 FNVLFSTVFPPT FNVLFSTVFPLT 4116 110
HLA-A*02:11 FSTVFPPTSFGPLV FSTVFPLTSFGPLV 6695 180
HLA-A*02:01 FNVLFSTVFPPTS FNVLFSTVFPLTS 11451 311
HLA-A*02:06 VLFSTVFPP VLFSTVFPL 368 10
HLA-A*02:11 ANFNVLFSTVFPPT ANFNVLFSTVFPLT 14639 409
HLA-A*02:01 FSTVFPPTSFGPLV FSTVFPLTSFGPLV 12596 425
HLA-A*68:01 PTSFGPLVR LTSFGPLVR 908 36
HLA-A*02:06 NVLFSTVFPP NVLFSTVFPL 1611 66
HLA-B*15:01 VLFSTVFPP VLFSTVFPL 5731 243
HLA-B*35:01 FPPTSFGPL FPLTSFGPL 304 13
HLA-B*53:01 FPPTSFGPL FPLTSFGPL 3581 154
HLA-C*01:02 FPPTSFGPL FPLTSFGPL 217 4855
HLA-A*02:01 CANFNVLFSTVFPP CANFNVLFSTVFPL 8519 384
HLA-A*02:02 FNVLFSTVFPPTS FNVLFSTVFPLTS 10920 497
HLA-A*02:02 FSTVFPPTSFGPLV FSTVFPLTSFGPLV 6958 322
HLA-A*02:11 VFPPTSFGPLV VFPLTSFGPLV 4242 199
HLA-A*02:02 CANFNVLFSTVFPP CANFNVLFSTVFPL 8183 391
HLA-A*02:11 NFNVLFSTVFPPT NFNVLFSTVFPLT 9111 472
HLA-A*02:06 ANFNVLFSTVFPP ANFNVLFSTVFPL 5191 304
HLA-A*02:06 NFNVLFSTVFPP NFNVLFSTVFPL 4220 274
HLA-A*02:06 FNVLFSTVFPPT FNVLFSTVFPLT 4868 388
HLA-B*35:03 FPPTSFGPL FPLTSFGPL 286 24
HLA-A*03:01 PTSFGPLVRK LTSFGPLVRK 554 47
HLA-A*31:01 PTSFGPLVR LTSFGPLVR 4402 390
HLA-A*11:01 PTSFGPLVR LTSFGPLVR 4068 379
HLA-A*03:02 PTSFGPLVRK LTSFGPLVRK 868 88
HLA-B*07:02 STVFPPTSFGPL STVFPLTSFGPL 777 79
HLA-A*68:01 PTSFGPLVRK LTSFGPLVRK 308 34
HLA-B*07:02 TVFPPTSFGPL TVFPLTSFGPL 1498 171
HLA-A*02:11 STVFPPTSFGPLV STVFPLTSFGPLV 2427 285
HLA-A*02:11 NVLFSTVFPPT NVLFSTVFPLT 1183 139
HLA-A*33:03 PTSFGPLVR LTSFGPLVR 3228 381
HLA-A*26:01 STVFPPTSF STVFPLTSF 786 95
HLA-B*07:02 VFPPTSFGPL VFPLTSFGPL 339 43
HLA-A*02:01 NVLFSTVFPPT NVLFSTVFPLT 2111 290
HLA-B*42:01 FSTVFPPTSFGPL FSTVFPLTSFGPL 1320 185
HLA-B*42:01 STVFPPTSFGPL STVFPLTSFGPL 738 111
HLA-A*02:01 VLFSTVFPPTSF VLFSTVFPLTSF 2225 342
HLA-B*08:01 FPPTSFGPL FPLTSFGPL 973 153
HLA-B*42:01 TVFPPTSFGPL TVFPLTSFGPL 843 142
HLA-A*11:01 PTSFGPLVRK LTSFGPLVRK 123 21
HLA-B*42:01 VFPPTSFGPL VFPLTSFGPL 274 47
HLA-A*02:01 VLFSTVFPPTS VLFSTVFPLTS 708 124
HLA-B*07:02 FSTVFPPTSFGPL FSTVFPLTSFGPL 2537 466
HLA-B*07:02 FPPTSFGPL FPLTSFGPL 42 8
HLA-A*02:11 VLFSTVFPPTSF VLFSTVFPLTSF 1019 195
HLA-A*25:01 STVFPPTSF STVFPLTSF 1533 296
HLA-B*07:02 FPPTSFGPLV FPLTSFGPLV 1131 236
HLA-B*42:01 FPPTSFGPL FPLTSFGPL 21 5
HLA-A*26:01 FSTVFPPTSF FSTVFPLTSF 1667 398
HLA-B*51:01 FPPTSFGPL FPLTSFGPL 1809 433
HLA-A*02:11 VLFSTVFPPTS VLFSTVFPLTS 309 74
HLA-B*42:01 FPPTSFGPLV FPLTSFGPLV 368 89
HLA-A*02:02 VLFSTVFPPTS VLFSTVFPLTS 1210 377
HLA-C*03:02 FPPTSFGPL FPLTSFGPL 960 313
HLA-A*32:01 STVFPPTSF STVFPLTSF 230 86
HLA-B*58:01 FSTVFPPTSF FSTVFPLTSF 88 33
HLA-B*15:01 STVFPPTSF STVFPLTSF 130 49
HLA-A*02:01 VLFSTVFPPT VLFSTVFPLT 61 23
HLA-C*03:03 FPPTSFGPL FPLTSFGPL 375 145
HLA-C*03:04 FPPTSFGPL FPLTSFGPL 375 145
HLA-A*02:02 VLFSTVFPPT VLFSTVFPLT 113 44
HLA-C*16:01 FSTVFPPTS FSTVFPLTS 1127 460
HLA-C*14:02 LFSTVFPPTSF LFSTVFPLTSF 396 950
HLA-C*01:02 VFPPTSFGPL VFPLTSFGPL 429 997
HLA-A*02:02 TVFPPTSFGPLV TVFPLTSFGPLV 789 343
HLA-A*68:02 STVFPPTSFGPLV STVFPLTSFGPLV 169 74
HLA-A*02:11 VLFSTVFPPT VLFSTVFPLT 25 11
HLA-A*03:01 TVFPPTSFGPLVRK TVFPLTSFGPLVRK 92 198
HLA-C*14:02 VFPPTSFGPL VFPLTSFGPL 47 99
HLA-A*23:01 LFSTVFPPTSF LFSTVFPLTSF 370 179