Summary

This strain contains 18 protein-level mutations:

  • 9 mutations in Spike protein: D80A, D215G, LLA 241-243 deletion, A260X, K417N, E484K, N501Y, D614G, A701V
  • 1 mutation in N protein: T205I
  • 1 mutation in E protein: P71L
  • 2 mutations in NS3 protein: Q57H, S171L
  • 1 mutation in NS9c protein: L52F
  • 1 mutation in NSP2 protein: T85I
  • 1 mutation in NSP3 protein: K837N
  • 1 mutation in NSP6 protein: SGF 106-108 deletion
  • 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

D80A

Reference  FLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWI
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    FLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWI

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*03:02 FDNPVLPF FANPVLPF 4198 5
HLA-C*16:01 FDNPVLPF FANPVLPF 9054 16
HLA-C*03:03 FDNPVLPF FANPVLPF 15346 35
HLA-C*03:04 FDNPVLPF FANPVLPF 15346 35
HLA-C*12:02 FDNPVLPF FANPVLPF 12779 39
HLA-C*12:03 FDNPVLPF FANPVLPF 16585 52
HLA-C*03:02 FDNPVLPFNDGVY FANPVLPFNDGVY 12724 65
HLA-C*02:02 FDNPVLPF FANPVLPF 16957 120
HLA-C*02:10 FDNPVLPF FANPVLPF 16957 120
HLA-B*35:01 FDNPVLPF FANPVLPF 14924 111
HLA-C*16:01 FDNPVLPFNDGVY FANPVLPFNDGVY 20775 308
HLA-C*12:02 FDNPVLPFNDGVY FANPVLPFNDGVY 13459 202
HLA-B*15:03 FDNPVLPF FANPVLPF 3927 66
HLA-A*30:01 GTNGTKRFD GTNGTKRFA 11372 201
HLA-C*02:02 FDNPVLPFNDGVY FANPVLPFNDGVY 17854 318
HLA-C*02:10 FDNPVLPFNDGVY FANPVLPFNDGVY 17854 318
HLA-C*12:03 FDNPVLPFNDGVY FANPVLPFNDGVY 18712 334
HLA-B*35:01 FDNPVLPFNDGVY FANPVLPFNDGVY 11216 207
HLA-C*03:02 FDNPVLPFNDGVYF FANPVLPFNDGVYF 6446 128
HLA-C*02:02 FDNPVLPFNDGVYF FANPVLPFNDGVYF 15611 499
HLA-C*02:10 FDNPVLPFNDGVYF FANPVLPFNDGVYF 15611 499
HLA-C*12:02 FDNPVLPFNDGVYF FANPVLPFNDGVYF 11675 421
HLA-B*15:01 RFDNPVLPF RFANPVLPF 4355 183
HLA-A*23:01 RFDNPVLPF RFANPVLPF 327 23
HLA-A*24:02 RFDNPVLPF RFANPVLPF 457 34
HLA-C*04:01 RFDNPVLPF RFANPVLPF 411 5105
HLA-C*14:02 FDNPVLPF FANPVLPF 3648 294
HLA-B*15:03 RFDNPVLPF RFANPVLPF 171 16
HLA-A*24:02 KRFDNPVLPF KRFANPVLPF 2713 316
HLA-A*23:01 KRFDNPVLPF KRFANPVLPF 1220 146
HLA-A*32:01 RFDNPVLPF RFANPVLPF 1028 133
HLA-C*14:02 RFDNPVLPF RFANPVLPF 36 6
HLA-A*30:01 GTKRFDNPV GTKRFANPV 120 25
HLA-C*03:02 RFDNPVLPF RFANPVLPF 1091 250
HLA-A*29:02 RFDNPVLPF RFANPVLPF 1026 276
HLA-A*30:01 GTKRFDNPVL GTKRFANPVL 352 110
HLA-A*68:02 FDNPVLPFNDGV FANPVLPFNDGV 503 164
HLA-A*30:02 RFDNPVLPFNDGVY RFANPVLPFNDGVY 686 246
HLA-C*14:02 KRFDNPVLPF KRFANPVLPF 405 152
HLA-C*16:01 RFDNPVLPF RFANPVLPF 1270 485
HLA-C*07:02 RFDNPVLPF RFANPVLPF 1004 412

D215G

Reference  REFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    REFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQT

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 DLPQGFSALEPL GLPQGFSALEPL 2822 38
HLA-A*02:01 DLPQGFSALEPL GLPQGFSALEPL 5739 78
HLA-A*02:02 DLPQGFSALEPL GLPQGFSALEPL 1894 30
HLA-A*02:11 DLPQGFSAL GLPQGFSAL 1553 28
HLA-A*02:02 DLPQGFSAL GLPQGFSAL 1520 31
HLA-B*40:02 RDLPQGFSAL RGLPQGFSAL 386 13573
HLA-A*02:11 DLPQGFSALEPLV GLPQGFSALEPLV 6434 216
HLA-A*02:01 DLPQGFSAL GLPQGFSAL 7889 307
HLA-A*02:02 DLPQGFSALEPLV GLPQGFSALEPLV 6875 269
HLA-A*02:06 DLPQGFSALEPL GLPQGFSALEPL 6309 284
HLA-A*02:06 DLPQGFSAL GLPQGFSAL 3505 186
HLA-A*68:02 HTPINLVRDL HTPINLVRGL 1815 188
HLA-C*01:02 DLPQGFSAL GLPQGFSAL 196 46
HLA-C*14:02 DLPQGFSAL GLPQGFSAL 1350 490

LLA 241-243 deletion

Reference  LPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVG
           |||||||||||||||||||||||||   |||||||||||||||||||||||||
Mutated    LPQGFSALEPLVDLPIGINITRFQT‑‑‑LHRSYLTPGDSSSGWTXGAAAYYVG

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*27:05 GINITRFQTLLAL - 99 -
HLA-B*27:05 INITRFQTLLAL - 213 -
HLA-B*27:05 NITRFQTLLAL - 258 -
HLA-A*30:01 INITRFQTLLA - 356 -
HLA-C*03:03 FQTLLALHRSYL FQTLHRSYL 10000 100
HLA-C*03:04 FQTLLALHRSYL FQTLHRSYL 10000 100
HLA-C*14:02 RFQTLLALHRSY RFQTLHRSY 1204 14
HLA-A*31:01 RFQTLLALHRS RFQTLHRS 348 22003
HLA-C*12:03 FQTLLALHRSYL FQTLHRSYL 7447 141
HLA-C*16:01 FQTLLALHRSYL FQTLHRSYL 8479 186
HLA-C*03:02 FQTLLALHRSYL FQTLHRSYL 7964 177
HLA-C*12:02 FQTLLALHRSYL FQTLHRSYL 5579 197
HLA-A*31:01 TRFQTLLALHR TRFQTLHR 145 3975
HLA-C*14:02 FQTLLALHRSYL FQTLHRSYL 4687 175
HLA-C*07:02 RFQTLLALHRSY RFQTLHRSY 10625 440
HLA-A*30:01 ITRFQTLLALHR ITRFQTLHR 3274 136
HLA-A*68:01 NITRFQTLLALHR NITRFQTLHR 652 30
HLA-C*14:02 TRFQTLLALHRSY TRFQTLHRSY 5428 255
HLA-B*15:03 FQTLLALHRSYL FQTLHRSYL 592 28
HLA-C*17:01 FQTLLALHRSYL FQTLHRSYL 8472 445
HLA-C*02:02 FQTLLALHRSYL FQTLHRSYL 8235 440
HLA-C*02:10 FQTLLALHRSYL FQTLHRSYL 8235 440
HLA-B*15:03 RFQTLLALHRSYL RFQTLHRSYL 7029 419
HLA-C*14:02 RFQTLLALHRSYL RFQTLHRSYL 1277 99
HLA-A*33:03 ITRFQTLLALHR ITRFQTLHR 656 60
HLA-B*27:05 TRFQTLLALHR TRFQTLHR 191 1873
HLA-A*68:01 ITRFQTLLALHR ITRFQTLHR 1475 155
HLA-A*33:03 NITRFQTLLALHR NITRFQTLHR 548 59
HLA-A*30:01 RFQTLLALHRSYL RFQTLHRSYL 2049 249
HLA-A*30:01 ITRFQTLLALHRS ITRFQTLHRS 3352 466
HLA-A*31:01 INITRFQTLLALHR INITRFQTLHR 2345 336
HLA-A*29:02 TRFQTLLALHRSY TRFQTLHRSY 2415 407
HLA-A*31:01 ITRFQTLLALHR ITRFQTLHR 134 26
HLA-A*31:01 NITRFQTLLALHR NITRFQTLHR 1001 227
HLA-B*15:01 FQTLLALHRSYL FQTLHRSYL 1826 446
HLA-B*15:03 TRFQTLLALHRSY TRFQTLHRSY 396 103
HLA-B*27:05 TRFQTLLALHRSY TRFQTLHRSY 511 146
HLA-A*30:02 TRFQTLLALHRSY TRFQTLHRSY 1004 366
HLA-B*15:01 FQTLLALHRSY FQTLHRSY 126 344
HLA-A*29:02 RFQTLLALHRSY RFQTLHRSY 489 188
HLA-B*27:05 TRFQTLLALHRSYL TRFQTLHRSYL 500 196
HLA-A*02:06 FQTLLALHRSYL FQTLHRSYL 579 257
HLA-A*30:02 RFQTLLALHRSY RFQTLHRSY 140 66

A260X

Reference  ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTI
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    ITRFQT‑‑‑LHRSYLTPGDSSSGWTXGAAAYYVGYLQPRTFLLKYNENGTI

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 YLTPGDSSSGWTA YLTPGDSSSGWTX 79 3190
HLA-A*02:02 YLTPGDSSSGWTA YLTPGDSSSGWTX 106 2993
HLA-C*16:01 TAGAAAYYV TXGAAAYYV 374 9769
HLA-A*02:01 YLTPGDSSSGWTA YLTPGDSSSGWTX 262 6132
HLA-A*68:02 TAGAAAYYV TXGAAAYYV 30 454
HLA-B*15:03 AGAAAYYVGY XGAAAYYVGY 388 1417
HLA-B*15:01 AGAAAYYVGY XGAAAYYVGY 360 1274
HLA-A*02:06 TAGAAAYYV TXGAAAYYV 186 584
HLA-A*30:02 AGAAAYYVGY XGAAAYYVGY 100 313
HLA-A*25:01 WTAGAAAYY WTXGAAAYY 112 298
HLA-A*02:11 TAGAAAYYV TXGAAAYYV 107 284
HLA-A*26:01 DSSSGWTAGAAAYY DSSSGWTXGAAAYY 344 899
HLA-A*26:01 SSGWTAGAAAYY SSGWTXGAAAYY 438 1112
HLA-A*68:02 GWTAGAAAYYV GWTXGAAAYYV 215 537
HLA-A*26:01 GWTAGAAAYY GWTXGAAAYY 318 773
HLA-A*26:01 WTAGAAAYYVGY WTXGAAAYYVGY 166 391
HLA-C*16:01 SSSGWTAGAAAY SSSGWTXGAAAY 1106 478
HLA-A*68:02 WTAGAAAYYVGYL WTXGAAAYYVGYL 90 192
HLA-C*14:02 SGWTAGAAAY SGWTXGAAAY 616 297
HLA-A*01:01 GWTAGAAAYY GWTXGAAAYY 258 532
HLA-A*02:02 TAGAAAYYV TXGAAAYYV 340 700
HLA-A*68:02 DSSSGWTAGA DSSSGWTXGA 418 839

K417N

Reference  FTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLD
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    FTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLD

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*03:01 RQIAPGQTGK RQIAPGQTGN 49 23809
HLA-A*11:01 RQIAPGQTGK RQIAPGQTGN 103 29063
HLA-A*68:01 EVRQIAPGQTGK EVRQIAPGQTGN 144 32767
HLA-A*03:02 RQIAPGQTGK RQIAPGQTGN 123 26438
HLA-A*68:01 QIAPGQTGK QIAPGQTGN 136 27997
HLA-A*11:01 QIAPGQTGK QIAPGQTGN 165 32767
HLA-A*03:02 QIAPGQTGK QIAPGQTGN 278 32767
HLA-A*03:01 QIAPGQTGK QIAPGQTGN 296 32767
HLA-A*32:01 KIADYNYKL NIADYNYKL 58 4480
HLA-A*30:01 RQIAPGQTGK RQIAPGQTGN 275 9067
HLA-A*68:02 KIADYNYKL NIADYNYKL 1274 39
HLA-A*03:02 KIADYNYK NIADYNYK 476 6850
HLA-A*02:06 KIADYNYKL NIADYNYKL 20 101
HLA-A*02:01 KIADYNYKL NIADYNYKL 23 110
HLA-C*17:01 KIADYNYKL NIADYNYKL 155 669
HLA-A*30:01 TGKIADYNYK TGNIADYNYK 292 1164
HLA-A*02:11 KIADYNYKL NIADYNYKL 5 19
HLA-A*68:01 TGKIADYNYK TGNIADYNYK 957 343
HLA-A*01:01 QTGKIADYNY QTGNIADYNY 580 270

E484K

Reference  SNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYR
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    SNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYR

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*40:02 VEGFNCYFPL VKGFNCYFPL 31 7011
HLA-B*40:01 VEGFNCYFPL VKGFNCYFPL 76 15210
HLA-A*11:01 GSTPCNGVE GSTPCNGVK 32767 444
HLA-A*68:02 EGFNCYFPL KGFNCYFPL 117 3877
HLA-A*30:01 EGFNCYFPL KGFNCYFPL 5413 164
HLA-A*32:01 EGFNCYFPL KGFNCYFPL 6548 210
HLA-A*30:02 EGFNCYFPLQSY KGFNCYFPLQSY 1806 72
HLA-B*15:01 GVEGFNCYF GVKGFNCYF 3125 132
HLA-A*31:01 EGFNCYFPL KGFNCYFPL 4227 226
HLA-B*15:03 EGFNCYFPL KGFNCYFPL 2980 212
HLA-A*02:11 EGFNCYFPL KGFNCYFPL 2508 259
HLA-B*15:03 GVEGFNCYF GVKGFNCYF 1657 199
HLA-A*02:06 EGFNCYFPL KGFNCYFPL 1266 169
HLA-B*35:01 TPCNGVEGF TPCNGVKGF 319 1754
HLA-B*15:03 VEGFNCYFPLQSY VKGFNCYFPLQSY 1081 208
HLA-B*35:01 NGVEGFNCY NGVKGFNCY 346 1439
HLA-C*16:01 EGFNCYFPL KGFNCYFPL 1861 498
HLA-B*15:03 VEGFNCYFPL VKGFNCYFPL 943 280

N501Y

Reference  GSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    GSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCG

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*29:02 QSYGFQPTN QSYGFQPTY 26152 24
HLA-A*29:02 YFPLQSYGFQPTN YFPLQSYGFQPTY 19514 25
HLA-B*15:01 LQSYGFQPTN LQSYGFQPTY 6135 8
HLA-B*35:01 FPLQSYGFQPTN FPLQSYGFQPTY 8715 15
HLA-C*03:02 QSYGFQPTN QSYGFQPTY 12903 23
HLA-B*15:03 LQSYGFQPTN LQSYGFQPTY 2045 4
HLA-B*15:03 QSYGFQPTN QSYGFQPTY 6543 13
HLA-C*16:01 QSYGFQPTN QSYGFQPTY 10868 27
HLA-B*35:01 QSYGFQPTN QSYGFQPTY 24615 71
HLA-C*12:03 QSYGFQPTN QSYGFQPTY 12696 38
HLA-B*15:03 PLQSYGFQPTN PLQSYGFQPTY 22802 80
HLA-C*14:02 TNGVGYQPY TYGVGYQPY 5468 21
HLA-A*29:02 LQSYGFQPTN LQSYGFQPTY 28458 133
HLA-C*03:02 FPLQSYGFQPTN FPLQSYGFQPTY 23840 113
HLA-C*03:02 LQSYGFQPTN LQSYGFQPTY 23421 125
HLA-A*30:02 LQSYGFQPTN LQSYGFQPTY 7508 42
HLA-A*30:02 QSYGFQPTN QSYGFQPTY 5297 30
HLA-B*15:03 FPLQSYGFQPTN FPLQSYGFQPTY 20159 137
HLA-C*03:02 YFPLQSYGFQPTN YFPLQSYGFQPTY 27639 198
HLA-A*29:02 CYFPLQSYGFQPTN CYFPLQSYGFQPTY 27182 196
HLA-C*14:02 SYGFQPTN SYGFQPTY 20230 162
HLA-A*29:02 FPLQSYGFQPTN FPLQSYGFQPTY 32767 264
HLA-B*15:01 QSYGFQPTN QSYGFQPTY 21529 195
HLA-C*14:02 YFPLQSYGFQPTN YFPLQSYGFQPTY 18230 169
HLA-B*15:03 YFPLQSYGFQPTN YFPLQSYGFQPTY 22168 206
HLA-A*11:01 QSYGFQPTN QSYGFQPTY 22068 241
HLA-C*16:01 LQSYGFQPTN LQSYGFQPTY 27149 326
HLA-C*12:02 QSYGFQPTN QSYGFQPTY 21029 267
HLA-B*15:01 PLQSYGFQPTN PLQSYGFQPTY 32767 449
HLA-B*35:01 YFPLQSYGFQPTN YFPLQSYGFQPTY 28375 395
HLA-C*12:03 FPLQSYGFQPTN FPLQSYGFQPTY 27893 431
HLA-C*16:01 FPLQSYGFQPTN FPLQSYGFQPTY 27733 434
HLA-C*02:02 QSYGFQPTN QSYGFQPTY 26598 425
HLA-C*02:10 QSYGFQPTN QSYGFQPTY 26598 425
HLA-A*30:02 YFPLQSYGFQPTN YFPLQSYGFQPTY 18743 310
HLA-B*15:03 LQSYGFQPTNG LQSYGFQPTYG 6387 109
HLA-B*53:01 FPLQSYGFQPTN FPLQSYGFQPTY 8451 151
HLA-C*12:03 LQSYGFQPTN LQSYGFQPTY 26641 480
HLA-A*32:01 QSYGFQPTN QSYGFQPTY 16619 311
HLA-A*30:02 FPLQSYGFQPTN FPLQSYGFQPTY 21475 466
HLA-C*03:02 NGVGYQPY YGVGYQPY 10463 451
HLA-B*57:01 QSYGFQPTN QSYGFQPTY 4070 215
HLA-B*58:01 QSYGFQPTN QSYGFQPTY 1532 83
HLA-A*02:11 NGVGYQPYRV YGVGYQPYRV 5989 327
HLA-B*57:01 LQSYGFQPTN LQSYGFQPTY 3839 244
HLA-B*58:01 LQSYGFQPTN LQSYGFQPTY 1885 155
HLA-B*15:03 NGVGYQPY YGVGYQPY 4677 467
HLA-A*31:01 TNGVGYQPYR TYGVGYQPYR 811 84
HLA-A*33:03 TNGVGYQPYR TYGVGYQPYR 573 62
HLA-A*29:02 TNGVGYQPY TYGVGYQPY 2031 237
HLA-A*29:02 PTNGVGYQPY PTYGVGYQPY 1211 177
HLA-A*02:11 YGFQPTNGV YGFQPTYGV 307 49
HLA-A*02:01 YGFQPTNGV YGFQPTYGV 2160 459
HLA-A*68:01 PTNGVGYQPYR PTYGVGYQPYR 1073 242
HLA-A*02:11 LQSYGFQPTNGV LQSYGFQPTYGV 1446 396
HLA-A*31:01 PTNGVGYQPYR PTYGVGYQPYR 1377 406
HLA-A*02:06 YGFQPTNGV YGFQPTYGV 174 52
HLA-A*33:03 PTNGVGYQPYR PTYGVGYQPYR 1345 407
HLA-A*02:02 YGFQPTNGV YGFQPTYGV 868 287
HLA-A*02:06 QSYGFQPTNGV QSYGFQPTYGV 1121 407
HLA-A*68:02 YGFQPTNGV YGFQPTYGV 73 28
HLA-A*68:02 QSYGFQPTNGV QSYGFQPTYGV 122 48
HLA-B*15:01 GFQPTNGVGY GFQPTYGVGY 774 311
HLA-A*29:02 YGFQPTNGVGY YGFQPTYGVGY 1158 486
HLA-A*31:01 NGVGYQPYR YGVGYQPYR 438 185
HLA-A*02:06 LQSYGFQPTNGV LQSYGFQPTYGV 249 111
HLA-A*30:02 PTNGVGYQPY PTYGVGYQPY 465 210
HLA-B*15:03 FQPTNGVGY FQPTYGVGY 63 29
HLA-A*02:02 LQSYGFQPTNGV LQSYGFQPTYGV 594 280
HLA-B*15:03 GFQPTNGVGY GFQPTYGVGY 769 363

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

A701V

Reference  TQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEI
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    TQTNSPRRARSVASQSIIAYTMSLGVENSVAYSNNSIAIPTNFTISVTTEI

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*15:02 IAYTMSLGA IAYTMSLGV 1895 45
HLA-A*02:11 SIIAYTMSLGA SIIAYTMSLGV 954 32
HLA-A*02:11 IIAYTMSLGA IIAYTMSLGV 834 30
HLA-A*02:11 IAYTMSLGA IAYTMSLGV 2062 76
HLA-C*17:01 IAYTMSLGA IAYTMSLGV 4933 248
HLA-C*12:03 IAYTMSLGA IAYTMSLGV 289 16
HLA-A*02:01 SIIAYTMSLGA SIIAYTMSLGV 1860 107
HLA-A*02:01 IIAYTMSLGA IIAYTMSLGV 1312 91
HLA-A*02:06 IAYTMSLGA IAYTMSLGV 739 57
HLA-C*16:01 IAYTMSLGA IAYTMSLGV 553 43
HLA-C*03:03 IAYTMSLGA IAYTMSLGV 1287 101
HLA-C*03:04 IAYTMSLGA IAYTMSLGV 1287 101
HLA-A*02:01 IAYTMSLGA IAYTMSLGV 3643 300
HLA-A*68:02 IIAYTMSLGA IIAYTMSLGV 1653 144
HLA-B*51:01 IAYTMSLGA IAYTMSLGV 5547 488
HLA-A*02:06 SIIAYTMSLGA SIIAYTMSLGV 706 64
HLA-B*44:02 AENSVAYSNNSI VENSVAYSNNSI 154 1676
HLA-C*02:02 IAYTMSLGA IAYTMSLGV 3671 343
HLA-C*02:10 IAYTMSLGA IAYTMSLGV 3671 343
HLA-A*02:02 IIAYTMSLGA IIAYTMSLGV 401 38
HLA-A*68:02 SIIAYTMSLGA SIIAYTMSLGV 3371 320
HLA-B*45:01 AENSVAYSNNSIA VENSVAYSNNSIA 83 849
HLA-A*02:02 SIIAYTMSLGA SIIAYTMSLGV 1180 122
HLA-A*02:06 IIAYTMSLGA IIAYTMSLGV 819 87
HLA-A*68:02 IAYTMSLGA IAYTMSLGV 2063 226
HLA-B*44:02 AENSVAYSN VENSVAYSN 233 1867
HLA-B*44:03 AENSVAYSNNSI VENSVAYSNNSI 367 2921
HLA-A*02:06 SQSIIAYTMSLGA SQSIIAYTMSLGV 2545 336
HLA-A*02:02 IAYTMSLGA IAYTMSLGV 2768 367
HLA-C*12:02 IAYTMSLGA IAYTMSLGV 1418 192
HLA-B*44:03 AENSVAYSN VENSVAYSN 237 1574
HLA-B*45:01 AENSVAYSN VENSVAYSN 392 2480
HLA-C*03:02 IAYTMSLGA IAYTMSLGV 530 93
HLA-A*68:02 MSLGAENSV MSLGVENSV 95 32
HLA-A*02:11 TMSLGAENSV TMSLGVENSV 110 41
HLA-A*02:11 MSLGAENSV MSLGVENSV 513 192
HLA-A*02:02 TMSLGAENSV TMSLGVENSV 74 30
HLA-A*02:01 TMSLGAENSV TMSLGVENSV 455 186
HLA-B*40:02 AENSVAYSNNSI VENSVAYSNNSI 463 1070
HLA-A*02:06 MSLGAENSV MSLGVENSV 188 92
HLA-A*30:02 LGAENSVAY LGVENSVAY 367 745

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

E protein

E

P71L

Reference  IVNVSLVKPSFYVYSRVKNLNSSRVPDLLV
           ||||||||||||||||||||||||| ||||
Mutated    IVNVSLVKPSFYVYSRVKNLNSSRVLDLLV

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*15:03 VKNLNSSRVP VKNLNSSRVL 13920 189
HLA-B*15:03 KNLNSSRVP KNLNSSRVL 17021 397
HLA-A*30:01 RVKNLNSSRVP RVKNLNSSRVL 1083 219
HLA-A*68:02 NSSRVPDLL NSSRVLDLL 1072 280
HLA-A*02:02 NLNSSRVPDLL NLNSSRVLDLL 657 201
HLA-A*68:02 NSSRVPDLLV NSSRVLDLLV 608 206
HLA-A*02:02 NLNSSRVPDLLV NLNSSRVLDLLV 740 327

NS3 protein

NS3

Q57H

Reference  TATIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCN
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    TATIPIQASLPFGWLIVGVALLAVFHSASKIITLKKRWQLALSKGVHFVCN

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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

S171L

Reference  FLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESG
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    FLCWHTNCYDYCIPYNSVTSSIVITLGDGTTSPISEHDYQIGGYTEKWESG

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*17:01 VTSSIVITS VTSSIVITL 13914 69
HLA-C*03:03 VTSSIVITS VTSSIVITL 19726 117
HLA-C*03:04 VTSSIVITS VTSSIVITL 19726 117
HLA-A*32:01 VTSSIVITS VTSSIVITL 13457 98
HLA-C*16:01 VTSSIVITS VTSSIVITL 4293 36
HLA-A*02:11 TSGDGTTSPI TLGDGTTSPI 10425 92
HLA-A*02:11 VTSSIVITS VTSSIVITL 8785 89
HLA-A*02:02 TSGDGTTSPI TLGDGTTSPI 8938 95
HLA-C*12:03 VTSSIVITS VTSSIVITL 4793 51
HLA-C*15:02 VTSSIVITS VTSSIVITL 7397 89
HLA-C*03:02 VTSSIVITS VTSSIVITL 9955 175
HLA-A*02:02 VTSSIVITS VTSSIVITL 5314 103
HLA-C*16:01 TSSIVITS TSSIVITL 18534 362
HLA-B*42:01 IPYNSVTSSIVITS IPYNSVTSSIVITL 14524 360
HLA-A*02:11 SVTSSIVITS SVTSSIVITL 12237 410
HLA-A*02:02 YNSVTSSIVITS YNSVTSSIVITL 8810 301
HLA-A*02:02 SVTSSIVITS SVTSSIVITL 5294 197
HLA-C*12:02 VTSSIVITS VTSSIVITL 9810 369
HLA-B*58:01 VTSSIVITS VTSSIVITL 2482 96
HLA-A*02:06 VTSSIVITS VTSSIVITL 4179 183
HLA-A*68:02 SVTSSIVITS SVTSSIVITL 1418 92
HLA-A*68:02 YNSVTSSIVITS YNSVTSSIVITL 2711 182
HLA-A*68:02 VTSSIVITS VTSSIVITL 911 63
HLA-A*68:02 NSVTSSIVITS NSVTSSIVITL 5500 388
HLA-C*08:02 SGDGTTSPI LGDGTTSPI 222 110

NS9c protein

NS9c

L52F

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

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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

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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

NSP3 protein

NSP3

K837N

Reference  EAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATAL
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    EAFEYYHTTDPSFLGRYMSALNHTKNWKYPQVNGLTSIKWADNNCYLATAL

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 MSALNHTKK MSALNHTKN 25 16109
HLA-A*11:01 MSALNHTKK MSALNHTKN 55 28173
HLA-A*03:02 MSALNHTKK MSALNHTKN 225 30854
HLA-A*03:01 MSALNHTKK MSALNHTKN 352 32755
HLA-A*30:01 MSALNHTKK MSALNHTKN 101 7035
HLA-A*68:01 YMSALNHTKK YMSALNHTKN 159 3833
HLA-A*11:01 YMSALNHTKK YMSALNHTKN 170 3650
HLA-A*30:01 KWKYPQVNG NWKYPQVNG 220 4236
HLA-A*03:01 YMSALNHTKK YMSALNHTKN 135 2562
HLA-A*30:01 KWKYPQVNGL NWKYPQVNGL 419 7410
HLA-A*03:02 YMSALNHTKK YMSALNHTKN 52 729
HLA-A*31:01 RYMSALNHTKK RYMSALNHTKN 106 777
HLA-A*03:02 SALNHTKKWK SALNHTKNWK 1062 167
HLA-A*30:01 RYMSALNHTKK RYMSALNHTKN 171 1048
HLA-A*11:01 SALNHTKKWK SALNHTKNWK 673 117
HLA-A*11:01 ALNHTKKWK ALNHTKNWK 1758 323
HLA-A*03:02 ALNHTKKWK ALNHTKNWK 266 53
HLA-A*68:02 HTKKWKYPQV HTKNWKYPQV 1273 380
HLA-A*30:02 ALNHTKKWKY ALNHTKNWKY 693 278
HLA-A*03:01 SALNHTKKWK SALNHTKNWK 506 204
HLA-B*27:05 GRYMSALNHTKK GRYMSALNHTKN 140 336
HLA-A*03:01 ALNHTKKWK ALNHTKNWK 132 60
HLA-A*30:01 SALNHTKKWK SALNHTKNWK 535 251

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

NSP12 protein

NSP12

P323L

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

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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