Summary

This strain contains 20 protein-level mutations:

  • 9 mutations in Spike protein: HV 69-70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H
  • 3 mutations in N protein: D3L, 203-204 RG->KR, S235F
  • 1 mutation in NS8 protein: Q27stop
  • 1 mutation in NS9c protein: G50N
  • 3 mutations in NSP3 protein: T183I, A890D, I1412T
  • 1 mutation in NSP6 protein: SGF 106-108 deletion
  • 1 mutation in NSP9 protein: D78N
  • 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

HV 69-70 deletion

Reference  RSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFAST
           |||||||||||||||||||||||||  |||||||||||||||||||||||||
Mutated    RSSVLHSTQDLFLPFFSNVTWFHAI‑‑SGTNGTKRFDNPVLPFNDGVYFAST

Export table to csv 
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

Y144 deletion

Reference  IVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFE
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    IVNNATNVVIKVCEFQFCNDPFLGVYHKNNKSWMESEFRVYSSANNCTFE

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*14:02 YYHKNNKSWM - 19 -
HLA-B*15:03 FQFCNDPFLGVYY - 47 -
HLA-C*14:02 YYHKNNKSW - 52 -
HLA-A*29:02 QFCNDPFLGVYY - 113 -
HLA-A*24:02 YYHKNNKSW - 116 -
HLA-B*15:01 FQFCNDPFLGVYY - 129 -
HLA-A*23:01 YYHKNNKSW - 150 -
HLA-A*29:02 FQFCNDPFLGVYY - 184 -
HLA-A*01:01 CNDPFLGVYY - 202 -
HLA-C*14:02 YYHKNNKSWMESEF - 227 -
HLA-A*29:02 CNDPFLGVYY - 439 -
HLA-A*11:01 GVYYHKNNK GVYHKNNK 51 5741
HLA-A*03:01 GVYYHKNNK GVYHKNNK 27 2231
HLA-A*30:01 GVYYHKNNK GVYHKNNK 51 3606
HLA-A*03:01 LGVYYHKNNK LGVYHKNNK 131 8411
HLA-A*03:02 GVYYHKNNK GVYHKNNK 119 6497
HLA-A*68:01 GVYYHKNNK GVYHKNNK 363 17786
HLA-A*31:01 GVYYHKNNK GVYHKNNK 375 9671
HLA-A*33:03 DPFLGVYYHK DPFLGVYHK 280 4172
HLA-A*68:01 LGVYYHKNNK LGVYHKNNK 494 3973
HLA-C*14:02 VYYHKNNKSW VYHKNNKSW 1115 238
HLA-B*15:03 FQFCNDPFLGVYYH FQFCNDPFLGVYH 1280 298
HLA-C*14:02 VYYHKNNKSWM VYHKNNKSWM 327 108
HLA-A*68:01 DPFLGVYYHK DPFLGVYHK 398 969
HLA-A*03:01 FLGVYYHKNNK FLGVYHKNNK 455 1078

N501Y

Reference  GSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    GSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCG

Export table to csv 
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

A570D

Reference  GLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGV
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    GLTGTGVLTESNKKFLPFQQFGRDIDDTTDAVRDPQTLEILDITPCSFGGV

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:02 DIADTTDAV DIDDTTDAV 24 2016
HLA-C*08:02 IADTTDAV IDDTTDAV 260 12788
HLA-A*68:01 DIADTTDAVR DIDDTTDAVR 28 961
HLA-A*02:02 FGRDIADTTDAV FGRDIDDTTDAV 26 819
HLA-A*68:02 FGRDIADTTDAV FGRDIDDTTDAV 216 5617
HLA-A*02:02 RDIADTTDAV RDIDDTTDAV 109 2346
HLA-B*15:03 FQQFGRDIA FQQFGRDID 491 8882
HLA-A*02:02 FLPFQQFGRDIA FLPFQQFGRDID 379 4318
HLA-A*02:06 FGRDIADTTDAV FGRDIDDTTDAV 85 852
HLA-A*02:06 RDIADTTDAV RDIDDTTDAV 301 2023
HLA-A*02:01 FGRDIADTTDAV FGRDIDDTTDAV 318 1833
HLA-A*02:11 FGRDIADTTDAV FGRDIDDTTDAV 81 356
HLA-A*02:11 RDIADTTDAV RDIDDTTDAV 303 798

D614G

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

Export table to csv 
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

P681H

Reference  VNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVA
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    VNNSYECDIPIGAGICASYQTQTNSHRRARSVASQSIIAYTMSLGAENSVA

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*07:02 SPRRARSVA SHRRARSVA 4 4721
HLA-B*42:01 SPRRARSVA SHRRARSVA 8 6169
HLA-B*07:02 SPRRARSVASQSI SHRRARSVASQSI 17 11433
HLA-B*07:02 SPRRARSV SHRRARSV 24 12728
HLA-B*07:02 SPRRARSVAS SHRRARSVAS 37 14758
HLA-B*07:02 SPRRARSVASQSII SHRRARSVASQSII 55 17736
HLA-B*42:01 SPRRARSV SHRRARSV 38 11622
HLA-B*42:01 SPRRARSVASQSI SHRRARSVASQSI 48 14418
HLA-B*07:02 TNSPRRARSVA TNSHRRARSVA 125 20078
HLA-B*42:01 SPRRARSVAS SHRRARSVAS 158 17461
HLA-B*07:02 NSPRRARSVA NSHRRARSVA 69 7270
HLA-B*42:01 SPRRARSVASQSII SHRRARSVASQSII 321 21521
HLA-B*07:02 TQTNSPRRARSVA TQTNSHRRARSVA 270 17880
HLA-B*07:02 QTNSPRRARSVA QTNSHRRARSVA 249 13539
HLA-B*42:01 TNSPRRARSVA TNSHRRARSVA 437 21599
HLA-B*42:01 NSPRRARSVA NSHRRARSVA 217 8330
HLA-C*14:02 SYQTQTNSP SYQTQTNSH 3691 139
HLA-B*08:01 NSPRRARSV NSHRRARSV 881 69
HLA-B*08:01 SPRRARSVA SHRRARSVA 372 3831
HLA-B*08:01 SPRRARSV SHRRARSV 428 2448
HLA-C*16:01 NSPRRARSV NSHRRARSV 1247 314
HLA-C*12:03 NSPRRARSV NSHRRARSV 1110 365
HLA-A*11:01 ASYQTQTNSPR ASYQTQTNSHR 346 1041
HLA-A*68:01 CASYQTQTNSPR CASYQTQTNSHR 142 401
HLA-A*68:01 TQTNSPRRAR TQTNSHRRAR 254 710
HLA-A*31:01 YQTQTNSPR YQTQTNSHR 441 1214
HLA-A*68:01 YQTQTNSPRR YQTQTNSHRR 206 78
HLA-A*33:03 QTQTNSPRR QTQTNSHRR 445 176
HLA-A*33:03 YQTQTNSPRR YQTQTNSHRR 967 411
HLA-A*68:01 QTQTNSPRR QTQTNSHRR 119 51
HLA-A*68:01 QTNSPRRAR QTNSHRRAR 95 216
HLA-A*31:01 ASYQTQTNSPR ASYQTQTNSHR 139 311

T716I

Reference  SIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMY
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    SIIAYTMSLGAENSVAYSNNSIAIPINFTISVTTEILPVSMTKTSVDCTMY

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*15:02 YSNNSIAIPT YSNNSIAIPI 8151 360
HLA-A*68:02 SVAYSNNSIAIPT SVAYSNNSIAIPI 3003 172
HLA-C*16:01 YSNNSIAIPT YSNNSIAIPI 5899 374
HLA-A*68:02 YSNNSIAIPT YSNNSIAIPI 990 78
HLA-B*58:01 YSNNSIAIPT YSNNSIAIPI 4346 439
HLA-A*02:06 YSNNSIAIPT YSNNSIAIPI 2074 359
HLA-A*02:01 AIPTNFTISV AIPINFTISV 173 30
HLA-A*68:02 IAIPTNFTI IAIPINFTI 505 97
HLA-A*02:06 AIPTNFTISV AIPINFTISV 79 16
HLA-A*68:02 TNFTISVTTEI INFTISVTTEI 199 905
HLA-A*02:02 IAIPTNFTI IAIPINFTI 1142 295
HLA-A*02:11 AIPTNFTISV AIPINFTISV 42 11
HLA-A*02:02 SIAIPTNFTI SIAIPINFTI 167 46
HLA-A*02:11 IAIPTNFTI IAIPINFTI 182 58
HLA-A*02:01 IAIPTNFTI IAIPINFTI 923 325
HLA-A*02:11 SIAIPTNFTI SIAIPINFTI 129 46
HLA-A*02:06 IAIPTNFTI IAIPINFTI 99 37
HLA-A*32:01 IAIPTNFTI IAIPINFTI 370 143
HLA-A*68:02 SIAIPTNFTI SIAIPINFTI 128 50
HLA-A*02:06 SIAIPTNFTISV SIAIPINFTISV 148 58
HLA-C*12:03 IPTNFTISV IPINFTISV 1235 488
HLA-A*02:02 AIPTNFTISV AIPINFTISV 75 30
HLA-A*02:06 SIAIPTNFTI SIAIPINFTI 257 105
HLA-A*02:01 SIAIPTNFTI SIAIPINFTI 541 237
HLA-B*35:01 IPTNFTISV IPINFTISV 182 80
HLA-A*68:02 AIPTNFTISV AIPINFTISV 420 190
HLA-B*42:01 SIAIPTNFTISV SIAIPINFTISV 925 436
HLA-B*15:03 IAIPTNFTI IAIPINFTI 279 559

S982A

Reference  QALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTY
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    QALNTLVKQLSSNFGAISSVLNDILARLDKVEAEVQIDRLITGRLQSLQTY

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*30:01 LSRLDKVEA LARLDKVEA 324 1357
HLA-A*02:11 GAISSVLNDILSRL GAISSVLNDILARL 1085 403
HLA-A*02:01 ISSVLNDILSRL ISSVLNDILARL 1063 399
HLA-A*02:11 VLNDILSRLD VLNDILARLD 274 104
HLA-A*02:01 SVLNDILSRL SVLNDILARL 281 107
HLA-A*02:11 AISSVLNDILSRL AISSVLNDILARL 235 92
HLA-A*02:01 SSVLNDILSRL SSVLNDILARL 920 364
HLA-A*02:02 LNDILSRL LNDILARL 793 331
HLA-A*02:11 SSVLNDILSRL SSVLNDILARL 85 39
HLA-A*02:11 ISSVLNDILSRL ISSVLNDILARL 105 49
HLA-A*68:02 SVLNDILSRL SVLNDILARL 702 331
HLA-A*02:02 GAISSVLNDILSRL GAISSVLNDILARL 262 124
HLA-A*02:02 SSVLNDILSRLD SSVLNDILARLD 902 448
HLA-A*02:11 SVLNDILSRL SVLNDILARL 22 11

D1118H

Reference  GVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQP
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    GVFVSNGTHWFVTQRNFYEPQIITTHNTFVSGNCDVVIGIVNNTVYDPLQP

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*30:01 TTDNTFVSG TTHNTFVSG 13098 346
HLA-A*68:02 TTDNTFVSGNCDV TTHNTFVSGNCDV 2752 249
HLA-C*03:02 QIITTDNTF QIITTHNTF 886 205
HLA-B*18:01 YEPQIITTDNTF YEPQIITTHNTF 1026 250
HLA-B*15:03 QIITTDNTF QIITTHNTF 144 51
HLA-C*14:02 FYEPQIITTDNTF FYEPQIITTHNTF 308 110
HLA-A*02:11 IITTDNTFV IITTHNTFV 105 47

N protein

N

D3L

Reference  MSDNGPQNQRNAPRITFGGPSDSTGSNQ
           || |||||||||||||||||||||||||
Mutated    MSLNGPQNQRNAPRITFGGPSDSTGSNQ

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*03:02 SDNGPQNQR SLNGPQNQR 21742 265
HLA-A*31:01 SDNGPQNQR SLNGPQNQR 7217 137
HLA-A*33:03 SDNGPQNQR SLNGPQNQR 8619 290
HLA-A*68:01 SDNGPQNQR SLNGPQNQR 3572 198
HLA-A*68:01 MSDNGPQNQRNAPR MSLNGPQNQRNAPR 1120 225
HLA-A*31:01 MSDNGPQNQRNAPR MSLNGPQNQRNAPR 627 178
HLA-A*33:03 MSDNGPQNQRNAPR MSLNGPQNQRNAPR 565 181
HLA-A*31:01 SDNGPQNQRNAPR SLNGPQNQRNAPR 1101 415
HLA-A*33:03 MSDNGPQNQR MSLNGPQNQR 290 129
HLA-A*31:01 MSDNGPQNQR MSLNGPQNQR 217 98

203-204 RG->KR

Reference  GGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQ
           |||||||||||||||||||||||||  |||||||||||||||||||||||||
Mutated    GGSQASSRSSSRSRNSSRNSTPGSSKRTSPARMAGNGGDAALALLLLDRLNQ

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 NSTPGSSRG NSTPGSSKR 32767 34
HLA-A*33:03 NSTPGSSRG NSTPGSSKR 32767 300
HLA-B*15:03 SRGTSPARM SKRTSPARM 2669 106
HLA-A*31:01 RNSTPGSSRG RNSTPGSSKR 7013 340
HLA-A*30:01 SSRNSTPGSSR SSRNSTPGSSK 356 20
HLA-A*30:01 GTSPARMAG RTSPARMAG 493 30
HLA-A*31:01 SSRNSTPGSSRG SSRNSTPGSSKR 3757 231
HLA-A*30:01 GTSPARMAGNGG RTSPARMAGNGG 6051 411
HLA-A*31:01 SSRNSTPGSSR SSRNSTPGSSK 127 1853
HLA-A*30:01 NSSRNSTPGSSR NSSRNSTPGSSK 4255 353
HLA-A*30:01 RNSTPGSSR RNSTPGSSK 2120 188
HLA-A*31:01 RNSTPGSSR RNSTPGSSK 123 1335
HLA-A*03:01 SSRNSTPGSSR SSRNSTPGSSK 4753 442
HLA-A*11:01 SSRNSTPGSSR SSRNSTPGSSK 2231 263
HLA-A*68:01 NSSRNSTPGSSR NSSRNSTPGSSK 270 1385
HLA-A*30:01 GSSRGTSPA GSSKRTSPA 555 145
HLA-A*30:01 SSRNSTPGSSRG SSRNSTPGSSKR 1625 469
HLA-A*30:01 SSRGTSPARMAG SSKRTSPARMAG 449 1031

S235F

Reference  MAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQ
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    MAGNGGDAALALLLLDRLNQLESKMFGKGQQQQGQTVTKKSAAEASKKPRQ

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*15:01 RLNQLESKMS RLNQLESKMF 11543 128
HLA-B*15:03 RLNQLESKMS RLNQLESKMF 15810 402
HLA-A*02:11 KMSGKGQQQQGQTV KMFGKGQQQQGQTV 4223 179
HLA-A*11:01 NQLESKMSGK NQLESKMFGK 1477 282
HLA-A*03:02 QLESKMSGK QLESKMFGK 782 156
HLA-A*11:01 QLESKMSGK QLESKMFGK 1994 407
HLA-A*03:02 RLNQLESKMSGK RLNQLESKMFGK 319 129

NS8 protein

NS8

Q27stop

Reference  KFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIELCVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDFI
           |||||||||||||||||||||||||                                                                                               
Mutated    KFLVFLGIITTVAAFHQECSLQSCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 YIDIGNYTV - 3 -
HLA-A*29:02 SFYEDFLEY - 3 -
HLA-A*31:01 HFYSKWYIR - 4 -
HLA-A*02:11 FLEYHDVRV - 5 -
HLA-A*33:03 HFYSKWYIR - 5 -
HLA-A*02:06 YIDIGNYTV - 6 -
HLA-B*15:03 IQYIDIGNY - 6 -
HLA-A*68:01 FTINCQEPK - 7 -
HLA-A*02:01 YIDIGNYTV - 8 -
HLA-A*02:02 FLEYHDVRV - 9 -
HLA-A*02:06 YVVDDPCPI - 10 -
HLA-A*02:11 FLEYHDVRVV - 10 -
HLA-C*14:02 SFYEDFLEY - 10 -
HLA-A*02:11 YVVDDPCPI - 13 -
HLA-A*31:01 IHFYSKWYIR - 13 -
HLA-B*53:01 CPIHFYSKW - 13 -
HLA-C*14:02 NYTVSCLPF - 13 -
HLA-A*29:02 CSFYEDFLEY - 15 -
HLA-A*02:02 YIDIGNYTV - 16 -
HLA-C*05:01 YIDIGNYTV - 16 -
HLA-A*02:06 YTVSCLPFTI - 18 -
HLA-A*68:02 TVSCLPFTI - 19 -
HLA-A*02:01 FLEYHDVRV - 22 -
HLA-A*31:01 KWYIRVGAR - 22 -
HLA-A*02:02 FLEYHDVRVV - 24 -
HLA-A*68:02 YTVSCLPFTI - 24 -
HLA-A*02:02 YVVDDPCPI - 29 -
HLA-A*02:11 YTVSCLPFTI - 29 -
HLA-C*03:03 YVVDDPCPI - 29 -
HLA-C*03:04 YVVDDPCPI - 29 -
HLA-A*11:01 FTINCQEPK - 30 -
HLA-C*08:02 YIDIGNYTV - 30 -
HLA-A*31:01 HFYSKWYIRVGAR - 31 -
HLA-A*02:11 TVSCLPFTI - 32 -
HLA-A*33:03 HFYSKWYIRVGAR - 32 -
HLA-B*15:01 IQYIDIGNY - 32 -
HLA-B*40:01 LEYHDVRVVL - 32 -
HLA-A*33:03 IHFYSKWYIR - 35 -
HLA-A*02:02 YTVSCLPFTI - 36 -
HLA-C*14:02 EYHDVRVVL - 38 -
HLA-A*30:02 IQYIDIGNY - 39 -
HLA-B*15:03 SFYEDFLEY - 39 -
HLA-A*02:01 FLEYHDVRVV - 46 -
HLA-A*24:02 NYTVSCLPF - 47 -
HLA-A*30:01 GSKSPIQYI - 47 -
HLA-B*40:02 LEYHDVRVVL - 49 -
HLA-C*03:02 YTVSCLPF - 52 -
HLA-A*23:01 NYTVSCLPF - 53 -
HLA-A*30:02 GSLVVRCSFY - 54 -
HLA-A*29:02 VRCSFYEDFLEY - 55 -
HLA-A*30:01 GARKSAPLI - 55 -
HLA-B*08:01 YIRVGARKSAPL - 55 -
HLA-C*03:02 YVVDDPCPI - 55 -
HLA-A*68:02 YVVDDPCPI - 57 -
HLA-A*02:01 YVVDDPCPI - 59 -
HLA-A*02:06 YTVSCLPFT - 59 -
HLA-B*15:03 RKSAPLIEL - 59 -
HLA-A*29:02 RCSFYEDFLEY - 60 -
HLA-A*29:02 VVRCSFYEDFLEY - 61 -
HLA-A*02:02 TVSCLPFTI - 63 -
HLA-A*31:01 CPIHFYSKWYIR - 74 -
HLA-A*30:01 RVGARKSAPLI - 75 -
HLA-A*01:01 CSFYEDFLEY - 76 -
HLA-A*02:06 FLEYHDVRV - 80 -
HLA-A*29:02 SLVVRCSFY - 84 -
HLA-A*02:06 TVSCLPFTI - 85 -
HLA-A*02:02 FLEYHDVRVVL - 86 -
HLA-A*30:02 CSFYEDFLEY - 89 -
HLA-A*30:02 SFYEDFLEY - 90 -
HLA-C*14:02 LEYHDVRVVL - 90 -
HLA-A*02:01 YTVSCLPFTI - 93 -
HLA-B*58:01 YTVSCLPFTI - 94 -
HLA-C*12:03 YVVDDPCPI - 97 -
HLA-A*29:02 YVVDDPCPIHFY - 98 -
HLA-A*31:01 HFYSKWYIRV - 98 -
HLA-A*02:11 KLGSLVVRC - 101 -
HLA-B*15:03 GNYTVSCLPF - 101 -
HLA-A*30:02 SLVVRCSFY - 103 -
HLA-A*26:01 YVVDDPCPIHFY - 106 -
HLA-A*29:02 SFYEDFLEYH - 110 -
HLA-A*68:02 FTINCQEPKL - 113 -
HLA-B*15:01 SLVVRCSFY - 115 -
HLA-C*14:02 FYEDFLEY - 116 -
HLA-A*33:03 DFLEYHDVR - 117 -
HLA-B*42:01 EPKLGSLVV - 118 -
HLA-A*31:01 YSKWYIRVGAR - 120 -
HLA-A*03:02 FTINCQEPK - 121 -
HLA-A*30:02 KSPIQYIDIGNY - 122 -
HLA-B*40:02 LEYHDVRVV - 122 -
HLA-A*33:03 CPIHFYSKWYIR - 123 -
HLA-C*14:02 FLEYHDVRVVL - 126 -
HLA-B*15:03 CSFYEDFLEY - 128 -
HLA-B*35:01 SFYEDFLEY - 128 -
HLA-A*68:01 PFTINCQEPK - 130 -
HLA-B*15:03 SLVVRCSFY - 130 -
HLA-A*33:03 FYSKWYIRVGAR - 133 -
HLA-B*15:03 GSLVVRCSF - 133 -
HLA-A*02:06 FTINCQEPKL - 134 -
HLA-A*02:11 QYIDIGNYTV - 135 -
HLA-A*02:11 FLEYHDVRVVL - 137 -
HLA-B*57:01 LGSLVVRCSF - 138 -
HLA-A*02:02 FTINCQEPKL - 140 -
HLA-A*31:01 KWYIRVGARK - 145 -
HLA-A*68:01 HFYSKWYIR - 146 -
HLA-A*30:01 KWYIRVGARK - 149 -
HLA-C*03:02 SFYEDFLEY - 152 -
HLA-C*12:02 YVVDDPCPI - 156 -
HLA-A*31:01 PIHFYSKWYIR - 158 -
HLA-B*15:03 YTVSCLPF - 158 -
HLA-C*07:02 SFYEDFLEY - 160 -
HLA-A*33:03 YSKWYIRVGAR - 162 -
HLA-C*17:01 YVVDDPCPI - 163 -
HLA-B*38:01 IHFYSKWYI - 168 -
HLA-A*23:01 FYSKWYIRV - 171 -
HLA-A*29:02 LVVRCSFYEDFLEY - 171 -
HLA-A*23:01 QYIDIGNYTV - 174 -
HLA-A*33:03 FYSKWYIR - 174 -
HLA-A*33:03 HFYSKWYIRV - 176 -
HLA-B*58:01 KSAPLIELCV - 177 -
HLA-C*17:01 YIDIGNYTV - 181 -
HLA-B*58:01 LGSLVVRCSF - 182 -
HLA-A*31:01 SKWYIRVGAR - 183 -
HLA-B*38:01 YHDVRVVLDF - 184 -
HLA-A*02:06 FLEYHDVRVV - 192 -
HLA-A*30:01 AGSKSPIQYI - 192 -
HLA-C*08:01 YIDIGNYTV - 192 -
HLA-A*11:01 SCLPFTINCQEPK - 193 -
HLA-A*29:02 FYEDFLEY - 195 -
HLA-A*31:01 FYSKWYIR - 195 -
HLA-A*30:02 KLGSLVVRCSFY - 199 -
HLA-B*15:03 SPIQYIDIGNY - 201 -
HLA-B*58:01 GSLVVRCSF - 201 -
HLA-C*14:02 FYSKWYIRV - 207 -
HLA-B*58:01 CSFYEDFLEY - 208 -
HLA-C*03:02 CSFYEDFLEY - 211 -
HLA-B*58:01 KSAPLIELC - 217 -
HLA-B*42:01 QEPKLGSLVV - 218 -
HLA-A*24:02 NYTVSCLPFTI - 221 -
HLA-B*50:01 LEYHDVRVV - 221 -
HLA-B*40:01 YEDFLEYHDVRVVL - 224 -
HLA-A*01:01 VVDDPCPIHFY - 225 -
HLA-B*07:02 RVGARKSAPL - 225 -
HLA-A*30:01 YSKWYIRVGA - 229 -
HLA-C*16:01 YVVDDPCPI - 229 -
HLA-A*23:01 NYTVSCLPFTI - 231 -
HLA-A*30:02 RCSFYEDFLEY - 236 -
HLA-A*68:02 DVRVVLDFI - 236 -
HLA-A*33:03 DPCPIHFYSKWYIR - 238 -
HLA-C*16:01 YTVSCLPF - 240 -
HLA-A*02:01 TVSCLPFTI - 244 -
HLA-A*31:01 FYSKWYIRVGAR - 244 -
HLA-C*05:01 FLEYHDVRV - 244 -
HLA-A*68:02 YTVSCLPFT - 245 -
HLA-C*05:01 VVDDPCPIHF - 247 -
HLA-B*15:03 KSPIQYIDIGNY - 252 -
HLA-A*68:02 FTINCQEPKLGSLV - 254 -
HLA-B*15:01 CSFYEDFLEY - 256 -
HLA-A*24:02 FYSKWYIRV - 261 -
HLA-A*68:02 YSKWYIRVGA - 262 -
HLA-B*57:01 KLGSLVVRCSF - 263 -
HLA-A*01:01 CVDEAGSKSPIQY - 264 -
HLA-A*33:03 EDFLEYHDVR - 264 -
HLA-A*23:01 IGNYTVSCLPF - 272 -
HLA-C*02:02 YVVDDPCPI - 275 -
HLA-C*02:10 YVVDDPCPI - 275 -
HLA-B*57:01 GSLVVRCSF - 276 -
HLA-A*32:01 TVSCLPFTI - 294 -
HLA-A*02:02 SLVVRCSFYEDFL - 298 -
HLA-A*02:11 IQYIDIGNYTV - 299 -
HLA-A*30:02 PIQYIDIGNY - 304 -
HLA-A*24:02 QYIDIGNYTV - 310 -
HLA-A*02:11 YIDIGNYTVS - 313 -
HLA-A*02:06 IQYIDIGNYTV - 320 -
HLA-B*15:01 VVRCSFYEDF - 326 -
HLA-B*40:01 LEYHDVRVV - 328 -
HLA-B*15:03 RCSFYEDFLEY - 332 -
HLA-C*14:02 YEDFLEYHDVRVVL - 333 -
HLA-A*68:01 YVVDDPCPIHFYSK - 335 -
HLA-A*31:01 IHFYSKWYIRVGAR - 336 -
HLA-B*08:01 VGARKSAPL - 346 -
HLA-C*14:02 YHDVRVVL - 346 -
HLA-A*33:03 KWYIRVGAR - 347 -
HLA-B*15:01 SPIQYIDIGNY - 352 -
HLA-B*40:02 YEDFLEYHDV - 352 -
HLA-A*33:03 WYIRVGARK - 359 -
HLA-A*33:03 SKWYIRVGAR - 361 -
HLA-C*03:02 YVVDDPCPIHF - 364 -
HLA-A*30:01 KWYIRVGAR - 382 -
HLA-C*16:01 IGNYTVSCL - 383 -
HLA-B*15:03 SKSPIQYIDIGNY - 384 -
HLA-B*15:03 PIQYIDIGNY - 390 -
HLA-A*11:01 CSFYEDFLEY - 395 -
HLA-A*68:01 FTINCQEPKL - 395 -
HLA-A*33:03 PIHFYSKWYIR - 398 -
HLA-B*08:01 SLVVRCSF - 399 -
HLA-C*16:01 GSLVVRCSF - 400 -
HLA-A*11:01 VVDDPCPIHFYSK - 401 -
HLA-A*29:02 GSLVVRCSFY - 402 -
HLA-A*68:01 YSKWYIRVGARK - 402 -
HLA-C*15:02 KSAPLIELCV - 403 -
HLA-C*07:02 EYHDVRVVL - 404 -
HLA-A*29:02 IQYIDIGNY - 410 -
HLA-A*02:11 YIDIGNYTVSCL - 412 -
HLA-B*40:06 LEYHDVRVV - 412 -
HLA-A*68:02 YIDIGNYTV - 413 -
HLA-B*15:03 YHDVRVVLDF - 413 -
HLA-A*33:03 FTINCQEPK - 416 -
HLA-B*38:01 YHDVRVVL - 417 -
HLA-A*24:02 IGNYTVSCLPF - 426 -
HLA-A*30:01 HFYSKWYIR - 430 -
HLA-C*15:02 YTVSCLPFTI - 430 -
HLA-B*15:03 CQEPKLGSL - 432 -
HLA-C*12:03 SFYEDFLEY - 443 -
HLA-B*42:01 YIRVGARKSAPL - 448 -
HLA-B*15:03 VRCSFYEDFLEY - 449 -
HLA-B*58:01 KLGSLVVRCSF - 450 -
HLA-C*14:02 CSFYEDFLEY - 454 -
HLA-B*15:01 YTVSCLPF - 456 -
HLA-A*30:02 SKSPIQYIDIGNY - 458 -
HLA-A*02:11 DFLEYHDVRVV - 459 -
HLA-A*11:01 LPFTINCQEPK - 466 -
HLA-B*40:02 YEDFLEYHDVRVVL - 468 -
HLA-B*15:03 IQYIDIGNYT - 483 -
HLA-B*58:01 TVSCLPFTI - 484 -
HLA-C*16:01 SFYEDFLEY - 486 -
HLA-A*30:02 SPIQYIDIGNY - 491 -
HLA-A*02:06 FTINCQEPKLGSL - 492 -
HLA-A*23:01 GNYTVSCLPF - 495 -
HLA-A*33:03 IHFYSKWYIRVGAR - 497 -
HLA-C*14:02 FYEDFLEYH - 497 -
HLA-A*02:01 FLEYHDVRVVL - 499 -
HLA-A*31:01 WYIRVGARK - 500 -

NS9c protein

NS9c

G50N

Reference  AAVKPLLVPHHVVATVQEIQLQAAVGELLLLEWLAMAVMLLLLCCCLTD
           ||||||||||||||||||||||||| |||||||||||||||||||||||
Mutated    AAVKPLLVPHHVVATVQEIQLQAAVNELLLLEWLAMAVMLLLLCCCLTD

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*18:01 GELLLLEWLAM NELLLLEWLAM 4979 247
HLA-B*18:01 GELLLLEW NELLLLEW 3915 401
HLA-B*40:01 GELLLLEWL NELLLLEWL 28 140
HLA-A*02:11 QLQAAVGEL QLQAAVNEL 120 27
HLA-A*02:11 IQLQAAVGEL IQLQAAVNEL 338 81
HLA-B*40:02 GELLLLEWL NELLLLEWL 52 204
HLA-B*40:02 GELLLLEWLAM NELLLLEWLAM 201 772
HLA-A*02:01 QLQAAVGEL QLQAAVNEL 1290 358
HLA-A*02:02 QLQAAVGEL QLQAAVNEL 92 28
HLA-B*58:01 VGELLLLEW VNELLLLEW 330 1071
HLA-A*02:02 IQLQAAVGEL IQLQAAVNEL 170 58
HLA-A*02:01 LQAAVGELL LQAAVNELL 938 352
HLA-A*02:02 LQAAVGELL LQAAVNELL 44 17
HLA-B*40:06 GELLLLEWLA NELLLLEWLA 268 677
HLA-B*40:02 GELLLLEWLA NELLLLEWLA 475 1195
HLA-A*02:11 LQAAVGELL LQAAVNELL 386 154
HLA-A*02:01 IQLQAAVGEL IQLQAAVNEL 1138 475
HLA-A*02:01 QLQAAVGELL QLQAAVNELL 961 403
HLA-A*02:01 GELLLLEWLAMA NELLLLEWLAMA 109 258
HLA-A*02:02 QLQAAVGELL QLQAAVNELL 35 15
HLA-A*02:02 IQLQAAVGELL IQLQAAVNELL 724 313
HLA-A*02:11 QLQAAVGELL QLQAAVNELL 303 131
HLA-B*58:01 AVGELLLLEW AVNELLLLEW 196 87
HLA-A*02:11 GELLLLEWLAMA NELLLLEWLAMA 29 61
HLA-B*57:01 AVGELLLLEW AVNELLLLEW 432 206
HLA-A*68:02 EIQLQAAVGELL EIQLQAAVNELL 697 346

NSP3 protein

NSP3

T183I

Reference  EEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVN
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    EEDWLDDDSQQTVGQQDGSEDNQTTIIQTIVEVQPQLEMELTPVVQTIEVN

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:02 NQTTTIQTIVEV NQTTIIQTIVEV 131 1642
HLA-A*68:02 EDNQTTTIQTIVEV EDNQTTIIQTIVEV 209 2184
HLA-A*02:11 TTTIQTIVEV TTIIQTIVEV 926 101
HLA-A*02:01 TTIQTIVEV TIIQTIVEV 449 53
HLA-C*15:02 TTIQTIVEV TIIQTIVEV 148 1212
HLA-A*68:02 TTIQTIVEVQ TIIQTIVEVQ 486 3957
HLA-A*02:02 TTIQTIVEV TIIQTIVEV 586 86
HLA-C*16:01 TTIQTIVEV TIIQTIVEV 287 1681
HLA-A*02:11 TTIQTIVEV TIIQTIVEV 36 7
HLA-A*68:02 TTIQTIVEV TIIQTIVEV 8 36
HLA-C*12:03 TTIQTIVEV TIIQTIVEV 65 268
HLA-A*02:06 NQTTTIQTI NQTTIIQTI 966 325
HLA-A*02:06 TTTIQTIVEV TTIIQTIVEV 346 128
HLA-A*02:06 TTIQTIVEV TIIQTIVEV 28 14

A890D

Reference  LQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMS
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    LQQIELKFNPPALQDAYYRARAGEADNFCALILAYCNKTVGELGDVRETMS

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*16:01 AANFCALIL ADNFCALIL 71 26218
HLA-C*03:03 AANFCALIL ADNFCALIL 163 32767
HLA-C*03:04 AANFCALIL ADNFCALIL 163 32767
HLA-C*03:02 AANFCALIL ADNFCALIL 249 32767
HLA-C*12:03 AANFCALIL ADNFCALIL 327 31906
HLA-A*68:02 EAANFCALI EADNFCALI 5 445
HLA-C*17:01 AANFCALIL ADNFCALIL 417 28330
HLA-C*15:02 AANFCALIL ADNFCALIL 444 23260
HLA-A*68:02 EAANFCALIL EADNFCALIL 39 1878
HLA-B*15:03 ANFCALILAY DNFCALILAY 99 3738
HLA-B*15:03 AANFCALIL ADNFCALIL 401 11495
HLA-A*68:02 GEAANFCALI GEADNFCALI 256 6356
HLA-A*01:01 EAANFCALILAY EADNFCALILAY 2565 144
HLA-A*26:01 EAANFCALILAY EADNFCALILAY 318 5414
HLA-B*15:01 ANFCALILAY DNFCALILAY 400 5972
HLA-A*30:02 ANFCALILAY DNFCALILAY 167 2346
HLA-A*02:06 AANFCALILA ADNFCALILA 441 4505
HLA-B*07:02 RARAGEAANF RARAGEADNF 420 3711
HLA-A*30:01 RARAGEAAN RARAGEADN 425 2806
HLA-A*68:02 EAANFCALILA EADNFCALILA 262 1482
HLA-B*15:03 ARAGEAANF ARAGEADNF 191 929
HLA-B*15:03 RARAGEAANF RARAGEADNF 72 338
HLA-B*15:01 RARAGEAANF RARAGEADNF 132 605
HLA-A*29:02 ANFCALILAY DNFCALILAY 55 231
HLA-A*24:02 YYRARAGEAANF YYRARAGEADNF 167 684
HLA-A*23:01 YYRARAGEAANF YYRARAGEADNF 209 819
HLA-A*30:01 RARAGEAANF RARAGEADNF 344 1332
HLA-B*15:03 GEAANFCAL GEADNFCAL 162 420
HLA-A*23:01 AYYRARAGEAANF AYYRARAGEADNF 278 625
HLA-A*30:01 RARAGEAANFCA RARAGEADNFCA 258 518

I1412T

Reference  SVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMS
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    SVGKFCLEASFNYLKSPNFSKLINITIWFLLLSVCLGSLIYSTAALGVLMS

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:02 IIIWFLLLSV ITIWFLLLSV 2073 142
HLA-A*68:02 IIWFLLLSV TIWFLLLSV 2625 320
HLA-B*15:03 KLINIIIWF KLINITIWF 568 90
HLA-B*15:01 KLINIIIWF KLINITIWF 1157 248
HLA-A*02:02 YLKSPNFSKLINII YLKSPNFSKLINIT 334 1554
HLA-C*03:03 FSKLINIII FSKLINITI 2108 478
HLA-C*03:04 FSKLINIII FSKLINITI 2108 478
HLA-C*16:01 FSKLINIII FSKLINITI 527 137
HLA-C*12:03 FSKLINIII FSKLINITI 247 65
HLA-C*03:02 FSKLINIII FSKLINITI 1536 421
HLA-A*32:01 KLINIIIWFL KLINITIWFL 488 141
HLA-A*02:01 SKLINIIIWFL SKLINITIWFL 312 91
HLA-A*32:01 KLINIIIWF KLINITIWF 161 47
HLA-B*58:01 FSKLINIIIW FSKLINITIW 51 15
HLA-A*68:02 FSKLINIII FSKLINITI 1131 345
HLA-A*02:06 SKLINIIIWFL SKLINITIWFL 940 293
HLA-A*02:06 LINIIIWFL LINITIWFL 432 137
HLA-A*02:02 SKLINIIIWFL SKLINITIWFL 609 195
HLA-A*02:11 LINIIIWFLL LINITIWFLL 444 146
HLA-A*23:01 KLINIIIWF KLINITIWF 1357 449
HLA-A*23:01 INIIIWFLL INITIWFLL 1280 432
HLA-B*57:01 FSKLINIIIW FSKLINITIW 79 27
HLA-A*02:11 SKLINIIIWFL SKLINITIWFL 88 32
HLA-C*15:02 FSKLINIII FSKLINITI 1149 428
HLA-A*02:11 YLKSPNFSKLINII YLKSPNFSKLINIT 314 833
HLA-A*02:02 LINIIIWFLL LINITIWFLL 447 169
HLA-A*02:01 LINIIIWFL LINITIWFL 335 127
HLA-B*57:01 KSPNFSKLINIIIW KSPNFSKLINITIW 454 176
HLA-B*58:01 KSPNFSKLINIIIW KSPNFSKLINITIW 382 150
HLA-B*42:01 SPNFSKLINIII SPNFSKLINITI 633 254
HLA-B*15:03 SKLINIIIWF SKLINITIWF 222 90
HLA-A*02:01 FSKLINIIIWFL FSKLINITIWFL 1189 487
HLA-C*12:02 FSKLINIII FSKLINITI 1099 482
HLA-A*02:02 SKLINIIIWFLL SKLINITIWFLL 810 365
HLA-A*02:11 NFSKLINIIIWFL NFSKLINITIWFL 909 417
HLA-A*02:02 FSKLINIIIWFL FSKLINITIWFL 853 394
HLA-A*02:02 KLINIIIWFLLL KLINITIWFLLL 114 53
HLA-B*58:01 KLINIIIW KLINITIW 930 441
HLA-A*02:11 FSKLINIIIWFL FSKLINITIWFL 198 94
HLA-A*02:02 KLINIIIWF KLINITIWF 815 387
HLA-A*02:11 NIIIWFLLL NITIWFLLL 245 511
HLA-A*02:02 KLINIIIWFLL KLINITIWFLL 76 38

NSP6 protein

NSP6

SGF 106-108 deletion

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

Export table to csv 
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

NSP9 protein

NSP9

D78N

Reference  WARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVL
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    WARFPKSDGTGTIYTELEPPCRFVTNTPKGPKVKYLYFIKGLNNLNRGMVL

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*01:01 VTDTPKGPKVKYLY VTNTPKGPKVKYLY 57 2541
HLA-A*30:01 VTDTPKGPK VTNTPKGPK 1758 46
HLA-A*01:01 VTDTPKGPKVKY VTNTPKGPKVKY 277 6463
HLA-A*68:01 VTDTPKGPK VTNTPKGPK 2219 277
HLA-A*03:01 VTDTPKGPK VTNTPKGPK 694 102
HLA-A*30:01 RFVTDTPKGPK RFVTNTPKGPK 959 142
HLA-A*03:01 RFVTDTPKGPK RFVTNTPKGPK 1503 399
HLA-A*03:01 FVTDTPKGPK FVTNTPKGPK 948 323
HLA-B*27:05 LEPPCRFVTDTPK LEPPCRFVTNTPK 1066 368
HLA-A*03:02 VTDTPKGPK VTNTPKGPK 713 268
HLA-A*11:01 VTDTPKGPK VTNTPKGPK 137 57

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