Summary

This strain contains 20 protein-level mutations:

  • 8 mutations in Spike protein: Q52R, A67V, HV 69-70 deletion, Y144 deletion, E484K, D614G, Q677H, F888L
  • 4 mutations in N protein: S2 deletion, D3Y, A12G, T205I
  • 1 mutation in M protein: I82T
  • 1 mutation in E protein: L21F
  • 1 mutation in NS6 protein: F2 deletion
  • 1 mutation in NS9b protein: H9D
  • 1 mutation in NS9c protein: L52F
  • 1 mutation in NSP3 protein: T1189I
  • 1 mutation in NSP6 protein: SGF 106-108 deletion
  • 1 mutation in NSP12 protein: P323F

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

Q52R

Reference  AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTK
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    AYTNSFTRGVYYPDKVFRSSVLHSTRDLFLPFFSNVTWFHVI‑‑SGTNGTK

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*31:01 RSSVLHSTQ RSSVLHSTR 7157 7
HLA-A*31:01 KVFRSSVLHSTQ KVFRSSVLHSTR 11964 15
HLA-A*68:01 FRSSVLHSTQ FRSSVLHSTR 9279 25
HLA-A*31:01 FRSSVLHSTQ FRSSVLHSTR 21936 75
HLA-A*31:01 VFRSSVLHSTQ VFRSSVLHSTR 14990 60
HLA-A*33:03 FRSSVLHSTQ FRSSVLHSTR 23602 97
HLA-A*31:01 DKVFRSSVLHSTQ DKVFRSSVLHSTR 29057 192
HLA-A*33:03 RSSVLHSTQ RSSVLHSTR 24802 229
HLA-A*31:01 RSSVLHSTQD RSSVLHSTRD 27209 280
HLA-A*33:03 VFRSSVLHSTQ VFRSSVLHSTR 23512 265
HLA-A*68:01 RSSVLHSTQ RSSVLHSTR 18086 261
HLA-A*74:01 KVFRSSVLHSTQ KVFRSSVLHSTR 17684 281
HLA-A*33:03 KVFRSSVLHSTQ KVFRSSVLHSTR 29777 500
HLA-A*02:06 TQDLFLPFFSNV TRDLFLPFFSNV 107 6293
HLA-A*30:01 STQDLFLPF STRDLFLPF 2886 58
HLA-A*68:01 KVFRSSVLHSTQ KVFRSSVLHSTR 22789 463
HLA-A*03:02 KVFRSSVLHSTQ KVFRSSVLHSTR 11050 243
HLA-A*11:01 KVFRSSVLHSTQ KVFRSSVLHSTR 11835 266
HLA-A*74:01 RSSVLHSTQ RSSVLHSTR 18484 447
HLA-A*30:01 STQDLFLPFF STRDLFLPFF 3497 105
HLA-A*03:01 KVFRSSVLHSTQ KVFRSSVLHSTR 9334 284
HLA-A*11:01 RSSVLHSTQ RSSVLHSTR 9744 302
HLA-A*30:01 STQDLFLPFFS STRDLFLPFFS 6813 321
HLA-B*15:03 TQDLFLPF TRDLFLPF 47 920
HLA-A*30:01 HSTQDLFLPF HSTRDLFLPF 7213 402
HLA-A*30:01 STQDLFLPFFSNV STRDLFLPFFSNV 4042 240
HLA-B*27:05 FRSSVLHSTQ FRSSVLHSTR 1533 115
HLA-B*15:03 TQDLFLPFF TRDLFLPFF 185 1800
HLA-B*42:01 STQDLFLPF STRDLFLPF 2706 447
HLA-A*30:01 RSSVLHSTQ RSSVLHSTR 677 129
HLA-A*23:01 STQDLFLPF STRDLFLPF 258 1243
HLA-B*57:01 STQDLFLPF STRDLFLPF 1089 319
HLA-A*29:02 STQDLFLPF STRDLFLPF 168 564
HLA-C*12:03 STQDLFLPF STRDLFLPF 279 85
HLA-B*57:01 STQDLFLPFF STRDLFLPFF 647 203
HLA-C*12:02 STQDLFLPF STRDLFLPF 316 113
HLA-B*38:01 LHSTQDLFL LHSTRDLFL 99 270
HLA-A*26:01 STQDLFLPF STRDLFLPF 627 249
HLA-B*57:01 HSTQDLFLPF HSTRDLFLPF 164 69
HLA-B*57:01 HSTQDLFLPFF HSTRDLFLPFF 394 169
HLA-B*15:01 STQDLFLPF STRDLFLPF 48 21
HLA-B*15:01 STQDLFLPFF STRDLFLPFF 230 104
HLA-C*02:02 STQDLFLPF STRDLFLPF 443 212
HLA-C*02:10 STQDLFLPF STRDLFLPF 443 212
HLA-A*30:02 STQDLFLPF STRDLFLPF 923 459

A67V

Reference  VFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYF
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    VFRSSVLHSTRDLFLPFFSNVTWFHVI‑‑SGTNGTKRFDNPVLPFNDGVYF

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:02 NVTWFHAIHV NVTWFHVI 16 5547
HLA-A*02:11 NVTWFHAIHV NVTWFHVI 125 10192
HLA-A*02:06 NVTWFHAIHV NVTWFHVI 263 10869
HLA-C*15:02 FSNVTWFHAIH FSNVTWFHVI 15930 389
HLA-A*68:02 FSNVTWFHAIH FSNVTWFHVI 13953 418
HLA-A*02:02 NVTWFHAIHV NVTWFHVI 468 14619
HLA-B*58:01 FSNVTWFHAIH FSNVTWFHVI 7866 292
HLA-B*51:01 LPFFSNVTWFHAIH LPFFSNVTWFHVI 11466 430
HLA-B*58:01 FSNVTWFHAIHV FSNVTWFHVI 6877 292
HLA-A*11:01 HAIHVSGTNGTK HVISGTNGTK 2998 135
HLA-C*12:03 FSNVTWFHAIH FSNVTWFHVI 8069 365
HLA-A*02:06 FSNVTWFHAIH FSNVTWFHVI 7820 387
HLA-C*15:02 FSNVTWFHA FSNVTWFHV 1444 73
HLA-A*68:01 AIHVSGTNGTKR VISGTNGTKR 5916 313
HLA-A*68:02 HAIHVSGTNGT HVISGTNGT 7705 415
HLA-C*16:01 FSNVTWFHAIH FSNVTWFHVI 5156 295
HLA-B*42:01 LPFFSNVTWFHAIH LPFFSNVTWFHVI 7318 437
HLA-A*03:01 HAIHVSGTNGTK HVISGTNGTK 3368 205
HLA-A*02:11 FSNVTWFHA FSNVTWFHV 366 23
HLA-C*03:02 FSNVTWFHAIHV FSNVTWFHVI 7468 494
HLA-C*16:01 FSNVTWFHAIHV FSNVTWFHVI 4412 295
HLA-C*12:03 FSNVTWFHAIHV FSNVTWFHVI 4736 365
HLA-A*03:02 HAIHVSGTNGTK HVISGTNGTK 4597 368
HLA-C*03:02 FSNVTWFHAIH FSNVTWFHVI 4526 494
HLA-A*68:02 FSNVTWFHA FSNVTWFHV 189 22
HLA-A*02:01 FSNVTWFHA FSNVTWFHV 1863 240
HLA-A*68:02 FFSNVTWFHAIHV FFSNVTWFHVI 492 3778
HLA-A*02:06 FSNVTWFHA FSNVTWFHV 182 24
HLA-C*12:03 FSNVTWFHA FSNVTWFHV 1369 181
HLA-A*02:11 FFSNVTWFHA FFSNVTWFHV 362 50
HLA-C*15:02 FSNVTWFHAIHV FSNVTWFHVI 2711 389
HLA-A*02:02 FSNVTWFHA FSNVTWFHV 741 115
HLA-A*02:11 FLPFFSNVTWFHA FLPFFSNVTWFHV 93 15
HLA-C*16:01 FSNVTWFHA FSNVTWFHV 906 156
HLA-A*68:01 HAIHVSGTNGTK HVISGTNGTK 174 30
HLA-A*68:02 FFSNVTWFHA FFSNVTWFHV 639 128
HLA-A*02:11 FFSNVTWFHAIHV FFSNVTWFHVI 219 1076
HLA-A*02:01 FFSNVTWFHA FFSNVTWFHV 1440 306
HLA-A*02:01 FLPFFSNVTWFHA FLPFFSNVTWFHV 424 94
HLA-A*02:06 FFSNVTWFHA FFSNVTWFHV 972 227
HLA-A*02:02 FFSNVTWFHA FFSNVTWFHV 328 79
HLA-A*02:11 FSNVTWFHAIHV FSNVTWFHVI 250 973
HLA-A*68:02 SNVTWFHAI SNVTWFHVI 196 729
HLA-A*02:02 FLPFFSNVTWFHA FLPFFSNVTWFHV 117 32
HLA-A*03:02 AIHVSGTNGTK VISGTNGTK 1179 326
HLA-A*02:06 SNVTWFHAI SNVTWFHVI 317 1145
HLA-A*02:06 FLPFFSNVTWFHA FLPFFSNVTWFHV 608 172
HLA-C*03:02 FSNVTWFHA FSNVTWFHV 1383 404
HLA-A*68:02 FSNVTWFHAI FSNVTWFHVI 124 418
HLA-A*02:11 FLPFFSNVTWFHAI FLPFFSNVTWFHVI 54 176
HLA-A*02:06 FLPFFSNVTWFHAI FLPFFSNVTWFHVI 457 1475
HLA-A*02:06 FSNVTWFHAI FSNVTWFHVI 123 387
HLA-B*58:01 FSNVTWFHA FSNVTWFHV 1061 354
HLA-A*02:01 FLPFFSNVTWFHAI FLPFFSNVTWFHVI 484 1319
HLA-A*02:02 FLPFFSNVTWFHAI FLPFFSNVTWFHVI 151 392
HLA-A*02:11 FSNVTWFHAI FSNVTWFHVI 398 973
HLA-B*42:01 LPFFSNVTWFHAI LPFFSNVTWFHVI 199 437
HLA-A*11:01 AIHVSGTNGTK VISGTNGTK 742 341
HLA-A*03:01 AIHVSGTNGTK VISGTNGTK 534 251

HV 69-70 deletion

Reference  RSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFAST
           |||||||||||||||||||||||||  |||||||||||||||||||||||||
Mutated    RSSVLHSTRDLFLPFFSNVTWFHVI‑‑SGTNGTKRFDNPVLPFNDGVYFAST

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 HVSGTNGTKR - 42 -
HLA-A*68:02 NVTWFHAIHV NVTWFHVI 16 5547
HLA-A*02:11 NVTWFHAIHV NVTWFHVI 125 10192
HLA-A*02:06 NVTWFHAIHV NVTWFHVI 263 10869
HLA-C*15:02 FSNVTWFHAIH FSNVTWFHVI 15930 389
HLA-A*68:02 FSNVTWFHAIH FSNVTWFHVI 13953 418
HLA-A*02:02 NVTWFHAIHV NVTWFHVI 468 14619
HLA-B*58:01 FSNVTWFHAIH FSNVTWFHVI 7866 292
HLA-B*51:01 LPFFSNVTWFHAIH LPFFSNVTWFHVI 11466 430
HLA-B*58:01 FSNVTWFHAIHV FSNVTWFHVI 6877 292
HLA-A*11:01 HAIHVSGTNGTK HVISGTNGTK 2998 135
HLA-C*12:03 FSNVTWFHAIH FSNVTWFHVI 8069 365
HLA-A*02:06 FSNVTWFHAIH FSNVTWFHVI 7820 387
HLA-A*68:01 AIHVSGTNGTKR VISGTNGTKR 5916 313
HLA-A*68:02 HAIHVSGTNGT HVISGTNGT 7705 415
HLA-C*16:01 FSNVTWFHAIH FSNVTWFHVI 5156 295
HLA-B*42:01 LPFFSNVTWFHAIH LPFFSNVTWFHVI 7318 437
HLA-A*03:01 HAIHVSGTNGTK HVISGTNGTK 3368 205
HLA-C*03:02 FSNVTWFHAIHV FSNVTWFHVI 7468 494
HLA-C*16:01 FSNVTWFHAIHV FSNVTWFHVI 4412 295
HLA-C*12:03 FSNVTWFHAIHV FSNVTWFHVI 4736 365
HLA-A*03:02 HAIHVSGTNGTK HVISGTNGTK 4597 368
HLA-C*03:02 FSNVTWFHAIH FSNVTWFHVI 4526 494
HLA-A*68:02 FFSNVTWFHAIHV FFSNVTWFHVI 492 3778
HLA-C*15:02 FSNVTWFHAIHV FSNVTWFHVI 2711 389
HLA-A*68:01 HAIHVSGTNGTK HVISGTNGTK 174 30
HLA-A*02:11 FFSNVTWFHAIHV FFSNVTWFHVI 219 1076
HLA-A*02:11 FSNVTWFHAIHV FSNVTWFHVI 250 973
HLA-A*03:02 AIHVSGTNGTK VISGTNGTK 1179 326
HLA-A*11:01 AIHVSGTNGTK VISGTNGTK 742 341
HLA-A*03:01 AIHVSGTNGTK VISGTNGTK 534 251

Y144 deletion

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

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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

E484K

Reference  SNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYR
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    SNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTNGVGYQPYR

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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

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

Q677H

Reference  GAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAE
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    GAEHVNNSYECDIPIGAGICASYQTHTNSPRRARSVASQSIIAYTMSLGAE

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*31:01 ASYQTQTNSPRR ASYQTHTNSPRR 433 121
HLA-A*31:01 ASYQTQTNSPR ASYQTHTNSPR 139 45
HLA-A*30:01 QTNSPRRAR HTNSPRRAR 1146 391
HLA-B*07:02 QTNSPRRARSVA HTNSPRRARSVA 249 100
HLA-A*68:01 QTQTNSPRR QTHTNSPRR 119 51
HLA-A*30:01 QTNSPRRARSVA HTNSPRRARSVA 662 288
HLA-B*42:01 QTNSPRRARSVA HTNSPRRARSVA 842 369
HLA-A*68:01 QTNSPRRAR HTNSPRRAR 95 43
HLA-A*33:03 QTNSPRRAR HTNSPRRAR 48 22
HLA-A*68:01 YQTQTNSPRR YQTHTNSPRR 206 99
HLA-A*31:01 YQTQTNSPR YQTHTNSPR 441 220

F888L

Reference  PLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQ
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    PLLTDEMIAQYTSALLAGTITSGWTLGAGAALQIPFAMQMAYRFNGIGVTQ

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 ALLAGTITSGWTF ALLAGTITSGWTL 3766 20
HLA-A*02:11 LLAGTITSGWTF LLAGTITSGWTL 2814 15
HLA-A*02:02 LLAGTITSGWTF LLAGTITSGWTL 2639 26
HLA-A*02:01 ALLAGTITSGWTF ALLAGTITSGWTL 6503 67
HLA-A*02:01 LLAGTITSGWTF LLAGTITSGWTL 5299 62
HLA-C*14:02 TFGAGAAL TLGAGAAL 117 9056
HLA-A*02:02 ALLAGTITSGWTF ALLAGTITSGWTL 7387 110
HLA-A*02:11 TFGAGAALQI TLGAGAALQI 11512 264
HLA-A*02:02 TFGAGAALQI TLGAGAALQI 7571 192
HLA-B*15:01 LLAGTITSGWTF LLAGTITSGWTL 86 3256
HLA-A*02:11 GTITSGWTF GTITSGWTL 7105 250
HLA-B*15:01 GTITSGWTF GTITSGWTL 144 2911
HLA-B*15:01 AGTITSGWTF AGTITSGWTL 305 5944
HLA-A*02:06 LLAGTITSGWTF LLAGTITSGWTL 5077 270
HLA-B*15:03 GTITSGWTF GTITSGWTL 88 1485
HLA-A*02:06 ALLAGTITSGWTF ALLAGTITSGWTL 6727 447
HLA-A*23:01 GTITSGWTF GTITSGWTL 350 4926
HLA-A*68:02 TSGWTFGAGAAL TSGWTLGAGAAL 187 2442
HLA-B*15:03 AGTITSGWTF AGTITSGWTL 492 5538
HLA-C*03:03 FGAGAALQI LGAGAALQI 270 3033
HLA-C*03:04 FGAGAALQI LGAGAALQI 270 3033
HLA-A*02:06 GTITSGWTF GTITSGWTL 1481 149
HLA-A*68:02 GWTFGAGAAL GWTLGAGAAL 362 3498
HLA-C*12:03 FGAGAALQI LGAGAALQI 302 2807
HLA-A*02:02 LLAGTITSGWTFG LLAGTITSGWTLG 3915 444
HLA-B*58:01 GTITSGWTF GTITSGWTL 56 475
HLA-B*58:01 AGTITSGWTF AGTITSGWTL 140 1178
HLA-C*12:03 WTFGAGAAL WTLGAGAAL 31 256
HLA-B*57:01 AGTITSGWTF AGTITSGWTL 297 2383
HLA-A*02:11 ITSGWTFGA ITSGWTLGA 51 399
HLA-A*68:02 ITSGWTFGA ITSGWTLGA 32 247
HLA-B*57:01 GTITSGWTF GTITSGWTL 196 1443
HLA-C*17:01 GTITSGWTF GTITSGWTL 3213 442
HLA-B*58:01 LAGTITSGWTF LAGTITSGWTL 119 847
HLA-B*58:01 LLAGTITSGWTF LLAGTITSGWTL 220 1487
HLA-B*57:01 LLAGTITSGWTF LLAGTITSGWTL 393 2547
HLA-A*02:06 ITSGWTFGA ITSGWTLGA 82 527
HLA-A*26:01 WTFGAGAAL WTLGAGAAL 351 2179
HLA-C*17:01 FGAGAALQI LGAGAALQI 268 1642
HLA-B*57:01 LAGTITSGWTF LAGTITSGWTL 308 1848
HLA-C*12:02 WTFGAGAAL WTLGAGAAL 66 382
HLA-A*02:02 ITSGWTFGA ITSGWTLGA 257 1444
HLA-A*68:02 WTFGAGAAL WTLGAGAAL 13 73
HLA-A*68:02 WTFGAGAALQI WTLGAGAALQI 149 833
HLA-A*68:02 TITSGWTFGA TITSGWTLGA 56 312
HLA-A*02:01 ITSGWTFGA ITSGWTLGA 464 2512
HLA-B*15:01 WTFGAGAALQIPF WTLGAGAALQIPF 308 1443
HLA-C*16:01 FGAGAALQI LGAGAALQI 383 1788
HLA-B*15:03 WTFGAGAALQIPF WTLGAGAALQIPF 333 1473
HLA-B*15:03 WTFGAGAAL WTLGAGAAL 30 131
HLA-C*02:02 WTFGAGAAL WTLGAGAAL 308 1256
HLA-C*02:10 WTFGAGAAL WTLGAGAAL 308 1256
HLA-B*35:01 WTFGAGAAL WTLGAGAAL 240 955
HLA-B*15:01 WTFGAGAAL WTLGAGAAL 210 828
HLA-A*32:01 GTITSGWTF GTITSGWTL 115 411
HLA-C*03:02 GTITSGWTF GTITSGWTL 321 1104
HLA-A*02:11 LLAGTITSGWTFGA LLAGTITSGWTLGA 197 641
HLA-A*02:02 WTFGAGAAL WTLGAGAAL 146 473
HLA-C*15:02 FGAGAALQI LGAGAALQI 328 949
HLA-C*14:02 WTFGAGAAL WTLGAGAAL 106 296
HLA-C*16:01 WTFGAGAAL WTLGAGAAL 41 111
HLA-C*03:02 WTFGAGAAL WTLGAGAAL 10 25
HLA-A*02:11 WTFGAGAAL WTLGAGAAL 132 308
HLA-C*17:01 WTFGAGAAL WTLGAGAAL 108 247

N protein

N

S2 deletion

Reference  MSDNGPQNQRNAPRITFGGPSDSTGSN
           | |||||||||||||||||||||||||
Mutated    MYNGPQNQRNGPRITFGGPSDSTGSN

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 MSDNGPQNQR MYNGPQNQR 37 480
HLA-A*33:03 MSDNGPQNQR MYNGPQNQR 290 39
HLA-A*33:03 MSDNGPQNQRNAPR MYNGPQNQRNGPR 565 140
HLA-A*31:01 MSDNGPQNQR MYNGPQNQR 217 64
HLA-A*31:01 MSDNGPQNQRNAPR MYNGPQNQRNGPR 627 303

D3Y

Reference  MSDNGPQNQRNAPRITFGGPSDSTGSNQ
           || |||||||||||||||||||||||||
Mutated    M‑YNGPQNQRNGPRITFGGPSDSTGSNQ

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 MSDNGPQNQR MYNGPQNQR 37 480
HLA-A*33:03 MSDNGPQNQR MYNGPQNQR 290 39
HLA-A*33:03 MSDNGPQNQRNAPR MYNGPQNQRNGPR 565 140
HLA-A*31:01 MSDNGPQNQR MYNGPQNQR 217 64
HLA-A*31:01 MSDNGPQNQRNAPR MYNGPQNQRNGPR 627 303

A12G

Reference  MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARS
           ||||||||||| |||||||||||||||||||||||||
Mutated    M‑YNGPQNQRNGPRITFGGPSDSTGSNQNGERSGARS

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*07:02 GPQNQRNAPRI GPQNQRNGPRI 496 3951
HLA-A*33:03 MSDNGPQNQRNAPR MYNGPQNQRNGPR 565 140
HLA-B*07:02 APRITFGGPS GPRITFGGPS 191 673
HLA-A*31:01 MSDNGPQNQRNAPR MYNGPQNQRNGPR 627 303

T205I

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

Export table to csv 
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

M protein

M

I82T

Reference  LWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTR
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    LWPVTLACFVLAAVYRINWITGGIATAMACLVGLMWLSYFIASFRLFARTR

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-C*14:02 NWITGGIAI NWITGGIAT 109 4410
HLA-A*68:02 IAMACLVGL TAMACLVGL 424 40
HLA-B*27:05 YRINWITGGIAI YRINWITGGIAT 85 885
HLA-A*68:02 AIAMACLVGL ATAMACLVGL 1414 203
HLA-A*02:11 WITGGIAIA WITGGIATA 788 138
HLA-A*68:02 IAMACLVGLM TAMACLVGLM 2691 495
HLA-A*02:06 WITGGIAIA WITGGIATA 477 117
HLA-A*02:01 AIAMACLVGL ATAMACLVGL 97 388
HLA-A*02:06 IAIAMACLV IATAMACLV 90 359
HLA-A*02:11 AIAMACLVGL ATAMACLVGL 53 208
HLA-A*02:02 WITGGIAIA WITGGIATA 333 88
HLA-A*02:11 IAIAMACLV IATAMACLV 140 524
HLA-A*02:02 AIAMACLVGL ATAMACLVGL 41 133
HLA-B*58:01 IAMACLVGL TAMACLVGL 423 1182
HLA-A*02:11 GIAIAMACL GIATAMACL 350 144
HLA-A*68:02 WITGGIAIA WITGGIATA 918 378
HLA-B*58:01 IAMACLVGLM TAMACLVGLM 479 1090
HLA-C*12:03 IAIAMACLV IATAMACLV 47 105
HLA-A*02:02 GIAIAMACL GIATAMACL 110 50
HLA-B*57:01 IAMACLVGLMW TAMACLVGLMW 65 141
HLA-A*02:02 GIAIAMACLV GIATAMACLV 84 39
HLA-C*12:02 IAIAMACLV IATAMACLV 336 715
HLA-A*02:06 GIAIAMACL GIATAMACL 662 317
HLA-A*02:02 GGIAIAMACL GGIATAMACL 596 288
HLA-B*58:01 IAMACLVGLMW TAMACLVGLMW 19 39
HLA-A*68:02 IAIAMACLV IATAMACLV 168 339
HLA-A*02:01 IAMACLVGL TAMACLVGL 122 246
HLA-A*02:11 IAMACLVGL TAMACLVGL 70 141
HLA-B*57:01 AIAMACLVGLMW ATAMACLVGLMW 538 268

E protein

E

L21F

Reference  MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNI
           |||||||||||||||||||| |||||||||||||||||||||||||
Mutated    MYSFVSEETGTLIVNSVLLFFAFVVFLLVTLAILTALRLCAYCCNI

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 FLAFVVFL FFAFVVFL 21 5433
HLA-A*02:11 IVNSVLLFL IVNSVLLFF 16 3454
HLA-A*02:02 FLAFVVFL FFAFVVFL 24 3923
HLA-A*02:01 FLAFVVFLL FFAFVVFLL 5 777
HLA-A*02:02 IVNSVLLFL IVNSVLLFF 25 3332
HLA-A*02:11 FLAFVVFLLVTL FFAFVVFLLVTL 28 3402
HLA-A*02:01 FLAFVVFL FFAFVVFL 107 11823
HLA-A*02:11 FLAFVVFLLVTLAI FFAFVVFLLVTLAI 120 11658
HLA-A*02:11 TLIVNSVLLFL TLIVNSVLLFF 83 7335
HLA-A*02:01 IVNSVLLFL IVNSVLLFF 74 6206
HLA-A*02:02 LIVNSVLLFL LIVNSVLLFF 70 5517
HLA-A*02:02 LFLAFVVFLL LFFAFVVFLL 16 1201
HLA-A*02:02 FLAFVVFLLVTL FFAFVVFLLVTL 36 2659
HLA-A*02:11 LFLAFVVFLL LFFAFVVFLL 18 1305
HLA-A*02:11 FLAFVVFLLVT FFAFVVFLLVT 186 13267
HLA-A*02:11 FLAFVVFLLV FFAFVVFLLV 6 398
HLA-A*02:02 FLAFVVFLLV FFAFVVFLLV 12 792
HLA-A*02:11 LIVNSVLLFL LIVNSVLLFF 116 7571
HLA-A*02:02 FLAFVVFLLVTLAI FFAFVVFLLVTLAI 185 10954
HLA-A*02:01 FLAFVVFLLV FFAFVVFLLV 33 1870
HLA-A*02:06 FLAFVVFLL FFAFVVFLL 20 1108
HLA-A*02:11 FLAFVVFLL FFAFVVFLL 2 102
HLA-A*02:02 TLIVNSVLLFL TLIVNSVLLFF 147 7129
HLA-A*02:06 IVNSVLLFL IVNSVLLFF 43 1905
HLA-A*02:01 LFLAFVVFLL LFFAFVVFLL 87 3662
HLA-A*02:01 FLAFVVFLLVTL FFAFVVFLLVTL 180 7525
HLA-A*02:02 FLAFVVFLL FFAFVVFLL 3 125
HLA-A*02:02 FLAFVVFLLVT FFAFVVFLLVT 334 13428
HLA-A*02:11 FLAFVVFLLVTLA FFAFVVFLLVTLA 128 4980
HLA-A*02:02 FLAFVVFLLVTLA FFAFVVFLLVTLA 101 3916
HLA-A*02:01 TLIVNSVLLFL TLIVNSVLLFF 255 9664
HLA-A*02:01 LIVNSVLLFL LIVNSVLLFF 229 8576
HLA-A*02:06 LIVNSVLLFL LIVNSVLLFF 147 4187
HLA-A*68:02 IVNSVLLFL IVNSVLLFF 379 10374
HLA-A*29:02 IVNSVLLFL IVNSVLLFF 2008 77
HLA-A*02:11 LFLAFVVFLLV LFFAFVVFLLV 165 3596
HLA-C*14:02 FLAFVVFL FFAFVVFL 10352 482
HLA-C*14:02 FLAFVVFLL FFAFVVFLL 4203 199
HLA-B*15:01 IVNSVLLFL IVNSVLLFF 2718 133
HLA-C*15:02 IVNSVLLFL IVNSVLLFF 126 2497
HLA-B*15:01 LIVNSVLLFL LIVNSVLLFF 1903 97
HLA-A*02:02 LFLAFVVFLLV LFFAFVVFLLV 427 7784
HLA-A*02:01 FLAFVVFLLVTLA FFAFVVFLLVTLA 485 8803
HLA-C*17:01 IVNSVLLFL IVNSVLLFF 140 2532
HLA-A*02:02 LFLAFVVFLLVTL LFFAFVVFLLVTL 399 6794
HLA-B*15:03 IVNSVLLFL IVNSVLLFF 1562 100
HLA-A*23:01 IVNSVLLFL IVNSVLLFF 4286 322
HLA-A*23:01 FLAFVVFLL FFAFVVFLL 5681 432
HLA-C*17:01 FLAFVVFLL FFAFVVFLL 436 4229
HLA-B*15:03 LIVNSVLLFL LIVNSVLLFF 4086 471
HLA-B*58:01 IVNSVLLFL IVNSVLLFF 712 96
HLA-C*03:03 LAFVVFLLV FAFVVFLLV 1855 254
HLA-C*03:04 LAFVVFLLV FAFVVFLLV 1855 254
HLA-A*02:11 SVLLFLAFVVFLL SVLLFFAFVVFLL 141 1000
HLA-A*02:02 SVLLFLAFVVFLL SVLLFFAFVVFLL 157 1091
HLA-A*02:11 LAFVVFLLV FAFVVFLLV 349 56
HLA-C*12:03 LAFVVFLLV FAFVVFLLV 190 31
HLA-C*12:02 LAFVVFLLV FAFVVFLLV 1465 256
HLA-C*03:02 LAFVVFLLV FAFVVFLLV 1034 184
HLA-C*12:03 LAFVVFLL FAFVVFLL 2342 431
HLA-A*68:02 FLAFVVFLL FFAFVVFLL 169 801
HLA-A*02:06 LAFVVFLLV FAFVVFLLV 308 67
HLA-A*68:02 LAFVVFLLV FAFVVFLLV 390 89
HLA-A*02:01 LAFVVFLLV FAFVVFLLV 1554 358
HLA-C*16:01 LAFVVFLLV FAFVVFLLV 411 101
HLA-C*16:01 LAFVVFLL FAFVVFLL 1366 350
HLA-A*02:06 FLAFVVFLLV FFAFVVFLLV 169 651
HLA-A*02:02 LAFVVFLLV FAFVVFLLV 1446 408
HLA-A*29:02 FLAFVVFLL FFAFVVFLL 1280 366
HLA-A*32:01 IVNSVLLFL IVNSVLLFF 574 176
HLA-A*32:01 LLFLAFVVF LLFFAFVVF 1029 347
HLA-C*03:02 NSVLLFLAF NSVLLFFAF 93 270
HLA-B*15:03 NSVLLFLAF NSVLLFFAF 51 144
HLA-C*03:02 IVNSVLLFL IVNSVLLFF 483 182
HLA-B*15:03 VNSVLLFLAF VNSVLLFFAF 355 916
HLA-C*14:02 LFLAFVVFL LFFAFVVFL 452 179
HLA-B*15:01 NSVLLFLAF NSVLLFFAF 445 1122
HLA-A*02:01 NSVLLFLAFV NSVLLFFAFV 218 504
HLA-C*15:02 LAFVVFLLV FAFVVFLLV 725 323
HLA-C*12:03 IVNSVLLFL IVNSVLLFF 327 727
HLA-A*02:02 VLLFLAFVVFL VLLFFAFVVFL 934 457
HLA-A*02:01 SVLLFLAFV SVLLFFAFV 25 51
HLA-C*16:01 NSVLLFLAF NSVLLFFAF 264 537

NS6 protein

NS6

F2 deletion

Reference  MFHLVDFQVTIAEILLIIMRTFKVSIW
           | |||||||||||||||||||||||||
Mutated    MHLVDFQVTIAEILLIIMRTFKVSIW

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*02:11 FHLVDFQVTI - 5 -
HLA-A*02:02 FHLVDFQVTI - 9 -
HLA-A*02:01 FHLVDFQVTI - 13 -
HLA-A*02:06 FHLVDFQVTI - 46 -
HLA-B*38:01 FHLVDFQVTI - 152 -
HLA-A*02:11 FHLVDFQVTIA - 285 -
HLA-A*02:02 FHLVDFQVTIA - 411 -
HLA-B*38:01 MFHLVDFQVTI MHLVDFQVTI 6291 62
HLA-A*68:02 MFHLVDFQV MHLVDFQV 350 17340
HLA-A*02:11 MFHLVDFQV MHLVDFQV 281 3270
HLA-A*68:02 MFHLVDFQVTI MHLVDFQVTI 2857 329
HLA-A*02:02 MFHLVDFQV MHLVDFQV 403 3464
HLA-A*02:02 MFHLVDFQVTI MHLVDFQVTI 51 11
HLA-A*02:06 MFHLVDFQVTI MHLVDFQVTI 303 76
HLA-A*02:01 MFHLVDFQVTI MHLVDFQVTI 81 24
HLA-A*02:11 MFHLVDFQVTI MHLVDFQVTI 25 8

NS9b protein

NS9b

H9D

Reference  MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQ
           |||||||| |||||||||||||||||||||||||
Mutated    MDPKISEMDPALRLVDPQIQLAVTRMENAVGRDQ

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*42:01 HPALRLVDPQIQL DPALRLVDPQIQL 148 6460
HLA-B*42:01 HPALRLVDPQI DPALRLVDPQI 297 7325
HLA-C*16:01 ISEMHPAL ISEMDPAL 248 3759
HLA-A*30:01 KISEMHPAL KISEMDPAL 455 5696
HLA-A*31:01 ISEMHPALR ISEMDPALR 196 2247
HLA-B*42:01 KISEMHPAL KISEMDPAL 213 2223
HLA-B*07:02 KISEMHPAL KISEMDPAL 436 3836
HLA-C*16:01 KISEMHPAL KISEMDPAL 189 1661
HLA-A*32:01 KISEMHPAL KISEMDPAL 124 1005
HLA-A*33:03 ISEMHPALR ISEMDPALR 395 2809
HLA-A*02:11 ISEMHPALRLV ISEMDPALRLV 778 140
HLA-A*68:02 EMHPALRLV EMDPALRLV 211 1079
HLA-C*03:03 KISEMHPAL KISEMDPAL 177 809
HLA-C*03:04 KISEMHPAL KISEMDPAL 177 809
HLA-A*31:01 KISEMHPALR KISEMDPALR 28 126
HLA-A*02:11 EMHPALRLV EMDPALRLV 249 60
HLA-A*33:03 KISEMHPALR KISEMDPALR 308 1254
HLA-C*03:02 KISEMHPAL KISEMDPAL 371 1480
HLA-A*02:01 SEMHPALRLV SEMDPALRLV 975 279
HLA-A*02:11 SEMHPALRLV SEMDPALRLV 122 39
HLA-C*17:01 KISEMHPAL KISEMDPAL 241 721
HLA-A*02:11 KISEMHPAL KISEMDPAL 14 37
HLA-B*40:01 KISEMHPALRL KISEMDPALRL 664 253
HLA-B*15:03 KISEMHPAL KISEMDPAL 436 1138
HLA-A*74:01 KISEMHPALR KISEMDPALR 419 1090
HLA-A*02:06 EMHPALRLV EMDPALRLV 1042 425
HLA-A*03:01 KISEMHPALR KISEMDPALR 414 1011
HLA-B*40:01 ISEMHPALRL ISEMDPALRL 404 179

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

NSP3 protein

NSP3

T1189I

Reference  GAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSED
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    GAKLLHKPIVWHVNNATNKATYKPNIWCIRCLWSTKPVETSNSFDVLKSED

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*57:01 NTWCIRCLW NIWCIRCLW 17 423
HLA-B*57:01 YKPNTWCIRCLW YKPNIWCIRCLW 105 2607
HLA-B*58:01 NTWCIRCLW NIWCIRCLW 16 325
HLA-B*57:01 KPNTWCIRCLW KPNIWCIRCLW 28 517
HLA-B*57:01 TYKPNTWCIRCLW TYKPNIWCIRCLW 266 4183
HLA-B*57:01 PNTWCIRCLW PNIWCIRCLW 142 1929
HLA-B*58:01 YKPNTWCIRCLW YKPNIWCIRCLW 231 3000
HLA-B*58:01 KPNTWCIRCLW KPNIWCIRCLW 68 781
HLA-B*57:01 TWCIRCLW IWCIRCLW 460 3614
HLA-B*58:01 PNTWCIRCLW PNIWCIRCLW 394 2545
HLA-A*68:01 NTWCIRCLWSTK NIWCIRCLWSTK 67 375
HLA-A*11:01 NTWCIRCLWSTK NIWCIRCLWSTK 442 2283
HLA-A*30:01 NTWCIRCLWSTK NIWCIRCLWSTK 403 1527
HLA-A*32:01 NTWCIRCLW NIWCIRCLW 142 357
HLA-A*31:01 NTWCIRCLWSTK NIWCIRCLWSTK 313 707
HLA-A*02:11 ATYKPNTWCI ATYKPNIWCI 308 139
HLA-A*02:06 ATYKPNTWCI ATYKPNIWCI 645 304
HLA-A*32:01 KPNTWCIRCLW KPNIWCIRCLW 477 991

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

P323F

Reference  CVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    CVNCLDDRCILHCANFNVLFSTVFPFTSFGPLVRKIFVDGVPFVVSTGYHF

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*15:03 VLFSTVFPP VLFSTVFPF 3115 4
HLA-A*32:01 VLFSTVFPP VLFSTVFPF 5415 8
HLA-B*15:01 VLFSTVFPP VLFSTVFPF 5731 11
HLA-A*23:01 VLFSTVFPP VLFSTVFPF 17486 35
HLA-A*29:02 VLFSTVFPP VLFSTVFPF 13973 41
HLA-C*03:02 VLFSTVFPP VLFSTVFPF 20533 102
HLA-B*15:01 NVLFSTVFPP NVLFSTVFPF 16240 100
HLA-B*15:03 NVLFSTVFPP NVLFSTVFPF 20337 128
HLA-A*24:02 VLFSTVFPP VLFSTVFPF 25301 183
HLA-B*35:01 VLFSTVFPP VLFSTVFPF 21745 165
HLA-B*15:03 FNVLFSTVFPP FNVLFSTVFPF 16079 155
HLA-C*14:02 LFSTVFPP LFSTVFPF 11979 160
HLA-A*29:02 NVLFSTVFPP NVLFSTVFPF 21903 310
HLA-A*68:01 PTSFGPLVR FTSFGPLVR 908 13
HLA-A*32:01 NVLFSTVFPP NVLFSTVFPF 21364 323
HLA-A*23:01 NFNVLFSTVFPP NFNVLFSTVFPF 16444 252
HLA-B*15:01 FNVLFSTVFPP FNVLFSTVFPF 21004 331
HLA-C*14:02 VLFSTVFPP VLFSTVFPF 21407 342
HLA-A*23:01 LFSTVFPP LFSTVFPF 24191 413
HLA-B*15:03 LFSTVFPP LFSTVFPF 23012 399
HLA-B*35:01 NVLFSTVFPP NVLFSTVFPF 23419 426
HLA-A*29:02 NFNVLFSTVFPP NFNVLFSTVFPF 21013 409
HLA-B*35:01 FPPTSFGPL FPFTSFGPL 304 6
HLA-B*53:01 FPPTSFGPL FPFTSFGPL 3581 84
HLA-B*35:01 FPPTSFGPLVRKIF FPFTSFGPLVRKIF 7080 191
HLA-C*03:02 PTSFGPLVRKIF FTSFGPLVRKIF 14624 448
HLA-A*68:01 PTSFGPLVRK FTSFGPLVRK 308 11
HLA-A*68:01 PPTSFGPLVR PFTSFGPLVR 4035 158
HLA-A*33:03 PTSFGPLVR FTSFGPLVR 3228 161
HLA-B*35:03 FPPTSFGPL FPFTSFGPL 286 16
HLA-B*15:03 FPPTSFGPL FPFTSFGPL 4804 375
HLA-A*68:02 PTSFGPLVRKIFV FTSFGPLVRKIFV 1635 142
HLA-C*01:02 FPPTSFGPL FPFTSFGPL 217 2475
HLA-B*51:01 FPPTSFGPL FPFTSFGPL 1809 165
HLA-B*07:02 STVFPPTSFGPL STVFPFTSFGPL 777 78
HLA-A*68:01 PPTSFGPLVRK PFTSFGPLVRK 4812 493
HLA-A*11:01 PTSFGPLVR FTSFGPLVR 4068 420
HLA-C*03:02 FPPTSFGPL FPFTSFGPL 960 101
HLA-A*31:01 PTSFGPLVR FTSFGPLVR 4402 481
HLA-B*42:01 FSTVFPPTSFGPL FSTVFPFTSFGPL 1320 145
HLA-B*07:02 TVFPPTSFGPL TVFPFTSFGPL 1498 175
HLA-B*42:01 STVFPPTSFGPL STVFPFTSFGPL 738 87
HLA-A*26:01 STVFPPTSF STVFPFTSF 786 95
HLA-A*03:02 PTSFGPLVRK FTSFGPLVRK 868 107
HLA-C*03:03 FPPTSFGPL FPFTSFGPL 375 51
HLA-C*03:04 FPPTSFGPL FPFTSFGPL 375 51
HLA-B*07:02 VFPPTSFGPL VFPFTSFGPL 339 47
HLA-B*42:01 TVFPPTSFGPL TVFPFTSFGPL 843 119
HLA-B*42:01 LFSTVFPPTSFGPL LFSTVFPFTSFGPL 3265 483
HLA-A*03:01 PTSFGPLVRK FTSFGPLVRK 554 82
HLA-B*42:01 VFPPTSFGPL VFPFTSFGPL 274 43
HLA-B*07:02 FSTVFPPTSFGPL FSTVFPFTSFGPL 2537 435
HLA-A*02:02 TVFPPTSFGPLV TVFPFTSFGPLV 789 137
HLA-A*11:01 PTSFGPLVRK FTSFGPLVRK 123 24
HLA-B*07:02 FPPTSFGPLV FPFTSFGPLV 1131 232
HLA-B*42:01 FPPTSFGPLV FPFTSFGPLV 368 76
HLA-B*08:01 FPPTSFGPL FPFTSFGPL 973 203
HLA-B*07:02 FPPTSFGPL FPFTSFGPL 42 9
HLA-B*15:01 STVFPPTSF STVFPFTSF 130 28
HLA-A*25:01 STVFPPTSF STVFPFTSF 1533 348
HLA-A*02:01 TVFPPTSFGPLV TVFPFTSFGPLV 1358 315
HLA-B*51:01 FPPTSFGPLV FPFTSFGPLV 363 86
HLA-B*42:01 FPPTSFGPL FPFTSFGPL 21 5
HLA-A*68:02 FPPTSFGPL FPFTSFGPL 1395 346
HLA-A*02:11 VLFSTVFPP VLFSTVFPF 78 20
HLA-A*32:01 STVFPPTSF STVFPFTSF 230 59
HLA-C*12:03 FPPTSFGPL FPFTSFGPL 1422 385
HLA-A*02:11 TVFPPTSFGPLV TVFPFTSFGPLV 306 86
HLA-A*31:01 STVFPPTSFGPLVR STVFPFTSFGPLVR 1475 417
HLA-A*68:02 STVFPPTSFGPLV STVFPFTSFGPLV 169 48
HLA-A*02:06 TVFPPTSFGPLV TVFPFTSFGPLV 277 79
HLA-A*26:01 FSTVFPPTSF FSTVFPFTSF 1667 479
HLA-C*16:01 FPPTSFGPL FPFTSFGPL 993 296
HLA-A*68:02 TVFPPTSFG TVFPFTSFG 443 133
HLA-B*58:01 FSTVFPPTSF FSTVFPFTSF 88 27
HLA-A*68:02 FPPTSFGPLV FPFTSFGPLV 991 312
HLA-A*02:06 TVFPPTSFGPL TVFPFTSFGPL 1253 414
HLA-B*15:03 STVFPPTSF STVFPFTSF 60 20
HLA-B*57:01 FSTVFPPTSF FSTVFPFTSF 648 220
HLA-A*02:06 VLFSTVFPP VLFSTVFPF 368 126
HLA-B*53:01 FPPTSFGPLV FPFTSFGPLV 767 282
HLA-A*02:11 FNVLFSTVFPP FNVLFSTVFPF 413 155
HLA-A*02:02 VLFSTVFPP VLFSTVFPF 269 106
HLA-A*31:01 TVFPPTSFGPLVR TVFPFTSFGPLVR 106 42
HLA-A*02:11 NVLFSTVFPP NVLFSTVFPF 739 295
HLA-C*14:02 FPPTSFGPL FPFTSFGPL 255 104
HLA-B*15:03 TVFPPTSF TVFPFTSF 465 196
HLA-A*33:03 STVFPPTSFGPLVR STVFPFTSFGPLVR 671 284
HLA-C*12:02 STVFPPTSF STVFPFTSF 320 147
HLA-B*15:01 FSTVFPPTSF FSTVFPFTSF 150 69
HLA-A*68:02 TVFPPTSFGPL TVFPFTSFGPL 143 67
HLA-A*02:01 VLFSTVFPP VLFSTVFPF 179 87