Summary

This strain contains 11 protein-level mutations:

  • 4 mutations in Spike protein: S13I, W152C, L452R, D614G
  • 1 mutation in N protein: T205I
  • 2 mutations in NS3 protein: Q57H, A99V
  • 1 mutation in NS9c protein: L52F
  • 1 mutation in NSP2 protein: T85I
  • 1 mutation in NSP12 protein: P323L
  • 1 mutation in NSP13 protein: D260Y

We identified all possible linear viral peptides affected by these mutations. Whenever it was possible, we matched the reference peptide with the mutated one. For example, D -> L mutation transformed SDNGPQNQR to SLNGPQNQR. Cases when it was not meaningful included deletions and insertions at the flanks of the peptide, e.g., HV deletion in NVTWFHAIHV peptide.

Then, we predicted binding affinities between the selected peptides and frequent HLA alleles. Predictions were made with NetMHCpan-4.1 and NetMHCIIpan-4.0. The binding affinities were classifies into three groups:

  1. Tight binding (IC50 affinity ≤ 50 nM)
  2. Moderate binding (50 nM < IC50 affinity ≤ 500 nM)
  3. Weak/no binding (IC50 affinity > 500 nM)

Here we report HLA-peptide interactions whose affinity was altered by at least two folds. Note that mutations with empty set of altered interactions are not showed.

The total number of interactions between HLA-DPA1*01:03/DPB1*04:01 and peptides affected by the mutations

Weaker binding was found for 35 epitopes, while stronger binding was found for 36 entries. There are 777 tight binders for the HLA-DPA1*01:03/DPB1*04:01 in the reference immunopeptidome (IC50 affinity ≤ 50 nM); 0 of them became non-tight binders (0.0%) and 0 novel tight binders appeared (0.0%). To avoid possible divisions by zero, we used + 1 regularization term in denominators when calculating percentages.

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HLA-DPA1*01:03/DPB1*04:01

Spike protein

W152C

Reference  VIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM
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Mutated    VIKVCEFQFCNDPFLGVYYHKNNKSCMESEFRVYSSANNCTFEYVSQPFLM

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DPA1*01:03/DPB1*04:01 YYHKNNKSWMESEFRVYSSA YYHKNNKSCMESEFRVYSSA 219 1104
HLA-DPA1*01:03/DPB1*04:01 KNNKSWMESEFRVYSS KNNKSCMESEFRVYSS 302 1512
HLA-DPA1*01:03/DPB1*04:01 HKNNKSWMESEFRVYS HKNNKSCMESEFRVYS 330 1643
HLA-DPA1*01:03/DPB1*04:01 YHKNNKSWMESEFRVYSSAN YHKNNKSCMESEFRVYSSAN 221 1092
HLA-DPA1*01:03/DPB1*04:01 YHKNNKSWMESEFRVYSSA YHKNNKSCMESEFRVYSSA 310 1528
HLA-DPA1*01:03/DPB1*04:01 NNKSWMESEFRVYSSA NNKSCMESEFRVYSSA 257 1266
HLA-DPA1*01:03/DPB1*04:01 VYYHKNNKSWMESEFRVYSS VYYHKNNKSCMESEFRVYSS 284 1383
HLA-DPA1*01:03/DPB1*04:01 HKNNKSWMESEFRVYSSAN HKNNKSCMESEFRVYSSAN 319 1545
HLA-DPA1*01:03/DPB1*04:01 YYHKNNKSWMESEFRVYSS YYHKNNKSCMESEFRVYSS 395 1909
HLA-DPA1*01:03/DPB1*04:01 GVYYHKNNKSWMESEFRVYS GVYYHKNNKSCMESEFRVYS 337 1599
HLA-DPA1*01:03/DPB1*04:01 VYYHKNNKSWMESEFRVYS VYYHKNNKSCMESEFRVYS 455 2120
HLA-DPA1*01:03/DPB1*04:01 NKSWMESEFRVYSSAN NKSCMESEFRVYSSAN 288 1333
HLA-DPA1*01:03/DPB1*04:01 YHKNNKSWMESEFRVY YHKNNKSCMESEFRVY 459 2122
HLA-DPA1*01:03/DPB1*04:01 HKNNKSWMESEFRVYSS HKNNKSCMESEFRVYSS 363 1649
HLA-DPA1*01:03/DPB1*04:01 KNNKSWMESEFRVYSSA KNNKSCMESEFRVYSSA 300 1358
HLA-DPA1*01:03/DPB1*04:01 YHKNNKSWMESEFRVYS YHKNNKSCMESEFRVYS 409 1822
HLA-DPA1*01:03/DPB1*04:01 KNNKSWMESEFRVYS KNNKSCMESEFRVYS 254 1130
HLA-DPA1*01:03/DPB1*04:01 NNKSWMESEFRVYSS NNKSCMESEFRVYSS 243 1074
HLA-DPA1*01:03/DPB1*04:01 HKNNKSWMESEFRVY HKNNKSCMESEFRVY 331 1462
HLA-DPA1*01:03/DPB1*04:01 NNKSWMESEFRVYSSAN NNKSCMESEFRVYSSAN 323 1418
HLA-DPA1*01:03/DPB1*04:01 NKSWMESEFRVYSSA NKSCMESEFRVYSSA 219 914
HLA-DPA1*01:03/DPB1*04:01 LGVYYHKNNKSWMESEFRVY LGVYYHKNNKSCMESEFRVY 489 2020
HLA-DPA1*01:03/DPB1*04:01 HKNNKSWMESEFRVYSSANN HKNNKSCMESEFRVYSSANN 213 878
HLA-DPA1*01:03/DPB1*04:01 KNNKSWMESEFRVYSSANN KNNKSCMESEFRVYSSANN 327 1342
HLA-DPA1*01:03/DPB1*04:01 KSWMESEFRVYSSAN KSCMESEFRVYSSAN 258 1034
HLA-DPA1*01:03/DPB1*04:01 KNNKSWMESEFRVYSSANNC KNNKSCMESEFRVYSSANNC 226 902
HLA-DPA1*01:03/DPB1*04:01 NNKSWMESEFRVYSSANNC NNKSCMESEFRVYSSANNC 347 1373
HLA-DPA1*01:03/DPB1*04:01 NNKSWMESEFRVYSSANNCT NNKSCMESEFRVYSSANNCT 245 917
HLA-DPA1*01:03/DPB1*04:01 KSWMESEFRVYSSANN KSCMESEFRVYSSANN 361 1331
HLA-DPA1*01:03/DPB1*04:01 NKSWMESEFRVYSSANN NKSCMESEFRVYSSANN 351 1276
HLA-DPA1*01:03/DPB1*04:01 NKSWMESEFRVYSSANNCT NKSCMESEFRVYSSANNCT 390 1414
HLA-DPA1*01:03/DPB1*04:01 KSWMESEFRVYSSANNC KSCMESEFRVYSSANNC 435 1383
HLA-DPA1*01:03/DPB1*04:01 NKSWMESEFRVYSSANNCTF NKSCMESEFRVYSSANNCTF 262 805
HLA-DPA1*01:03/DPB1*04:01 KSWMESEFRVYSSANNCTF KSCMESEFRVYSSANNCTF 456 1346
HLA-DPA1*01:03/DPB1*04:01 KSWMESEFRVYSSANNCTFE KSCMESEFRVYSSANNCTFE 339 921

NS9c protein

L52F

Reference  VKPLLVPHHVVATVQEIQLQAAVGELLLLEWLAMAVMLLLLCCCLTD
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Mutated    VKPLLVPHHVVATVQEIQLQAAVGEFLLLEWLAMAVMLLLLCCCLTD

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DPA1*01:03/DPB1*04:01 IQLQAAVGELLLLEW IQLQAAVGEFLLLEW 395 186
HLA-DPA1*01:03/DPB1*04:01 AVGELLLLEWLAMAV AVGEFLLLEWLAMAV 552 267
HLA-DPA1*01:03/DPB1*04:01 QLQAAVGELLLLEWLAM QLQAAVGEFLLLEWLAM 387 188
HLA-DPA1*01:03/DPB1*04:01 VGELLLLEWLAMAVM VGEFLLLEWLAMAVM 712 347

NSP12 protein

P323L

Reference  CVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF
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Mutated    CVNCLDDRCILHCANFNVLFSTVFPLTSFGPLVRKIFVDGVPFVVSTGYHF

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DPA1*01:03/DPB1*04:01 FSTVFPPTSFGPLVRKIF FSTVFPLTSFGPLVRKIF 2095 292
HLA-DPA1*01:03/DPB1*04:01 STVFPPTSFGPLVRKI STVFPLTSFGPLVRKI 1006 147
HLA-DPA1*01:03/DPB1*04:01 FSTVFPPTSFGPLVRK FSTVFPLTSFGPLVRK 891 131
HLA-DPA1*01:03/DPB1*04:01 FSTVFPPTSFGPLVRKI FSTVFPLTSFGPLVRKI 1024 151
HLA-DPA1*01:03/DPB1*04:01 STVFPPTSFGPLVRKIFV STVFPLTSFGPLVRKIFV 2255 336
HLA-DPA1*01:03/DPB1*04:01 TVFPPTSFGPLVRKIFVD TVFPLTSFGPLVRKIFVD 3076 482
HLA-DPA1*01:03/DPB1*04:01 STVFPPTSFGPLVRK STVFPLTSFGPLVRK 671 106
HLA-DPA1*01:03/DPB1*04:01 STVFPPTSFGPLVRKIF STVFPLTSFGPLVRKIF 1036 165
HLA-DPA1*01:03/DPB1*04:01 LFSTVFPPTSFGPLVRKI LFSTVFPLTSFGPLVRKI 1549 252
HLA-DPA1*01:03/DPB1*04:01 TVFPPTSFGPLVRKIF TVFPLTSFGPLVRKIF 1288 217
HLA-DPA1*01:03/DPB1*04:01 TVFPPTSFGPLVRKI TVFPLTSFGPLVRKI 941 159
HLA-DPA1*01:03/DPB1*04:01 FSTVFPPTSFGPLVR FSTVFPLTSFGPLVR 811 138
HLA-DPA1*01:03/DPB1*04:01 STVFPPTSFGPLVRKIFVD STVFPLTSFGPLVRKIFVD 1238 223
HLA-DPA1*01:03/DPB1*04:01 FSTVFPPTSFGPLVRKIFV FSTVFPLTSFGPLVRKIFV 1028 186
HLA-DPA1*01:03/DPB1*04:01 TVFPPTSFGPLVRKIFV TVFPLTSFGPLVRKIFV 1336 247
HLA-DPA1*01:03/DPB1*04:01 TVFPPTSFGPLVRKIFVDG TVFPLTSFGPLVRKIFVDG 1823 340
HLA-DPA1*01:03/DPB1*04:01 VFPPTSFGPLVRKIFV VFPLTSFGPLVRKIFV 2019 394
HLA-DPA1*01:03/DPB1*04:01 VFPPTSFGPLVRKIFVD VFPLTSFGPLVRKIFVD 2231 438
HLA-DPA1*01:03/DPB1*04:01 VFPPTSFGPLVRKIF VFPLTSFGPLVRKIF 1460 287
HLA-DPA1*01:03/DPB1*04:01 FSTVFPPTSFGPLVRKIFVD FSTVFPLTSFGPLVRKIFVD 857 179
HLA-DPA1*01:03/DPB1*04:01 STVFPPTSFGPLVRKIFVDG STVFPLTSFGPLVRKIFVDG 1018 213
HLA-DPA1*01:03/DPB1*04:01 LFSTVFPPTSFGPLVRK LFSTVFPLTSFGPLVRK 584 123
HLA-DPA1*01:03/DPB1*04:01 LFSTVFPPTSFGPLVRKIF LFSTVFPLTSFGPLVRKIF 728 158
HLA-DPA1*01:03/DPB1*04:01 LFSTVFPPTSFGPLVR LFSTVFPLTSFGPLVR 623 144
HLA-DPA1*01:03/DPB1*04:01 TVFPPTSFGPLVRKIFVDGV TVFPLTSFGPLVRKIFVDGV 1356 328
HLA-DPA1*01:03/DPB1*04:01 LFSTVFPPTSFGPLVRKIFV LFSTVFPLTSFGPLVRKIFV 620 155
HLA-DPA1*01:03/DPB1*04:01 LFSTVFPPTSFGPLV LFSTVFPLTSFGPLV 536 147
HLA-DPA1*01:03/DPB1*04:01 VLFSTVFPPTSFGPLVRK VLFSTVFPLTSFGPLVRK 527 155
HLA-DPA1*01:03/DPB1*04:01 NVLFSTVFPPTSFGPLVR NVLFSTVFPLTSFGPLVR 314 120
HLA-DPA1*01:03/DPB1*04:01 VLFSTVFPPTSFGPLVRKI VLFSTVFPLTSFGPLVRKI 268 103
HLA-DPA1*01:03/DPB1*04:01 VLFSTVFPPTSFGPLVRKIF VLFSTVFPLTSFGPLVRKIF 259 108
HLA-DPA1*01:03/DPB1*04:01 VLFSTVFPPTSFGPLVR VLFSTVFPLTSFGPLVR 188 83