Summary

This strain contains 12 protein-level mutations:

  • 1 mutation in Spike protein: D614G
  • 3 mutations in N protein: 203-204 RG->KR, M234I, P279S
  • 1 mutation in NS8 protein: G8R
  • 1 mutation in NS9c protein: G50N
  • 1 mutation in NSP2 protein: K81N
  • 1 mutation in NSP12 protein: P323L
  • 2 mutations in NSP14 protein: P43L, D345Y
  • 1 mutation in NSP15 protein: H337Y
  • 1 mutation in NSP16 protein: R287I

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-DQA1*05:01/DQB1*02:01 and peptides affected by the mutations

Weaker binding was not found, while stronger binding was found for 19 entries. There is no tight binders for the HLA-DQA1*05:01/DQB1*02:01 in the reference immunopeptidome (IC50 affinity ≤ 50 nM). To avoid possible divisions by zero, we used + 1 regularization term in denominators when calculating percentages.

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HLA-DQA1*05:01/DQB1*02:01

NSP14 protein

P43L

Reference  LHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNG
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Mutated    LHPTQAPTHLSVDTKFKTEGLCVDILGIPKDMTYRRLISMMGFKMNYQVNG

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DQA1*05:01/DQB1*02:01 FKTEGLCVDIPGIPK FKTEGLCVDILGIPK 1852 481
HLA-DQA1*05:01/DQB1*02:01 KFKTEGLCVDIPGIP KFKTEGLCVDILGIP 1118 306
HLA-DQA1*05:01/DQB1*02:01 KFKTEGLCVDIPGIPKD KFKTEGLCVDILGIPKD 1636 453
HLA-DQA1*05:01/DQB1*02:01 TKFKTEGLCVDIPGIPK TKFKTEGLCVDILGIPK 1403 407
HLA-DQA1*05:01/DQB1*02:01 KFKTEGLCVDIPGIPK KFKTEGLCVDILGIPK 1150 337
HLA-DQA1*05:01/DQB1*02:01 DTKFKTEGLCVDIPGIP DTKFKTEGLCVDILGIP 1209 361
HLA-DQA1*05:01/DQB1*02:01 TKFKTEGLCVDIPGI TKFKTEGLCVDILGI 1165 349
HLA-DQA1*05:01/DQB1*02:01 TKFKTEGLCVDIPGIP TKFKTEGLCVDILGIP 996 300
HLA-DQA1*05:01/DQB1*02:01 DTKFKTEGLCVDIPG DTKFKTEGLCVDILG 1158 377
HLA-DQA1*05:01/DQB1*02:01 VDTKFKTEGLCVDIP VDTKFKTEGLCVDIL 973 321
HLA-DQA1*05:01/DQB1*02:01 DTKFKTEGLCVDIPGI DTKFKTEGLCVDILGI 991 339
HLA-DQA1*05:01/DQB1*02:01 VDTKFKTEGLCVDIPGI VDTKFKTEGLCVDILGI 1316 451
HLA-DQA1*05:01/DQB1*02:01 TKFKTEGLCVDIPGIPKDM TKFKTEGLCVDILGIPKDM 1364 471
HLA-DQA1*05:01/DQB1*02:01 SVDTKFKTEGLCVDIP SVDTKFKTEGLCVDIL 967 337
HLA-DQA1*05:01/DQB1*02:01 VDTKFKTEGLCVDIPG VDTKFKTEGLCVDILG 1098 385
HLA-DQA1*05:01/DQB1*02:01 LSVDTKFKTEGLCVDIP LSVDTKFKTEGLCVDIL 1288 458
HLA-DQA1*05:01/DQB1*02:01 DTKFKTEGLCVDIPGIPKD DTKFKTEGLCVDILGIPKD 1148 410
HLA-DQA1*05:01/DQB1*02:01 SVDTKFKTEGLCVDIPGIP SVDTKFKTEGLCVDILGIP 1071 388
HLA-DQA1*05:01/DQB1*02:01 VDTKFKTEGLCVDIPGIPK VDTKFKTEGLCVDILGIPK 1093 401