Summary

This strain contains 26 protein-level mutations:

  • 9 mutations in Spike protein: T95I, 144-145 YY->SN, R346K, E484K, N501Y, D614G, Q677H, P681H, D950N
  • 2 mutations in N protein: T205I, Q241K
  • 1 mutation in NS3 protein: Q57H
  • 3 mutations in NS8 protein: T11K, P38S, S67F
  • 1 mutation in NS9b protein: R32L
  • 1 mutation in NS9c protein: L52F
  • 3 mutations in NSP3 protein: T237A, T720I, E997K
  • 1 mutation in NSP4 protein: T492I
  • 1 mutation in NSP6 protein: Q160R
  • 1 mutation in NSP12 protein: P323L
  • 2 mutations in NSP13 protein: P419S, L581F
  • 1 mutation in NSP14 protein: V125F

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*01:02/DQB1*06:09 and peptides affected by the mutations

Weaker binding was not found, while stronger binding was found for 37 entries. There is no tight binders for the HLA-DQA1*01:02/DQB1*06:09 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*01:02/DQB1*06:09

Spike protein

T95I

Reference  VSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
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Mutated    VSGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIV

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DQA1*01:02/DQB1*06:09 FNDGVYFASTEKSNI FNDGVYFASIEKSNI 922 339
HLA-DQA1*01:02/DQB1*06:09 PFNDGVYFASTEKSN PFNDGVYFASIEKSN 1083 402
HLA-DQA1*01:02/DQB1*06:09 FNDGVYFASTEKSNIIRG FNDGVYFASIEKSNIIRG 1320 493
HLA-DQA1*01:02/DQB1*06:09 PFNDGVYFASTEKSNIIRG PFNDGVYFASIEKSNIIRG 795 311
HLA-DQA1*01:02/DQB1*06:09 LPFNDGVYFASTEKS LPFNDGVYFASIEKS 922 364
HLA-DQA1*01:02/DQB1*06:09 NDGVYFASTEKSNIIRGWI NDGVYFASIEKSNIIRGWI 886 352
HLA-DQA1*01:02/DQB1*06:09 FNDGVYFASTEKSNIIRGW FNDGVYFASIEKSNIIRGW 809 325
HLA-DQA1*01:02/DQB1*06:09 NDGVYFASTEKSNIIRG NDGVYFASIEKSNIIRG 904 368
HLA-DQA1*01:02/DQB1*06:09 DGVYFASTEKSNIIRGW DGVYFASIEKSNIIRGW 951 390
HLA-DQA1*01:02/DQB1*06:09 NDGVYFASTEKSNII NDGVYFASIEKSNII 807 338
HLA-DQA1*01:02/DQB1*06:09 LPFNDGVYFASTEKSNII LPFNDGVYFASIEKSNII 1065 449
HLA-DQA1*01:02/DQB1*06:09 LPFNDGVYFASTEKSN LPFNDGVYFASIEKSN 786 334
HLA-DQA1*01:02/DQB1*06:09 LPFNDGVYFASTEKSNI LPFNDGVYFASIEKSNI 804 342
HLA-DQA1*01:02/DQB1*06:09 PFNDGVYFASTEKSNII PFNDGVYFASIEKSNII 754 321
HLA-DQA1*01:02/DQB1*06:09 FNDGVYFASTEKSNIIR FNDGVYFASIEKSNIIR 788 338
HLA-DQA1*01:02/DQB1*06:09 DGVYFASTEKSNIIRG DGVYFASIEKSNIIRG 786 339
HLA-DQA1*01:02/DQB1*06:09 PFNDGVYFASTEKSNI PFNDGVYFASIEKSNI 740 321
HLA-DQA1*01:02/DQB1*06:09 GVYFASTEKSNIIRG GVYFASIEKSNIIRG 1023 444
HLA-DQA1*01:02/DQB1*06:09 VLPFNDGVYFASTEKSN VLPFNDGVYFASIEKSN 845 370
HLA-DQA1*01:02/DQB1*06:09 FNDGVYFASTEKSNIIRGWI FNDGVYFASIEKSNIIRGWI 635 286
HLA-DQA1*01:02/DQB1*06:09 DGVYFASTEKSNIIRGWIF DGVYFASIEKSNIIRGWIF 799 361
HLA-DQA1*01:02/DQB1*06:09 FNDGVYFASTEKSNII FNDGVYFASIEKSNII 615 278
HLA-DQA1*01:02/DQB1*06:09 DGVYFASTEKSNIIR DGVYFASIEKSNIIR 907 411
HLA-DQA1*01:02/DQB1*06:09 LPFNDGVYFASTEKSNIIR LPFNDGVYFASIEKSNIIR 680 309
HLA-DQA1*01:02/DQB1*06:09 PFNDGVYFASTEKSNIIRGW PFNDGVYFASIEKSNIIRGW 631 288
HLA-DQA1*01:02/DQB1*06:09 GVYFASTEKSNIIRGWI GVYFASIEKSNIIRGWI 1004 462
HLA-DQA1*01:02/DQB1*06:09 LPFNDGVYFASTEKSNIIRG LPFNDGVYFASIEKSNIIRG 585 272
HLA-DQA1*01:02/DQB1*06:09 VLPFNDGVYFASTEKSNI VLPFNDGVYFASIEKSNI 1045 489
HLA-DQA1*01:02/DQB1*06:09 PVLPFNDGVYFASTEKS PVLPFNDGVYFASIEKS 824 386
HLA-DQA1*01:02/DQB1*06:09 VLPFNDGVYFASTEKS VLPFNDGVYFASIEKS 694 326
HLA-DQA1*01:02/DQB1*06:09 GVYFASTEKSNIIRGWIFG GVYFASIEKSNIIRGWIFG 960 454
HLA-DQA1*01:02/DQB1*06:09 NDGVYFASTEKSNIIR NDGVYFASIEKSNIIR 711 337
HLA-DQA1*01:02/DQB1*06:09 PVLPFNDGVYFASTEKSNI PVLPFNDGVYFASIEKSNI 679 324
HLA-DQA1*01:02/DQB1*06:09 GVYFASTEKSNIIRGW GVYFASIEKSNIIRGW 830 402
HLA-DQA1*01:02/DQB1*06:09 NPVLPFNDGVYFASTEKSN NPVLPFNDGVYFASIEKSN 738 358
HLA-DQA1*01:02/DQB1*06:09 VLPFNDGVYFASTEKSNII VLPFNDGVYFASIEKSNII 596 291
HLA-DQA1*01:02/DQB1*06:09 NDGVYFASTEKSNIIRGWIF NDGVYFASIEKSNIIRGWIF 636 318