Summary

This strain contains 15 protein-level mutations:

  • 2 mutations in Spike protein: M153T, D614G
  • 3 mutations in N protein: 203-204 RG->KR, G214C, P383L
  • 2 mutations in NS9c protein: G50N, M60I
  • 4 mutations in NSP3 protein: T428I, T725I, P1469S, F1569V
  • 1 mutation in NSP4 protein: L438P
  • 1 mutation in NSP6 protein: SGF 106-108 deletion
  • 1 mutation in NSP12 protein: P323L
  • 1 mutation in NSP16 protein: G213N

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*06:01 and peptides affected by the mutations

Weaker binding was found for 13 epitopes, while stronger binding was found for 8 entries. There are 89 tight binders for the HLA-DQA1*01:02/DQB1*06:01 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-DQA1*01:02/DQB1*06:01

NSP6 protein

SGF 106-108 deletion

Reference  FNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYD
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Mutated    FNMVYMPASWVMRIMTWLDMVDTSL‑‑‑KLKDCVMYASAVVLLILMTARTVYD

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DQA1*01:02/DQB1*06:01 FKLKDCVMYASAVVLLI - 296 -
HLA-DQA1*01:02/DQB1*06:01 GFKLKDCVMYASAVVLL - 310 -
HLA-DQA1*01:02/DQB1*06:01 FKLKDCVMYASAVVLL - 313 -
HLA-DQA1*01:02/DQB1*06:01 FKLKDCVMYASAVVL KLKDCVMYASAVVL 356 -
HLA-DQA1*01:02/DQB1*06:01 GFKLKDCVMYASAVVL KLKDCVMYASAVVL 365 -
HLA-DQA1*01:02/DQB1*06:01 SGFKLKDCVMYASAVVL KLKDCVMYASAVVL 392 -
HLA-DQA1*01:02/DQB1*06:01 SGFKLKDCVMYASAVVLLIL - 395 -
HLA-DQA1*01:02/DQB1*06:01 DTSLSGFKLKDCVMYASAVVLLI DTSLKLKDCVMYASAVVLLI - 402
HLA-DQA1*01:02/DQB1*06:01 GFKLKDCVMYASAVVLLILM - 412 -
HLA-DQA1*01:02/DQB1*06:01 TSLSGFKLKDCVMYASAVVLLIL TSLKLKDCVMYASAVVLLIL - 418
HLA-DQA1*01:02/DQB1*06:01 VDTSLSGFKLKDCVMYASAVVLL VDTSLKLKDCVMYASAVVLL - 425
HLA-DQA1*01:02/DQB1*06:01 SGFKLKDCVMYASAVVLLI - 429 -
HLA-DQA1*01:02/DQB1*06:01 SLSGFKLKDCVMYASAVVLLILM SLKLKDCVMYASAVVLLILM - 431
HLA-DQA1*01:02/DQB1*06:01 TSLSGFKLKDCVMYASAVVLLI TSLKLKDCVMYASAVVLLI - 453
HLA-DQA1*01:02/DQB1*06:01 GFKLKDCVMYASAVV KLKDCVMYASAVV 455 -
HLA-DQA1*01:02/DQB1*06:01 GFKLKDCVMYASAVVLLIL - 455 -
HLA-DQA1*01:02/DQB1*06:01 FKLKDCVMYASAVVLLILMT - 463 -
HLA-DQA1*01:02/DQB1*06:01 SLSGFKLKDCVMYASAVVLLIL SLKLKDCVMYASAVVLLIL - 477
HLA-DQA1*01:02/DQB1*06:01 LSGFKLKDCVMYASAVVLLILMT LKLKDCVMYASAVVLLILMT - 484
HLA-DQA1*01:02/DQB1*06:01 SGFKLKDCVMYASAVV KLKDCVMYASAVV 487 -
HLA-DQA1*01:02/DQB1*06:01 MVDTSLSGFKLKDCVMYASAVVL MVDTSLKLKDCVMYASAVVL - 495