Summary

This strain contains 46 protein-level mutations:

  • 29 mutations in Spike protein: A67V, HV 69-70 deletion, T95I, GVY 142-144 deletion, Y145D, N211 deletion, L212I, G339D, S371F, S373P, S375F, D405N, K417T, N440K, G446S, 477-478 ST->NK, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
  • 3 mutations in N protein: P13L, ERS 31-33 deletion, 203-204 RG->KR
  • 2 mutations in M protein: Q19E, A63T
  • 1 mutation in E protein: T9I
  • 1 mutation in NS3 protein: T223I
  • 2 mutations in NS9b protein: P10S, ENA 27-29 deletion
  • 1 mutation in NS9c protein: G50N
  • 1 mutation in NSP1 protein: S135R
  • 2 mutations in NSP4 protein: T327I, T492I
  • 1 mutation in NSP5 protein: P132H
  • 1 mutation in NSP6 protein: A88V
  • 2 mutations in NSP12 protein: R249M, P323L

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-B*50:01 and peptides affected by the mutations

Weaker binding was found for 2 epitopes, while stronger binding was found for 0 entries. There are 10 tight binders for the HLA-B*50:01 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-B*50:01

Spike protein

G339D

Reference  QTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVAD
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Mutated    QTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVAD

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*50:01 GEVFNATRFA DEVFNATRFA 147 4233

477-478 ST->NK

Reference  LYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGV
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Mutated    LYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGV

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-B*50:01 TEIYQAGSTP TEIYQAGNKP 464 1807