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-A*68:01 and peptides affected by the mutations

Weaker binding was found for 2 epitopes, while stronger binding was found for 13 entries. There are 385 tight binders for the HLA-A*68:01 in the reference immunopeptidome (IC50 affinity ≤ 50 nM); 0 of them became non-tight binders (0.0%) and 2 novel tight binders appeared (0.5%). To avoid possible divisions by zero, we used + 1 regularization term in denominators when calculating percentages.

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HLA-A*68:01

Spike protein

S13I

Reference  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYY
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Mutated    MFVFLVLLPLVSIQCVNLTTRTQLPPAYTNSFTRGVYY

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 LVSSQCVNLTTR LVSIQCVNLTTR 380 833

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-A*68:01 NKSWMESEFR NKSCMESEFR 75 226

L452R

Reference  DDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGS
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Mutated    DDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGS

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 SKVGGNYNYL SKVGGNYNYR 24692 119
HLA-A*68:01 KVGGNYNYL KVGGNYNYR 25432 286
HLA-A*68:01 DSKVGGNYNYL DSKVGGNYNYR 28915 378

N protein

T205I

Reference  SQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQL
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Mutated    SQASSRSSSRSRNSSRNSTPGSSRGISPARMAGNGGDAALALLLLDRLNQL

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 SSRGTSPAR SSRGISPAR 186 61
HLA-A*68:01 STPGSSRGTSPAR STPGSSRGISPAR 860 288
HLA-A*68:01 GSSRGTSPAR GSSRGISPAR 615 248

NS3 protein

Q57H

Reference  TATIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCN
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Mutated    TATIPIQASLPFGWLIVGVALLAVFHSASKIITLKKRWQLALSKGVHFVCN

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-A*68:01 QSASKIITLKK HSASKIITLKK 1356 322
HLA-A*68:01 QSASKIITLKKR HSASKIITLKKR 683 195
HLA-A*68:01 QSASKIITLK HSASKIITLK 35 10
HLA-A*68:01 AVFQSASKIITLK AVFHSASKIITLK 808 368

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-A*68:01 PTSFGPLVR LTSFGPLVR 908 36
HLA-A*68:01 PTSFGPLVRK LTSFGPLVRK 308 34