Summary

This strain contains 24 protein-level mutations:

• 10 mutations in Spike protein: T19R, K77T, G142D, EF 156-157 deletion, R158G, L452R, T478K, D614G, P681R, D950N
• 3 mutations in N protein: D63G, R203M, D377Y
• 1 mutation in M protein: I82T
• 1 mutation in NS3 protein: S26L
• 2 mutations in NS7a protein: V82A, T120I
• 1 mutation in NS9b protein: T60A
• 1 mutation in NS9c protein: G50W
• 1 mutation in NSP2 protein: P129L
• 1 mutation in NSP3 protein: P822L
• 2 mutations in NSP4 protein: D217N, F375S
• 1 mutation in NSP12 protein: P323L

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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*40:06 and peptides affected by the mutations

Weaker binding was found for 4 epitopes, while stronger binding was found for 2 entries. There are 9 tight binders for the HLA-B*40:06 in the reference immunopeptidome (IC₅₀ affinity ≤ 50 nM); 2 of them became non-tight binders (20.0%) and 0 novel tight binders appeared (0.0%). To avoid possible divisions by zero, we used + 1 regularization term in denominators when calculating percentages.

Spike protein

EF 156-157 deletion

Reference  CEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGK
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Mutated    CEFQFCNDPFLDVYYHKNNKSWMES‑‑GVYSSANNCTFEYVSQPFLMDLEGK

Export table to csv 

Allele	Reference peptide	Mutated peptide	Reference affinity (IC50, nM)	Mutated affinity (IC50, nM)
HLA-B*40:06	SEFRVYSSA	SGVYSSA	21	-
HLA-B*40:06	MESEFRVYS	MESGVYS	299	-
HLA-B*40:06	MESEFRVYSSA	MESGVYSSA	248	72

R158G

Reference  FQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQ
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Mutated    FQFCNDPFLDVYYHKNNKSWMES‑‑GVYSSANNCTFEYVSQPFLMDLEGKQ

Export table to csv 

Allele	Reference peptide	Mutated peptide	Reference affinity (IC50, nM)	Mutated affinity (IC50, nM)
HLA-B*40:06	SEFRVYSSA	SGVYSSA	21	-
HLA-B*40:06	MESEFRVYS	MESGVYS	299	-
HLA-B*40:06	MESEFRVYSSA	MESGVYSSA	248	72