Summary

This strain contains 20 protein-level mutations:

• 8 mutations in Spike protein: Q52R, A67V, HV 69-70 deletion, Y144 deletion, E484K, D614G, Q677H, F888L
• 4 mutations in N protein: S2 deletion, D3Y, A12G, T205I
• 1 mutation in M protein: I82T
• 1 mutation in E protein: L21F
• 1 mutation in NS6 protein: F2 deletion
• 1 mutation in NS9b protein: H9D
• 1 mutation in NS9c protein: L52F
• 1 mutation in NSP3 protein: T1189I
• 1 mutation in NSP6 protein: SGF 106-108 deletion
• 1 mutation in NSP12 protein: P323F

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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*40:01 and peptides affected by the mutations

Weaker binding was found for 2 epitopes, while stronger binding was found for 3 entries. There are 63 tight binders for the HLA-B*40:01 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.

Spike protein

E484K

Reference  SNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYR
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Mutated    SNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTNGVGYQPYR

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Allele	Reference peptide	Mutated peptide	Reference affinity (IC50, nM)	Mutated affinity (IC50, nM)
HLA-B*40:01	VEGFNCYFPL	VKGFNCYFPL	76	15210

NS9b protein

H9D

Reference  MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQ
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Mutated    MDPKISEMDPALRLVDPQIQLAVTRMENAVGRDQ

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Allele	Reference peptide	Mutated peptide	Reference affinity (IC50, nM)	Mutated affinity (IC50, nM)
HLA-B*40:01	KISEMHPALRL	KISEMDPALRL	664	253
HLA-B*40:01	ISEMHPALRL	ISEMDPALRL	404	179

NS9c protein

L52F

Reference  VKPLLVPHHVVATVQEIQLQAAVGELLLLEWLAMAVMLLLLCCCLTD
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Mutated    VKPLLVPHHVVATVQEIQLQAAVGEFLLLEWLAMAVMLLLLCCCLTD

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Allele	Reference peptide	Mutated peptide	Reference affinity (IC50, nM)	Mutated affinity (IC50, nM)
HLA-B*40:01	QEIQLQAAVGEL	QEIQLQAAVGEF	201	2708
HLA-B*40:01	GELLLLEWLAM	GEFLLLEWLAM	791	222