T-cell COVID-19 Atlas | Epsilon GH/452R.V1 (B.1.429+B.1.427)

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-DPA1*01:03/DPB1*06:01 and peptides affected by the mutations

Weaker binding was found for 5 epitopes, while stronger binding was found for 1 entrie. There are 31 tight binders for the HLA-DPA1*01:03/DPB1*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.

Download figure Export data to csv NSP12 protein

P323L

Reference CVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF ||||||||||||||||||||||||| ||||||||||||||||||||||||| Mutated CVNCLDDRCILHCANFNVLFSTVFPLTSFGPLVRKIFVDGVPFVVSTGYHF

Export table to csv

Allele	Reference peptide	Mutated peptide	Reference affinity (IC50, nM)	Mutated affinity (IC50, nM)
HLA-DPA1*01:03/DPB1*06:01	LFSTVFPPTSFGPLVRKIFV	LFSTVFPLTSFGPLVRKIFV	1256	472
HLA-DPA1*01:03/DPB1*06:01	LHCANFNVLFSTVFPPTSFG	LHCANFNVLFSTVFPLTSFG	366	965
HLA-DPA1*01:03/DPB1*06:01	ILHCANFNVLFSTVFPPTSF	ILHCANFNVLFSTVFPLTSF	346	875
HLA-DPA1*01:03/DPB1*06:01	HCANFNVLFSTVFPPTSFGP	HCANFNVLFSTVFPLTSFGP	359	888
HLA-DPA1*01:03/DPB1*06:01	CANFNVLFSTVFPPTSFGPL	CANFNVLFSTVFPLTSFGPL	357	803
HLA-DPA1*01:03/DPB1*06:01	LHCANFNVLFSTVFPPTSF	LHCANFNVLFSTVFPLTSF	486	1031