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-DRB1*11:01 and peptides affected by the mutations

Weaker binding was found for 20 epitopes, while stronger binding was found for 41 entries. There are 937 tight binders for the HLA-DRB1*11:01 in the reference immunopeptidome (IC50 affinity ≤ 50 nM); 2 of them became non-tight binders (0.2%) 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 
HLA-DRB1*11:01

Spike protein

L452R

Reference  DDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGS
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    DDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGS

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DRB1*11:01 GGNYNYLYRLFRKSN GGNYNYRYRLFRKSN 37 169
HLA-DRB1*11:01 KVGGNYNYLYRLFRKSN KVGGNYNYRYRLFRKSN 72 326
HLA-DRB1*11:01 VGGNYNYLYRLFRKSN VGGNYNYRYRLFRKSN 82 368
HLA-DRB1*11:01 KVGGNYNYLYRLFRK KVGGNYNYRYRLFRK 64 271
HLA-DRB1*11:01 SKVGGNYNYLYRLFRK SKVGGNYNYRYRLFRK 145 597
HLA-DRB1*11:01 DSKVGGNYNYLYRLFRK DSKVGGNYNYRYRLFRK 133 541
HLA-DRB1*11:01 SKVGGNYNYLYRLFR SKVGGNYNYRYRLFR 144 581
HLA-DRB1*11:01 DSKVGGNYNYLYRLFR DSKVGGNYNYRYRLFR 357 1364
HLA-DRB1*11:01 SKVGGNYNYLYRLFRKSN SKVGGNYNYRYRLFRKSN 281 1070
HLA-DRB1*11:01 LDSKVGGNYNYLYRLFR LDSKVGGNYNYRYRLFR 344 1295
HLA-DRB1*11:01 KVGGNYNYLYRLFRKS KVGGNYNYRYRLFRKS 114 416
HLA-DRB1*11:01 DSKVGGNYNYLYRLFRKSN DSKVGGNYNYRYRLFRKSN 134 485
HLA-DRB1*11:01 VGGNYNYLYRLFRKS VGGNYNYRYRLFRKS 50 179
HLA-DRB1*11:01 SKVGGNYNYLYRLFRKS SKVGGNYNYRYRLFRKS 102 357
HLA-DRB1*11:01 DSKVGGNYNYLYRLFRKS DSKVGGNYNYRYRLFRKS 383 1300
HLA-DRB1*11:01 LDSKVGGNYNYLYRLFRKSN LDSKVGGNYNYRYRLFRKSN 83 278
HLA-DRB1*11:01 NLDSKVGGNYNYLYRLFRK NLDSKVGGNYNYRYRLFRK 258 850
HLA-DRB1*11:01 LDSKVGGNYNYLYRLFRKS LDSKVGGNYNYRYRLFRKS 185 559
HLA-DRB1*11:01 NNLDSKVGGNYNYLYRLFRK NNLDSKVGGNYNYRYRLFRK 176 498
HLA-DRB1*11:01 NLDSKVGGNYNYLYRLFRKS NLDSKVGGNYNYRYRLFRKS 118 331

NS3 protein

Q57H

Reference  TATIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCN
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    TATIPIQASLPFGWLIVGVALLAVFHSASKIITLKKRWQLALSKGVHFVCN

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DRB1*11:01 IVGVALLAVFQSASK IVGVALLAVFHSASK 445 112
HLA-DRB1*11:01 VGVALLAVFQSASKII VGVALLAVFHSASKII 794 204
HLA-DRB1*11:01 VGVALLAVFQSASKI VGVALLAVFHSASKI 334 86
HLA-DRB1*11:01 IVGVALLAVFQSASKI IVGVALLAVFHSASKI 853 223
HLA-DRB1*11:01 GVALLAVFQSASKII GVALLAVFHSASKII 325 86
HLA-DRB1*11:01 LIVGVALLAVFQSASK LIVGVALLAVFHSASK 1141 316
HLA-DRB1*11:01 LIVGVALLAVFQSASKI LIVGVALLAVFHSASKI 567 170
HLA-DRB1*11:01 IVGVALLAVFQSASKII IVGVALLAVFHSASKII 505 153
HLA-DRB1*11:01 WLIVGVALLAVFQSASK WLIVGVALLAVFHSASK 755 240
HLA-DRB1*11:01 FGWLIVGVALLAVFQSASKI FGWLIVGVALLAVFHSASKI 1042 343
HLA-DRB1*11:01 GWLIVGVALLAVFQSASKII GWLIVGVALLAVFHSASKII 972 331
HLA-DRB1*11:01 WLIVGVALLAVFQSASKII WLIVGVALLAVFHSASKII 1372 479
HLA-DRB1*11:01 PFGWLIVGVALLAVFQSASK PFGWLIVGVALLAVFHSASK 1217 436
HLA-DRB1*11:01 LIVGVALLAVFQSASKIIT LIVGVALLAVFHSASKIIT 458 216
HLA-DRB1*11:01 WLIVGVALLAVFQSASKIIT WLIVGVALLAVFHSASKIIT 313 153

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-DRB1*11:01 STVFPPTSFGPLVRK STVFPLTSFGPLVRK 2376 314
HLA-DRB1*11:01 FSTVFPPTSFGPLVRKI FSTVFPLTSFGPLVRKI 2923 409
HLA-DRB1*11:01 TVFPPTSFGPLVRKI TVFPLTSFGPLVRKI 1773 257
HLA-DRB1*11:01 FSTVFPPTSFGPLVR FSTVFPLTSFGPLVR 2949 493
HLA-DRB1*11:01 LFSTVFPPTSFGPLVRK LFSTVFPLTSFGPLVRK 2782 492
HLA-DRB1*11:01 NVLFSTVFPPTSFGPLVRKI NVLFSTVFPLTSFGPLVRKI 1267 408
HLA-DRB1*11:01 TVFPPTSFGPLVRKIF TVFPLTSFGPLVRKIF 902 293
HLA-DRB1*11:01 STVFPPTSFGPLVRKIF STVFPLTSFGPLVRKIF 729 240
HLA-DRB1*11:01 LFSTVFPPTSFGPLVRKIF LFSTVFPLTSFGPLVRKIF 1150 447
HLA-DRB1*11:01 FNVLFSTVFPPTSFGPLVRK FNVLFSTVFPLTSFGPLVRK 1200 468
HLA-DRB1*11:01 VFPPTSFGPLVRKIF VFPLTSFGPLVRKIF 292 125
HLA-DRB1*11:01 VLFSTVFPPTSFGPLVRKIF VLFSTVFPLTSFGPLVRKIF 625 279
HLA-DRB1*11:01 VFPPTSFGPLVRKIFVD VFPLTSFGPLVRKIFVD 387 176
HLA-DRB1*11:01 NVLFSTVFPPTSFGP NVLFSTVFPLTSFGP 708 336
HLA-DRB1*11:01 TVFPPTSFGPLVRKIFV TVFPLTSFGPLVRKIFV 324 157
HLA-DRB1*11:01 FPPTSFGPLVRKIFVDG FPLTSFGPLVRKIFVDG 428 208
HLA-DRB1*11:01 VFPPTSFGPLVRKIFV VFPLTSFGPLVRKIFV 413 203
HLA-DRB1*11:01 FPPTSFGPLVRKIFVD FPLTSFGPLVRKIFVD 492 245

NSP13 protein

D260Y

Reference  LSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPG
           ||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated    LSAPTLVPQEHYVRITGLYPTLNISYEFSSNVANYQKVGMQKYSTLQGPPG

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DRB1*11:01 NISDEFSSNVANYQK NISYEFSSNVANYQK 1482 437
HLA-DRB1*11:01 YPTLNISDEFSSNVANYQKV YPTLNISYEFSSNVANYQKV 1261 472
HLA-DRB1*11:01 PTLNISDEFSSNVANYQKVG PTLNISYEFSSNVANYQKVG 1082 409
HLA-DRB1*11:01 ISDEFSSNVANYQKV ISYEFSSNVANYQKV 814 331
HLA-DRB1*11:01 TLNISDEFSSNVANYQKVGM TLNISYEFSSNVANYQKVGM 1000 407
HLA-DRB1*11:01 LNISDEFSSNVANYQKVGMQ LNISYEFSSNVANYQKVGMQ 954 418
HLA-DRB1*11:01 SDEFSSNVANYQKVG SYEFSSNVANYQKVG 792 375
HLA-DRB1*11:01 NISDEFSSNVANYQKVGMQK NISYEFSSNVANYQKVGMQK 867 433