Summary

This strain contains 12 protein-level mutations:

  • 1 mutation in Spike protein: D614G
  • 3 mutations in N protein: 203-204 RG->KR, M234I, P279S
  • 1 mutation in NS8 protein: G8R
  • 1 mutation in NS9c protein: G50N
  • 1 mutation in NSP2 protein: K81N
  • 1 mutation in NSP12 protein: P323L
  • 2 mutations in NSP14 protein: P43L, D345Y
  • 1 mutation in NSP15 protein: H337Y
  • 1 mutation in NSP16 protein: R287I

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 74 epitopes, while stronger binding was found for 52 entries. There are 937 tight binders for the HLA-DRB1*11:01 in the reference immunopeptidome (IC50 affinity ≤ 50 nM); 12 of them became non-tight binders (1.3%) and 0 novel tight binders appeared (0.0%). To avoid possible divisions by zero, we used + 1 regularization term in denominators when calculating percentages.

HLA-DRB1*11:01

NS8 protein

G8R

Reference  MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVV
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Mutated    MKFLVFLRIITTVAAFHQECSLQSCTQHQPYVV

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DRB1*11:01 FLGIITTVAAFHQEC FLRIITTVAAFHQEC 540 158
HLA-DRB1*11:01 FLGIITTVAAFHQECSL FLRIITTVAAFHQECSL 1144 347
HLA-DRB1*11:01 FLGIITTVAAFHQECS FLRIITTVAAFHQECS 1435 466
HLA-DRB1*11:01 VFLGIITTVAAFHQECS VFLRIITTVAAFHQECS 651 215
HLA-DRB1*11:01 VFLGIITTVAAFHQEC VFLRIITTVAAFHQEC 833 298
HLA-DRB1*11:01 MKFLVFLGIITTVAAFHQEC MKFLVFLRIITTVAAFHQEC 1319 487
HLA-DRB1*11:01 LGIITTVAAFHQECS LRIITTVAAFHQECS 788 307
HLA-DRB1*11:01 VFLGIITTVAAFHQE VFLRIITTVAAFHQE 236 94
HLA-DRB1*11:01 LVFLGIITTVAAFHQEC LVFLRIITTVAAFHQEC 534 224
HLA-DRB1*11:01 KFLVFLGIITTVAAFHQ KFLVFLRIITTVAAFHQ 428 188
HLA-DRB1*11:01 FLVFLGIITTVAAFHQE FLVFLRIITTVAAFHQE 413 185
HLA-DRB1*11:01 KFLVFLGIITTVAAF KFLVFLRIITTVAAF 501 240
HLA-DRB1*11:01 LVFLGIITTVAAFHQE LVFLRIITTVAAFHQE 587 283
HLA-DRB1*11:01 FLVFLGIITTVAAFHQ FLVFLRIITTVAAFHQ 612 301
HLA-DRB1*11:01 MKFLVFLGIITTVAAFH MKFLVFLRIITTVAAFH 498 245

NSP2 protein

K81N

Reference  HEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQP
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Mutated    HEIAWYTERSEKSYELQTPFEIKLANKFDTFNGECPNFVFPLNSIIKTIQP

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DRB1*11:01 EIKLAKKFDTFNGECPN EIKLANKFDTFNGECPN 183 636
HLA-DRB1*11:01 EIKLAKKFDTFNGECPNFVF EIKLANKFDTFNGECPNFVF 248 851
HLA-DRB1*11:01 FEIKLAKKFDTFNGECPNFV FEIKLANKFDTFNGECPNFV 96 326
HLA-DRB1*11:01 EIKLAKKFDTFNGECPNFV EIKLANKFDTFNGECPNFV 375 1261
HLA-DRB1*11:01 FEIKLAKKFDTFNGECPN FEIKLANKFDTFNGECPN 315 1040
HLA-DRB1*11:01 FEIKLAKKFDTFNGECPNF FEIKLANKFDTFNGECPNF 139 454
HLA-DRB1*11:01 FEIKLAKKFDTFNGECP FEIKLANKFDTFNGECP 69 225
HLA-DRB1*11:01 EIKLAKKFDTFNGECP EIKLANKFDTFNGECP 209 662
HLA-DRB1*11:01 YELQTPFEIKLAKKFDTF YELQTPFEIKLANKFDTF 271 854
HLA-DRB1*11:01 ELQTPFEIKLAKKFDTF ELQTPFEIKLANKFDTF 67 209
HLA-DRB1*11:01 PFEIKLAKKFDTFNGECPNF PFEIKLANKFDTFNGECPNF 56 173
HLA-DRB1*11:01 SYELQTPFEIKLAKKFDTF SYELQTPFEIKLANKFDTF 123 378
HLA-DRB1*11:01 ELQTPFEIKLAKKFDTFN ELQTPFEIKLANKFDTFN 207 634
HLA-DRB1*11:01 IKLAKKFDTFNGECP IKLANKFDTFNGECP 464 1405
HLA-DRB1*11:01 YELQTPFEIKLAKKFDT YELQTPFEIKLANKFDT 190 573
HLA-DRB1*11:01 PFEIKLAKKFDTFNGECP PFEIKLANKFDTFNGECP 237 710
HLA-DRB1*11:01 PFEIKLAKKFDTFNGECPN PFEIKLANKFDTFNGECPN 90 267
HLA-DRB1*11:01 TPFEIKLAKKFDTFNGEC TPFEIKLANKFDTFNGEC 205 607
HLA-DRB1*11:01 TPFEIKLAKKFDTFNGECPN TPFEIKLANKFDTFNGECPN 48 142
HLA-DRB1*11:01 YELQTPFEIKLAKKFDTFN YELQTPFEIKLANKFDTFN 83 245
HLA-DRB1*11:01 QTPFEIKLAKKFDTFNGECP QTPFEIKLANKFDTFNGECP 43 126
HLA-DRB1*11:01 FEIKLAKKFDTFNGEC FEIKLANKFDTFNGEC 77 225
HLA-DRB1*11:01 LQTPFEIKLAKKFDTF LQTPFEIKLANKFDTF 76 221
HLA-DRB1*11:01 SYELQTPFEIKLAKKFDTFN SYELQTPFEIKLANKFDTFN 53 154
HLA-DRB1*11:01 LQTPFEIKLAKKFDTFNGEC LQTPFEIKLANKFDTFNGEC 41 118
HLA-DRB1*11:01 LQTPFEIKLAKKFDTFN LQTPFEIKLANKFDTFN 49 141
HLA-DRB1*11:01 TPFEIKLAKKFDTFNGECP TPFEIKLANKFDTFNGECP 78 224
HLA-DRB1*11:01 QTPFEIKLAKKFDTFNGE QTPFEIKLANKFDTFNGE 193 554
HLA-DRB1*11:01 PFEIKLAKKFDTFNGEC PFEIKLANKFDTFNGEC 52 149
HLA-DRB1*11:01 YELQTPFEIKLAKKFDTFNG YELQTPFEIKLANKFDTFNG 42 120
HLA-DRB1*11:01 LQTPFEIKLAKKFDTFNG LQTPFEIKLANKFDTFNG 193 551
HLA-DRB1*11:01 ELQTPFEIKLAKKFDTFNGE ELQTPFEIKLANKFDTFNGE 41 117
HLA-DRB1*11:01 KSYELQTPFEIKLAKKFDTF KSYELQTPFEIKLANKFDTF 79 225
HLA-DRB1*11:01 QTPFEIKLAKKFDTFNGEC QTPFEIKLANKFDTFNGEC 71 201
HLA-DRB1*11:01 LQTPFEIKLAKKFDT LQTPFEIKLANKFDT 98 275
HLA-DRB1*11:01 LQTPFEIKLAKKFDTFNGE LQTPFEIKLANKFDTFNGE 69 193
HLA-DRB1*11:01 ELQTPFEIKLAKKFDTFNG ELQTPFEIKLANKFDTFNG 71 198
HLA-DRB1*11:01 EIKLAKKFDTFNGEC EIKLANKFDTFNGEC 92 256
HLA-DRB1*11:01 TPFEIKLAKKFDTFNGE TPFEIKLANKFDTFNGE 47 129
HLA-DRB1*11:01 ELQTPFEIKLAKKFDT ELQTPFEIKLANKFDT 229 628
HLA-DRB1*11:01 QTPFEIKLAKKFDTFN QTPFEIKLANKFDTFN 56 153
HLA-DRB1*11:01 QTPFEIKLAKKFDTFNG QTPFEIKLANKFDTFNG 46 123
HLA-DRB1*11:01 PFEIKLAKKFDTFNGE PFEIKLANKFDTFNGE 59 156
HLA-DRB1*11:01 QTPFEIKLAKKFDTF QTPFEIKLANKFDTF 37 96
HLA-DRB1*11:01 TPFEIKLAKKFDTFNG TPFEIKLANKFDTFNG 55 140
HLA-DRB1*11:01 KSYELQTPFEIKLAKKFDT KSYELQTPFEIKLANKFDT 335 845
HLA-DRB1*11:01 FEIKLAKKFDTFNGE FEIKLANKFDTFNGE 39 98
HLA-DRB1*11:01 TPFEIKLAKKFDTFN TPFEIKLANKFDTFN 30 71
HLA-DRB1*11:01 PFEIKLAKKFDTFNG PFEIKLANKFDTFNG 31 69
HLA-DRB1*11:01 EKSYELQTPFEIKLAKKFDT EKSYELQTPFEIKLANKFDT 188 383

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-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

NSP14 protein

P43L

Reference  LHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNG
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Mutated    LHPTQAPTHLSVDTKFKTEGLCVDILGIPKDMTYRRLISMMGFKMNYQVNG

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Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DRB1*11:01 CVDIPGIPKDMTYRR CVDILGIPKDMTYRR 3720 150
HLA-DRB1*11:01 VDIPGIPKDMTYRRL VDILGIPKDMTYRRL 2925 153
HLA-DRB1*11:01 LCVDIPGIPKDMTYR LCVDILGIPKDMTYR 3877 229
HLA-DRB1*11:01 GLCVDIPGIPKDMTYRR GLCVDILGIPKDMTYRR 4665 303
HLA-DRB1*11:01 LCVDIPGIPKDMTYRR LCVDILGIPKDMTYRR 5815 391
HLA-DRB1*11:01 LCVDIPGIPKDMTYRRL LCVDILGIPKDMTYRRL 4309 310
HLA-DRB1*11:01 CVDIPGIPKDMTYRRL CVDILGIPKDMTYRRL 5862 423
HLA-DRB1*11:01 KTEGLCVDIPGIPKDMTYRR KTEGLCVDILGIPKDMTYRR 3400 284
HLA-DRB1*11:01 TEGLCVDIPGIPKDMTYRRL TEGLCVDILGIPKDMTYRRL 3084 271
HLA-DRB1*11:01 GLCVDIPGIPKDMTY GLCVDILGIPKDMTY 3821 451
HLA-DRB1*11:01 EGLCVDIPGIPKDMTYRRLI EGLCVDILGIPKDMTYRRLI 2001 262
HLA-DRB1*11:01 CVDIPGIPKDMTYRRLI CVDILGIPKDMTYRRLI 2546 335
HLA-DRB1*11:01 VDIPGIPKDMTYRRLI VDILGIPKDMTYRRLI 3165 429
HLA-DRB1*11:01 DIPGIPKDMTYRRLI DILGIPKDMTYRRLI 1445 287
HLA-DRB1*11:01 GLCVDIPGIPKDMTYRRLIS GLCVDILGIPKDMTYRRLIS 1254 255
HLA-DRB1*11:01 VDIPGIPKDMTYRRLIS VDILGIPKDMTYRRLIS 1419 325
HLA-DRB1*11:01 LCVDIPGIPKDMTYRRLISM LCVDILGIPKDMTYRRLISM 799 248
HLA-DRB1*11:01 CVDIPGIPKDMTYRRLISMM CVDILGIPKDMTYRRLISMM 595 254
HLA-DRB1*11:01 VDIPGIPKDMTYRRLISMM VDILGIPKDMTYRRLISMM 951 458

NSP16 protein

R287I

Reference  LKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
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Mutated    LKEGQINDMILSLLSKGRLIIRENNIVVISSDVLVNN

Export table to csv 
Allele Reference peptide Mutated peptide Reference affinity (IC50, nM) Mutated affinity (IC50, nM)
HLA-DRB1*11:01 LIIRENNRVVISSDV LIIRENNIVVISSDV 483 1322
HLA-DRB1*11:01 RLIIRENNRVVISSDVLVNN RLIIRENNIVVISSDVLVNN 323 870
HLA-DRB1*11:01 GRLIIRENNRVVISSDVLVN GRLIIRENNIVVISSDVLVN 258 693
HLA-DRB1*11:01 RLIIRENNRVVISSD RLIIRENNIVVISSD 235 611
HLA-DRB1*11:01 GRLIIRENNRVVISS GRLIIRENNIVVISS 165 428
HLA-DRB1*11:01 KGRLIIRENNRVVISSDVLV KGRLIIRENNIVVISSDVLV 201 499
HLA-DRB1*11:01 RLIIRENNRVVISSDVL RLIIRENNIVVISSDVL 449 1105
HLA-DRB1*11:01 SKGRLIIRENNRVVISSDVL SKGRLIIRENNIVVISSDVL 180 440
HLA-DRB1*11:01 KGRLIIRENNRVVIS KGRLIIRENNIVVIS 128 305
HLA-DRB1*11:01 LSKGRLIIRENNRVVISSDV LSKGRLIIRENNIVVISSDV 164 389
HLA-DRB1*11:01 GRLIIRENNRVVISSDV GRLIIRENNIVVISSDV 377 888
HLA-DRB1*11:01 GRLIIRENNRVVISSDVLV GRLIIRENNIVVISSDVLV 491 1134
HLA-DRB1*11:01 LLSKGRLIIRENNRVVISSD LLSKGRLIIRENNIVVISSD 151 340
HLA-DRB1*11:01 KGRLIIRENNRVVISSDVL KGRLIIRENNIVVISSDVL 380 848
HLA-DRB1*11:01 KGRLIIRENNRVVISSD KGRLIIRENNIVVISSD 283 624
HLA-DRB1*11:01 SKGRLIIRENNRVVISSDV SKGRLIIRENNIVVISSDV 345 750
HLA-DRB1*11:01 RLIIRENNRVVISSDV RLIIRENNIVVISSDV 480 1041
HLA-DRB1*11:01 SKGRLIIRENNRVVISS SKGRLIIRENNIVVISS 234 502
HLA-DRB1*11:01 SKGRLIIRENNRVVI SKGRLIIRENNIVVI 149 310
HLA-DRB1*11:01 GRLIIRENNRVVISSD GRLIIRENNIVVISSD 412 855
HLA-DRB1*11:01 KGRLIIRENNRVVISS KGRLIIRENNIVVISS 278 575
HLA-DRB1*11:01 LSKGRLIIRENNRVVISSD LSKGRLIIRENNIVVISSD 314 639
HLA-DRB1*11:01 SKGRLIIRENNRVVIS SKGRLIIRENNIVVIS 291 587
HLA-DRB1*11:01 SLLSKGRLIIRENNRVVISS SLLSKGRLIIRENNIVVISS 137 274