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:
- Tight binding (IC50 affinity ≤ 50 nM)
- Moderate binding (50 nM < IC50 affinity ≤ 500 nM)
- 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.
NS8 protein
G8R
Reference MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVV
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Mutated MKFLVFLRIITTVAAFHQECSLQSCTQHQPYVV
| 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
| 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
| 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
| 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
| 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 |