This strain contains 25 protein-level mutations:
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:
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.
Weaker binding was found for 17 epitopes, while stronger binding was found for 13 entries. There are 150 tight binders for the HLA-B*58:01 in the reference immunopeptidome (IC50 affinity ≤ 50 nM); 0 of them became non-tight binders (0.0%) and 1 novel tight binder appeared (0.7%). To avoid possible divisions by zero, we used + 1 regularization term in denominators when calculating percentages.
Reference CEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQ
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated CEFQFCNDPFLGVYYHKNNKSWMES‑‑‑VYSSANNCTFEYVSQPFLMDLEGKQ
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | RVYSSANNCTF | - | 126 | - |
HLA-B*58:01 | KSWMESEFRV | KSWMESV | 187 | - |
HLA-B*58:01 | MESEFRVYSSANNCTF | MESVYSSANNCTF | - | 267 |
HLA-B*58:01 | KSWMESEF | KSWMES | 465 | - |
HLA-B*58:01 | KSWMESEFRVY | KSWMESVY | 167 | 832 |
Reference QSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSF
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated QSLQTYVTQQLIRAAEIRASANLAAIKMSECVLGQSKRVDFCGKGYHLMSF
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | RASANLAAT | RASANLAAI | 5883 | 333 |
Reference LWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTR
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated LWPVTLACFVLAAVYRINWITGGIATAMACLVGLMWLSYFIASFRLFARTR
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | IAMACLVGL | TAMACLVGL | 423 | 1182 |
HLA-B*58:01 | IAMACLVGLM | TAMACLVGLM | 479 | 1090 |
HLA-B*58:01 | IAMACLVGLMW | TAMACLVGLMW | 19 | 39 |
Reference FLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESG
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated FLCWHTNCYDYCIPYNSVTSSIVITLGDGTTSPISEHDYQIGGYTEKWESG
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | VTSSIVITS | VTSSIVITL | 2482 | 96 |
Reference AAVKPLLVPHHVVATVQEIQLQAAVGELLLLEWLAMAVMLLLLCCCLTD
||||||||||||||||||||||||| |||||||||||||||||||||||
Mutated AAVKPLLVPHHVVATVQEIQLQAAVNELLLLEWLAMAVMLLLLCCCLTD
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | VGELLLLEW | VNELLLLEW | 330 | 1071 |
HLA-B*58:01 | AVGELLLLEW | AVNELLLLEW | 196 | 87 |
Reference DAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPP
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated DAVIKTLQPVSELLTPLGIDLDEWSVATYYLFDESGEFKLASHMYCSFYPP
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | EWSMATYYLF | EWSVATYYLF | 157 | 467 |
HLA-B*58:01 | IDLDEWSMATYYLF | IDLDEWSVATYYLF | 380 | 1116 |
HLA-B*58:01 | SMATYYLF | SVATYYLF | 493 | 1427 |
HLA-B*58:01 | WSMATYYLFD | WSVATYYLFD | 490 | 1374 |
HLA-B*58:01 | LDEWSMATYYLF | LDEWSVATYYLF | 65 | 180 |
HLA-B*58:01 | WSMATYYLF | WSVATYYLF | 7 | 15 |
Reference VGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIAN
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated VGHTDLMAAYVDNSSLTIKKPNELSIVLGLKTLATHGLAAVNSVPWDTIAN
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | LSRVLGLKTL | LSIVLGLKTL | 1838 | 328 |
Reference FVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFK
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated FVKHKHAFLCLFLLPSLATVAYFNMFYMPASWVMRIMTWLDMVDTSLSGFK
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | LATVAYFNMV | LATVAYFNMF | 3556 | 279 |
HLA-B*58:01 | ATVAYFNMV | ATVAYFNMF | 5612 | 474 |
HLA-B*58:01 | MVYMPASWVM | MFYMPASWVM | 229 | 2515 |
HLA-B*58:01 | MVYMPASW | MFYMPASW | 112 | 464 |
HLA-B*58:01 | VAYFNMVYM | VAYFNMFYM | 878 | 222 |
HLA-B*58:01 | NMVYMPASW | NMFYMPASW | 167 | 70 |
HLA-B*58:01 | YFNMVYMPASW | YFNMFYMPASW | 507 | 249 |
Reference PKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREP
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated PKGFCDLKGKYVQIPTTCANDPVGFILKNTVCTVCGMWKGYGCSCDQLREP
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | FTLKNTVCTVCGMW | FILKNTVCTVCGMW | 345 | 5931 |
Reference CVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated CVNCLDDRCILHCANFNVLFSTVFPLTSFGPLVRKIFVDGVPFVVSTGYHF
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | FSTVFPPTSF | FSTVFPLTSF | 88 | 33 |
Reference APGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDN
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated APGCDVTDVTQLYLGGMSYYCKSHKLPISFPLCANGQVFGLYKNTCVGSDN
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*58:01 | MSYYCKSHKP | MSYYCKSHKL | 3227 | 360 |
HLA-B*58:01 | KSHKPPISFPL | KSHKLPISFPL | 716 | 187 |