This strain contains 24 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 24 epitopes, while stronger binding was found for 29 entries. There are 473 tight binders for the HLA-B*15:03 in the reference immunopeptidome (IC50 affinity ≤ 50 nM); 6 of them became non-tight binders (1.3%) and 6 novel tight binders appeared (1.3%). To avoid possible divisions by zero, we used + 1 regularization term in denominators when calculating percentages.
Reference MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFR
|||||||||||||||||| |||||||||||||||||||||||||
Mutated MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFR
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | TTRTQLPPAY | RTRTQLPPAY | 888 | 198 |
Reference QDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIR
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated QDLFLPFFSNVTWFHAIHVSGTNGTTRFDNPVLPFNDGVYFASTEKSNIIR
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | TKRFDNPVL | TTRFDNPVL | 162 | 3746 |
HLA-B*15:03 | TKRFDNPVLPF | TTRFDNPVLPF | 100 | 750 |
Reference CEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGK
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated CEFQFCNDPFLDVYYHKNNKSWMES‑‑GVYSSANNCTFEYVSQPFLMDLEGK
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | WMESEFRVY | WMESGVY | 10 | - |
HLA-B*15:03 | NKSWMESEF | NKSWMES | 126 | - |
HLA-B*15:03 | MESEFRVY | MESGVY | 180 | - |
HLA-B*15:03 | HKNNKSWMESEFRVY | HKNNKSWMESGVY | - | 224 |
HLA-B*15:03 | YHKNNKSWMESEFRVY | YHKNNKSWMESGVY | - | 418 |
HLA-B*15:03 | KSWMESEFRVY | KSWMESGVY | 250 | 9 |
HLA-B*15:03 | NKSWMESEFRVY | NKSWMESGVY | 1077 | 62 |
HLA-B*15:03 | SWMESEFRVY | SWMESGVY | 196 | 1469 |
HLA-B*15:03 | EFRVYSSANNCTF | GVYSSANNCTF | 1751 | 469 |
HLA-B*15:03 | FRVYSSANNCTF | GVYSSANNCTF | 131 | 469 |
Reference FQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQ
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated FQFCNDPFLDVYYHKNNKSWMES‑‑GVYSSANNCTFEYVSQPFLMDLEGKQ
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | WMESEFRVY | WMESGVY | 10 | - |
HLA-B*15:03 | MESEFRVY | MESGVY | 180 | - |
HLA-B*15:03 | HKNNKSWMESEFRVY | HKNNKSWMESGVY | - | 224 |
HLA-B*15:03 | YHKNNKSWMESEFRVY | YHKNNKSWMESGVY | - | 418 |
HLA-B*15:03 | KSWMESEFRVY | KSWMESGVY | 250 | 9 |
HLA-B*15:03 | NKSWMESEFRVY | NKSWMESGVY | 1077 | 62 |
HLA-B*15:03 | RVYSSANNCTF | GVYSSANNCTF | 41 | 469 |
HLA-B*15:03 | RVYSSANNCTFEY | GVYSSANNCTFEY | 203 | 2038 |
HLA-B*15:03 | SWMESEFRVY | SWMESGVY | 196 | 1469 |
HLA-B*15:03 | EFRVYSSANNCTF | GVYSSANNCTF | 1751 | 469 |
HLA-B*15:03 | FRVYSSANNCTF | GVYSSANNCTF | 131 | 469 |
Reference DDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGS
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated DDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGS
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | SKVGGNYNYLY | SKVGGNYNYRY | 313 | 720 |
Reference YRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGV
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated YRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGV
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | YQAGSTPCNGVEGF | YQAGSKPCNGVEGF | 217 | 656 |
Reference KQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYR
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated KQRRPQGLPNNTASWFTALTQHGKEGLKFPRGQGVPINTNSSPDDQIGYYR
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | TQHGKEDLKF | TQHGKEGLKF | 206 | 56 |
Reference GGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLN
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated GGSQASSRSSSRSRNSSRNSTPGSSMGTSPARMAGNGGDAALALLLLDRLN
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | RNSTPGSSR | RNSTPGSSM | 16125 | 70 |
HLA-B*15:03 | SRNSTPGSSR | SRNSTPGSSM | 25421 | 299 |
HLA-B*15:03 | SRGTSPARM | SMGTSPARM | 2669 | 248 |
HLA-B*15:03 | SSRGTSPARM | SSMGTSPARM | 1402 | 217 |
Reference LLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDD
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated LLNKHIDAYKTFPPTEPKKDKKKKAYETQALPQRQKKQQTVTLLPAADLDD
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | KKADETQAL | KKAYETQAL | 48 | 18 |
HLA-B*15:03 | KKKADETQAL | KKKAYETQAL | 560 | 253 |
Reference MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVA
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated MDLFMRIFTIGTVTLKQGEIKDATPLDFVRATATIPIQASLPFGWLIVGVA
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | KQGEIKDATPS | KQGEIKDATPL | 9550 | 310 |
HLA-B*15:03 | GEIKDATPS | GEIKDATPL | 11520 | 472 |
Reference NNVGPKVYPIILRLGSPLSLNMARKTLNSLEDKAFQLTPIAVQMTKLATTE
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated NNVGPKVYPIILRLGSPLSLNMARKALNSLEDKAFQLTPIAVQMTKLATTE
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | RKTLNSLEDKAF | RKALNSLEDKAF | 83 | 31 |
Reference IQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTG
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated IQPRVEKKKLDGFMGRIRSVYPVASLNECNQMCLSTLMKCDHCGETSWQTG
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | RSVYPVASP | RSVYPVASL | 5293 | 84 |
HLA-B*15:03 | PNECNQMCLSTLM | LNECNQMCLSTLM | 9595 | 269 |
Reference GKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLT
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated GKTFYVLPNDDTLRVEAFEYYHTTDLSFLGRYMSALNHTKKWKYPQVNGLT
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | FEYYHTTDP | FEYYHTTDL | 5699 | 46 |
HLA-B*15:03 | YHTTDPSF | YHTTDLSF | 1219 | 446 |
HLA-B*15:03 | YYHTTDPSF | YYHTTDLSF | 77 | 34 |
Reference TFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKR
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated TFYLTNDVSFLAHIQWMVMFTPLVPSWITIAYIICISTKHFYWFFSNYLKR
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | MVMFTPLVPF | MVMFTPLVPS | 5 | 1507 |
HLA-B*15:03 | IQWMVMFTPLVPF | IQWMVMFTPLVPS | 27 | 6363 |
HLA-B*15:03 | VMFTPLVPF | VMFTPLVPS | 2 | 342 |
HLA-B*15:03 | WMVMFTPLVPF | WMVMFTPLVPS | 54 | 8157 |
HLA-B*15:03 | QWMVMFTPLVPF | QWMVMFTPLVPS | 128 | 14472 |
HLA-B*15:03 | HIQWMVMFTPLVPF | HIQWMVMFTPLVPS | 153 | 16597 |
HLA-B*15:03 | MFTPLVPF | MFTPLVPS | 175 | 16680 |
HLA-B*15:03 | MVMFTPLVPFW | MVMFTPLVPSW | 362 | 2119 |
HLA-B*15:03 | VMFTPLVPFW | VMFTPLVPSW | 96 | 234 |
Reference CVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF
||||||||||||||||||||||||| |||||||||||||||||||||||||
Mutated CVNCLDDRCILHCANFNVLFSTVFPLTSFGPLVRKIFVDGVPFVVSTGYHF
Allele | Reference peptide | Mutated peptide | Reference affinity (IC50, nM) | Mutated affinity (IC50, nM) |
---|---|---|---|---|
HLA-B*15:03 | VLFSTVFPP | VLFSTVFPL | 3115 | 36 |