Table 2.
Mutated T cell epitopes in spike protein from variants of SARS-COV-2.
| CD8 native epitope | CD8 Mutant epitope | Variants |
|---|---|---|
| AEHVNNSY | AEYVNNSY | P.1, B.1.1.529 |
| DGVYFASTEK | DGVYFASIEK | B.1.617.2.1, B.1.1.529 |
| DSKVGGNYNY | DSKVSGNYNY | B.1.1.529 |
| GEVFNATRF | DEVFNATRF | B.1.1.529 |
| FQFCNDPFL | FQFCNYPFL | P.1 |
| GVYFASTEK | GVYFASIEK | B.1.617.2.1, B.1.1.529 |
| GVYYHKNNK | DVYYHKNNK | B.1.617.2.1 |
| DHKNNK | B.1.1.529 | |
| HVSGTNGTK | SGTNGTK | B.1.1.298 |
| HVISGTNGTK | B.1.1.529 | |
| IYKTPPIKDF | IYKTPPIKYF | B.1.1.529 |
| KIADYNYKL | NIADYNYKL | B.1.617.2.1 |
| TIADYNYKL | P.1 | |
| KVGGNYNYLY | KVGGNYNYRY | B.1.617.2.1 |
| KVGGNYNYLF | B.1.1.298 | |
| KVSGNYNYLY | B.1.1.529 | |
| LGAENSVAY | LGVENSVAY | B.1.1.529 |
| LPPAYTNSF | LPSAYTNSF | P.1 |
| NASVVNIQK | NASFVNIQK | P.1, P.2 |
| NESLIDLQEL | NESLIDLQQL | B.1.1.429 |
| NSASFSTFK | NLAPFFTFK | B.1.1.529 |
| NYNYLYRLF | NYNYLFRLF | B.1.1.298 |
| NYNYRYRLF | B.1.617.2.1 | |
| QELGKYEQY | QQLGKYEQY | B.1.1.429 |
| QIAPGQTGK | QIAPGQTGN | B.1.617.2.1 |
| QIAPGQTGT | P.1 | |
| QTNSPRRAR | QTNSRRRAR | B.1.617.2.1 |
| QTKSHRRAR | B.1.1.529 | |
| RASANLAATK | RASANLAAIK | P.1 |
| SFKEELDKY | LFKEELDKY | B.1.1.298 |
| SIIAYTMSL | SIIAYTMLL | P.2 |
| SPRRARSV | SRRRARSV | B.1.617.2.1 |
| SHRRARSV | B.1.1.529 | |
| SPRRARSVA | SRRRARSVA | B.1.617.2.1 |
| SHRRARSVA | B.1.1.529 | |
| SVLNDILSR | SVLNDIFSR | B.1.1.529 |
| SWMESEFRVY | SWMESGVY | B.1.617.2.1 |
| TEKSNIIRGW | IEKSNIIRGW | B.1.617.2.1, B.1.1.529 |
| TPINLVRDL | TPIIVREPEDL | B.1.1.529 |
| TVYDPLQPELDSFK | TVYDPLQPELDLFK | B.1.1.298 |
| VGGNYNYLY | VGGNYNYLF | B.1.1.298 |
| VGGNYNYRY | B.1.617.2.1 | |
| VSGNYNYLY | B.1.1.529 | |
| VLNDILSRL | VLNDIFSRL | B.1.1.529 |
| VYDPLQPELDSF | VYDPLQPELDLF | B.1.1.298 |
| WTAGAAAYY | LTAGAAAYY | B.1.617.2.1 |
| YFQPRTFLL | YLQPRTFLL | B.1.617.2.1, B.1.1.298, P.1, B.1.1.429, P.2, B.1.1.529 |
| YGFQPTNGV | YGFQPTYGV | P.1 |
| YSFRPTYGV | B.1.1.529 | |
| YNYLYRLFR | YNYLFRLFR | B.1.1.298 |
| YNYRYRLFR | B.1.617.2.1 | |
| YQDVNCTEV | YQGVNCTEV | B.1.617.2.1, B.1.1.298, P.1, B.1.1.429, P.2, B.1.1.529 |
| YTMSLGAENSVAY | YTMLLGAENSVAY | P.2 |
| YTMSLGVENSVAY | B.1.1.529 | |
| YYHKNNKSW | DHKNNKSW | B.1.1.529 |
| AENSVAYSNNSIAIP | VENSVAYSNNSIAIP | B.1.1.529 |
| ARDLICAQKFNGLTV | ARDLICAQKFKGLTV | B.1.1.529 |
| CAQKFNGLTVLPPLL | CAQKFKGLTVLPPLL | B.1.1.529 |
| CEFQFCNDPFLGVYY | CEFQFCNYPFLGVYY | P.1 |
| CEFQFCNDPFLDVYY | B.1.617.2.1 | |
| CEFQFCNDPFLD | B.1.1.529 | |
| CPFGEVFNATRFASV | CPFDEVFNATRFASV | B.1.1.529 |
| CVADYSVLYNSASFS | CVADYSVLYNLAPFF | B.1.1.529 |
| EIYQAGSTPCNGVEG | EIYQAGSTPCNGVKG | P.1 |
| EIYQAGNTPCNGVKG | P.2 | |
| EIYQAGSKPCNGVEG | B.1.617.2.1 | |
| EIYQAGNKPCNGVAG | B.1.1.529 | |
| FKIYSKHTPINLVRD | FKIYSKHTPIIVREPED | B.1.1.529 |
| FNCYFPLQSYGFQPT | FNCYFPLRSYSFRPT | B.1.1.529 |
| FNGLTVLPPLLTDEM | FKGLTVLPPLLTDEM | B.1.1.529 |
| GINASVVNIQKEIDR | GINASFVNIQKEIDR | P.1, P.2 |
| GKQGNFKNLREFVFK | GKQGNFKNLSEFVFK | P.1 |
| HKNNKSWMESEFRVY | HKNNKSWMESGVY | B.1.617.2.1 |
| IVRFPNITNLCPFGE | IVRFPNITNLCPFDE | B.1.1.529 |
| KHTPINLVRDLPQGF | KHTPIIVREPEDLPQGF | B.1.1.529 |
| LGVYYHKNNKSWMES | LDVYYHKNNKSWMES | B.1.617.2.1 |
| LDHKNNKSWMES | B.1.1.529 | |
| LMDLEGKQGNFKNLR | LMDLEGKQGNFKNLS | P.1 |
| LPFFSNVTWFHAIHV | LPFFSNVTWFHAI | B.1.1.298 |
| LPFFSNVTWFHVI | B.1.1.529 | |
| LQPELDSFKEELDKY | LQPELDLFKEELDKY | B.1.1.298 |
| LTGTGVLTESNKKFL | LKGTGVLTESNKKFL | B.1.1.529 |
| NLLLQYGSFCTQLNR | NLLLQYGSFCTQLKR | B.1.1.529 |
| NLVRDLPQGFSALEP | IVREPEDLPQGFSALEP | B.1.1.529 |
| NPVLPFNDGVYFAST | NPVLPFNDGVYFASI | B.1.617.2.1, B.1.1.529 |
| PINLVRDLPQGFSAL | PIIVREPEDLPQGFSAL | B.1.1.529 |
| QELGKYEQYIKWPWY | QQLGKYEQYIKWPWY | B.1.1.429 |
| QLIRAAEIRASANLAATK | QLIRAAEIRASANLAAIK | P.1 |
| SASFSTFKCYGVSPT | LAPFFTFKCYGVSPT | B.1.1.529 |
| SVLYNSASFSTFKCY | SVLYNLAPFFTFKCY | B.1.1.529 |
| TPPIKDFGGFNFSQI | TPPIKYFGGFNFSQI | B.1.1.529 |
| TQLNRALTGIAVEQD | TQLKRALTGIAVEQD | B.1.1.529 |
| WNSNNLDSKVGGNYN | WNSNKLDSKVSGNYN | B.1.1.529 |
| VNLTTRTQLPPAYTN | VNFTNRTQLPSAYTN | P.1 |
| VNLRTRTQLPPAYTN | B.1.617.2.1 | |
| VSSQCVNLTTRTQLP | VSSQCVNFTNRTQLP | P.1 |
| VSSQCVNLRTRTQLP | B.1.617.2.1 | |
| VVIKVCEFQFCNDPF | VVIKVCEFQFCNYPF | P.1 |
| YNYLYRLFRKSNLKP | YNYRYRLFRKSNLKP | B.1.617.2.1 |
| YNYLFRLFRKSNLKP | B.1.1.298 |
Footnote: Positions with mutations are highlighted in red. Red highlighted residues in native epitopes indicate the deletions. Yellow highlighted mutated epitopes were not used for further HLA analysis due to their length (less than 8 or more than 15 residues).