Table 3.
Dominant SARS-CoV-derived T cell epitopes and corresponding regions in nCoV
| SARS | 2019 nCoV | |||||
|---|---|---|---|---|---|---|
| Sequence | RF score | HLA restrictiona | Sequence | Proteinb | Mapped Start-End | Identity (%) |
| VRGWVFGSTMNNKSQSVI | 0.15 | DRB1*04:01 | IRGWIFGTTLDSKTQSLL | s | 101-118 | 50 |
| CTFEYISDAFSLD | 0.21 | DRB1*04:01 | CTFEYVSQPFLMD | S | 166-178 | 62 |
| DAFSLDVSEKSGN | 0.62 | DRB1*04:01 | QPFLMDLEGKQGN | s | 173-185 | 38 |
| TNFRAILTAFSPAQDIW | 0.32 | DRB1*04 01 | TRFQTLLALHRSYLTPGDSSSGW | s | 236-258 | 17 |
| KSFEIDKGIYQTSNFRW | 0.40 | DRB 1*04:01, DRB1*07:01 | KSFTVEKGIYQTSNFRVQ | s | 304-321 | 78 |
| STFFSTFKCYGVSATKL | 0.50 | DRB 1*07:01, DR8 | SASFSTFKCYGVSPTKL | s | 371-387 | 82 |
| KLPDDFMGCV | 0.55 | A*02:01 | KLPDDFTGCV | s | 424-433 | 90 |
| NIDATSTGNYNYKYRYLR | 0.29 | NLDSKVGGNYNYLYRLFR | g | 440-457 | 56 | |
| YLRHGKLRPFERDISNVP | 0.16 | DRB1*04:01 | YLYRLFRKSNLKPFERDI | s | 451-468 | 58 |
| RPFERDISNVPFS | 0.36 | DRB1*04:01 | KPFERDISTEIYQ | s | 462-474 | 54 |
| KSIVAYTMSLGADSSIAY | 0.15 | DRB1*04:01, DRB1*07:01 | QSIIAYTMSLGAENSVAY | s | 690-707 | 72 |
| SIVAYTMSL | 0.29 | A*02:01 | SIIAYTMSL | s | 691-699 | 89 |
| TECANLLLQYGSFCTQL | 0.50 | DR8 | TECSNLLLQYGSFCTQL | s | 747-763 | 94 |
| VKQMYKTPTLKYFGGFNF | 0.20 | DRB1*04:01 | VKQIYKTPPIKDFGGFNF | s | 785-802 | 78 |
| ESLTTTSTALGKLQDW | 0.42 | DRB1*04:01 | DSLSSTASALGKLQDW | s | 936-952 | 71 |
| ALNTLVKQL | 0.29 | A*02:01 | ALNTLVKQL | s | 958-966 | 100 |
| VLNDILSRL | 0.29 | A*02:01 | VLNDILSRL | s | 976-984 | 100 |
| LITGRLQSL | 0.42 | A*02:01 | LITGRLQSL | s | 996-1004 | 100 |
| QLIRAAEIRASANLAATK | 0.20 | DRB1*04:01 | QLIRAAEIRASANLAATK | s | 1011-1028 | 100 |
| SWFITQRNFFSPQII | 0.60 | DRB1*04:01 | HWFVTQRNFYEPQII | s | 1101-1115 | 73 |
| RLNEVAKNL | 0.42 | A*02:01 | RLNEVAKNL | s | 1185-1193 | 100 |
| NLNESLIDL | 0.29 | A*02:01 | NLNESLIDL | s | 1192-1200 | 100 |
| FIAGLIAIV | 0.80 | A*02:01 | FIAGLIAIV | s | 1220-1228 | 100 |
| RFFTLGSITAQPVKI | 0.18 | B*58:01 | RIFTIGTVTLKQGEI | Orf 3a | 6-20 | 40 |
| SITAQPVKI | 0.29 | B*58:01 | TVTLKQGEI | Orf 3a | 12-20 | 22 |
| TLACFVLAAV | 0.59 | A*02:01 | TLACFVLAAV | M | 61-70 | 100 |
| GLMWLSYFV | 0.59 | A*02:01 | GLMWLSYFI | M | 89-97 | 89 |
| HLRMAGHSL | 0.40 | Class I | HLRIAGHHL | M | 148-156 | 78 |
| ALNTPKDHI | 0.29 | A*02:01 | ALNTPKDHI | N | 138-146 | 100 |
| LQLPQGTTL | 0.29 | A*02:01 | LQLPQGTTL | N | 159-167 | 100 |
| GETALALLLL | 0.38 | B*40:01 | GDAALALLLL | N | 215-224 | 80 |
| LALLLLDRL | 0.29 | A*02:01 | LALLLLDRL | N | 219-227 | 100 |
| LLLDRLNQL | 0.42 | A*02:01 | LLLDRLNQL | N | 222-230 | 100 |
| RLNQLESKV | 0.42 | A*02:01 | RLNQLESKM | N | 226-234 | 89 |
| TKQYNVTQAF | 0.29 | Class I | TKAYNVTQAF | N | 265-274 | 90 |
| GMSRIGMEV | 0.42 | A*02:01 | GMSRIGMEV | N | 316-324 | 100 |
| MEVTPSGTWL | 0.42 | B*40:01 | MEVTPSGTWL | N | 322-331 | 100 |
| QFKDNVILL | 0.50 | A*24:02 | NFKDQVILL | N | 345-353 | 78 |
| CLDAGINYV | 0.42 | A*02:01 | CLEASFNYL | Orf lab | 2139-2147 | 56 |
| WLMWFIISI | 0.42 | A*02:01 | WLMWLIINL | Orf lab | 2292-2300 | 67 |
| ILLLDQVLV | 0.42 | A*02:01 | ILLLDQALV | Orf lab | 2498-2506 | 89 |
| LLCVLAALV | 0.42 | A*02:01 | SACVLAAEC | Orf lab | 2840-2848 | 56 |
| ALSGVFCGV | 0.42 | A*02:01 | SLPGVFCGV | Orf lab | 2942-2950 | 78 |
| TLMNVITLV | 0.42 | A*02:01 | TLMNVLTLV | Orf lab | 3639-3647 | 89 |
| SMWALVISV | 0.42 | A*02:01 | SMWALIISV | Orf lab | 3661-3669 | 89 |
a.
Restrictions defined only in HLA-transgenic mice are indicated by the italicized font.
b.
S= surface glycoprotein; M=membrane protein; N=nucleocapsid phosphoprotein.