Table 2. A list of SARS-CoV-2-derived CD4+ T-cell epitopes that have been tested in unexposed individuals or examined for cross-reactivity with human CCCoVs.
| Protein | AA sequence | Position | HLA allele | Epitope-reactive T cell response in unexposed individuals | Confirmed cross-reactivity with CCCoVs | Detection method | Ref. |
|---|---|---|---|---|---|---|---|
| N | MKDLSPRWYFYYLGT | 101-115 | ND | + | ND | Ex vivo IFN-γ ELISpot and ICS assay | (24) |
| N | PRWYFYYLGTGPEAG | 106-120 | ND | + | ND | ||
| ORF1a | SKLWAQCVQLHNDIL | 26-40 | ND | + | ND | ||
| ORF1a | HNDILLAKDTTEAFE | 36-50 | ND | + | − | ||
| S | ITRFQTLLALHRSYL | 235-249 | DRB1*01 | + | ND | Pre-expansion → IFN-γ ELISpot | (37) |
| M | LSYYKLGASQRVAGD | 176-190 | DRB1*04, DRB1*07 | − | ND | ||
| N | ASWFTALTQHGKEDL | 50-64 | DRB1*04, DRB1*11 | + | ND | ||
| N | IGYYRRATRRIRGGD | 84-98 | DRB1*04, DRB1*11 | − | ND | ||
| N | RWYFYYLGTGPEAGL | 107-121 | DRB1*04 | + | ND | ||
| N | KDGIIWVATEGALNT | 127-141 | DRB1*01, DRB1*04, DRB1*11 | + | ND | ||
| N | AIVLQLPQGTTLPKG | 156-170 | DRB1*01, DRB1*03 | − | ND | ||
| N | YKHWPQIAQFAPSAS | 298-312 | DRB1*01, DRB1*04, DRB1*11 | − | ND | ||
| N | ASAFFGMSRIGMEVT | 311-325 | DRB1*01, DRB1*04, DRB1*07, DRB1*11 | + | ND | ||
| N | GTWLTYTGAIKLDDK | 328-342 | DRB1*01, DRB1*07, DRB1*15 | + | ND | ||
| N | AIVLQLPQGTTLPKG | 156-170 | DRB1*01, DRB1*03 | − | ND | ||
| E | FYVYSRVKNLNSSRV | 56-70 | DRB1*04, DRB1*11 | + | ND | ||
| ORF1 | LDDFVEIIKSQDLSV | 6751-6765 | DRB1*11 | + | ND | ||
| ORF3 | FMRIFTIGTVTLKQG | 4-18 | DRB1*01, DRB1*03, DRB1*07 | + | ND | ||
| ORF6 | IWNLDYIINLIIKNL | 26-40 | DRB1*04, DRB1*07, DRB1*15 | + | ND | ||
| ORF7 | QEEVQELYSPIFLIV | 90-104 | DRB1*01, DRB1*07 | + | ND | ||
| ORF8 | SKWYIRVGARKSAPL | 43-57 | DRB1*01, DRB1*11 | + | ND | ||
| ORF10 | INVFAFPFTIYSLLL | 4-18 | DRB1*01, DRB1*04 | − | ND | ||
| N | LLLLDRLNQLESKMS | 221-235 | DRB1*04, DRB1*15 | + | ND | ||
| N | LLLLDRLNQLESKMS | 221-235 | DRB1*11:01, DQA1*01:01, DQB1*05:01 | + | ND | Pre-expansion → IFN-γ/IL-5 FluoroSPOT | (36) |
| S | SLLIVNNATNVVIKV | 116-130 | DRB1*07:01, *13:01, DQA1*01:03/DQB1*06:03 | + | − | ||
| S | NNATNVVIKVCEFQF | 121-135 | ND | + | ND | ||
| S | CEFQFCNDPFLGVYY | 131-145 | DQA1*02:01/DQB1*02:02, *01:01/*05:01 | + | ND | ||
| S | CTFEYVSQPFLMDLE | 166-180 | DQA1*01:02/DQB1*06:04 | + | − | ||
| S | IGINITRFQTLLALH | 231-245 | DRB1*07:01, *11:02, *13:01, *13:03, DQA1*01:03/DQB1*06:03 | + | ND | ||
| S | TRFQTLLALHRSYLT | 236-250 | DRB1*01:01, *07:01, *08:03, DRB1*11:02, *13:01, *13:02, *13:03, DRB1*15:01, DQA1*01:01/DQB1*05:01, *01:02/*06:02, *01:03/*06:03 | + | − | ||
| S | LLALHRSYLTPGDSS | 241-255 | DRB1*01:01, *07:01, *11:02, *15:01 | + | ND | ||
| S | FTVEKGIYQTSNFRV | 306-320 | ND | + | ND | ||
| S | SNFRVQPTESIVRFP | 316-330 | DRB1*03:01 | + | ND | ||
| S | QPTESIVRFPNITNL | 321-335 | DRB1*08:03, *15:01 | + | − | ||
| S | IVRFPNITNLCPFGE | 326-340 | ND | + | − | ||
| S | CPFGEVFNATRFASV | 336-350 | DRB1*01:01, *08:03, *11:01, *11:02, *13:03, DQA1*05:01/DQB1*03:01, *01:02/*06:02 | + | − | ||
| S | VFNATRFASVYAWNR | 341-355 | DRB1*01:01, *08:03, *11:01, *13:03, *15:01, DQA1*05:01/DQB1*03:01, *01:02/*06:02 | + | − | ||
| S | SIIAYTMSLGAENSV | 691-705 | DRB1*01:03, *07:01, DQA1*02:01/DQB1*02:02, *01:01/*05:01 | + | ND | ||
| S | AYSNNSIAIPTNFTI | 706-720 | DQA1*01:03/DQB1*06:03 | + | − | ||
| S | NLLLQYGSFCTQLNR | 751-765 | DRB1*01:01, *15:01, DQA1*01:01/DQB1*05:01 | + | ND | ||
| S | TQLNRALTGIAVEQD | 761-775 | DRB1*01:01, *09:01, DQA1*03:01/DQB1*03:03, *03:01/*04:02, *01:02/*06:02, *01:02/*06:04 | + | − | ||
| S | VFAQVKQIYKTPPIK | 781-795 | ND | + | − | ||
| S | NFSQILPDPSKPSKR | 801-815 | ND | + | ND | ||
| S | KPSKRSFIEDLLFNK | 811-825 | DRB1*03:01, DQA1*05:01/DQB1*02:01, *02:01/*02:02, *01:01/*05:01 | + | ND | ||
| S | SFIEDLLFNKVTLAD | 816-830 | DRB1*01:01, *01:03, *04:04, *11:02, *13:03, *14:01, *15:01, *16:02, DQA1*01:01/DQB1*05:01, *01:02, *05:02 | + | + | ||
| S | AQYTSALLAGTITSG | 871-885 | ND | + | ND | ||
| S | WTFGAGAALQIPFAM | 886-900 | DRB1*01:01, DQA1*05:01/DQB1*03:01 | + | ND | ||
| S | AQALNTLVKQLSSNF | 956-970 | DRB1*11:01, *13:03, DQA1*01:02/DQB1*06:02 | + | ND | ||
| S | GAISSVLNDILSRLD | 971-985 | DQA1*01:01/DQB1*05:01 | + | − | ||
| S | VQIDRLITGRLQSLQ | 991-1005 | DRB1*01:01, *03:01, *11:01, *13:03 | + | − | ||
| S | APHGVVFLHVTYVPA | 1056-1070 | DRB1*04:04, *10:01, DQA1*01:01/DQB1*05:01 | + | ND | ||
| S | ELDKYFKNHTSPDVD | 1151-1165 | ND | + | − | ||
| S | GINASVVNIQKEIDR | 1171-1185 | DQA1*05:01/DQB1*03:01 | + | − | ||
| S | LNEVAKNLNESLIDL | 1186-1200 | DRB1*13:02 | + | − | ||
| S | YEQYIKWPWYIWLGF | 1206-1220 | ND | + | + | ||
| N | DAALALLLLDRLNQL | 216-230 | DRB1*11:01, DQA1*01:01/DQB1*05:01 | + | − | ||
| N | PSGTWLTYTGAIKLD | 326-340 | DRB1*01:03, *07:01 | + | + | ||
| E | LAILTALRLCAYCCN | 31-45 | DRB1*01:01, *11:01 | + | ND | ||
| ORF1a | PLNSIIKTIQPRVEK | 276-290 | DRB1*01:01, *07:01 | + | − | ||
| ORF1a | EEIAIILASFSASTS | 471-485 | DRB1*04:10, *07:01, DQA1*02:01/DQB1*02:02, *03:01/*03:02 | + | − | ||
| ORF1a | SPLYAFASEAARVVR | 531-545 | DRB1*07:01, DQA1*02:01/DQB1*02:02 | + | − | ||
| ORF1a | QTFFKLVNKFLALCA | 676-690 | DRB1*01:03, *07:01, DQA1*01:01/DQB1*05:01 | + | − | ||
| ORF1a | GETFVTHSKGLYRKC | 706-720 | DRB1*07:01 | + | ND | ||
| ORF1a | KVTFFPDLNGDVVAI | 1956-1970 | DQA1*02:01/DQB1*02:02, *01:01/*05:01 | + | ND | ||
| ORF1a | SHNIALIWNVKDFMS | 2706-2720 | DRB1*04:10, DQA1*02:01/DQB1*02:02, *03:01/*03:02, *03:01/*04:02 | + | ND | ||
| ORF1a | KHFYWFFSNYLKRRV | 3151-3165 | DRB1*04:10, *0701, *09:01, DQA1*02:01/DQB1*02:02, *03:01/*04:02 | + | − | ||
| ORF1a | NHNFLVQAGNVQLRV | 3326-3340 | DRB1*01:01, *07:01, *08:03, *15:01, DQA1*05:01/DQB1*03:01, *01:02/*06:02 | + | − | ||
| ORF1a | QNCVLKLKVDTANPK | 3346-3360 | DRB1*04:10 | + | ND | ||
| ORF1a | NRYFRLTLGVYDYLV | 3801-3815 | DRB1*01:01, *01:03, *07:01, *08:03, *15:01, DQA1*02:01/DQB1*02:02, *01:01/*05:01, *01:02/*06:02 | + | − | ||
| ORF1a | VLKKLKKSLNVAKSE | 3976-3990 | DRB1*11:01, *13:03, DQA1*01:02/DQB1*06:02 | + | + | ||
| ORF1b | KLLKSIAATRGATVV | 4966-4980 | DRB1*04:04, *10:01 | + | + | ||
| ORF1b | EFYAYLRKHFSMMIL | 5136-5150 | DRB1*07:01, *09:01, *13:01, DQA1*03:01/DQB1*04:02 | + | + | ||
| ORF1b | GLVASIKNFKSVLYY | 5166-5180 | DRB1*08:03, *12:02, DQA1*01:03/DQB1*06:01 | + | ND | ||
| ORF1b | LMIERFVSLAIDAYP | 5246-5260 | DRB1*01:03, *07:01, *08:03, *12:02, DQA1*02:01/DQB1*02:02, *05:01/*03:01, *01:01/*05:01, *01:03/*06:01 | + | + | ||
| ORF1b | TSHKLVLSVNPYVCN | 5361-5375 | DRB1*07:01, *13:01, DQA1*01:03/DQB1*06:03 | + | + | ||
| ORF1b | ISPYNSQNAVASKIL | 5836-5850 | DRB1*01:01, DQA1*01:02/DQB1*06:02 | + | ND | ||
| ORF1b | NVNRFNVAITRAKVG | 5881-5895 | DRB1*08:03, *15:01, DQA1*05:01/DQB1*03:01, *01:02/*06:02 | + | + | ||
| ORF1b | REEAIRHVRAWIGFD | 6001-6015 | DRB1*01:03, *07:01 | + | ND | ||
| ORF1b | TQLCQYLNTLTLAVP | 6846-6860 | DRB1*01:01, *15:01, DQA1*01:01/DQB1*05:01, *01:02/*06:02 | + | ND | ||
| ORF3a | SDFVRATATIPIQAS | 26-40 | DRB1*07:01, DQA1*02:01/DQB1*02:02 | + | − | ||
| ORF3a | ALLAVFQSASKIITL | 51-65 | DRB1*07:01, *13:01, DQA1*01:03/DQB1*06:03 | + | − | ||
| ORF6 | MFHLVDFQVTIAEIL | 1-15 | DRB1*13:03 | + | − | ||
| ORF6 | TFKVSIWNLDYIINL | 21-35 | DRB1*01:03, *07:01, *15:01, DQA1*02:01/DQB1*02:02, *01:01/*05:01 | + | − | ||
| ORF6 | YIINLIIKNLSKSLT | 31-45 | DRB1*11:02, *13:03 | + | − | ||
| ORF7 | VKHVYQLRARSVSPK | 71-85 | DRB1*01:03, *07:01 | + | − | ||
| ORF8 | FYSKWYIRVGARKSA | 41-55 | DRB1*01:01, *07:01 | + | − |
AA, amino acid; HLA, human leukocyte antigen; E, envelope; +, positive response; −, negative response; ND, not determined.