Table 3.
The epitopes sequences, amino acid position and its presented HLA alleles of SARS-CoV-2 N protein by cluster analysis
| Cluster Number | Epitope Number | Alignment | Epitope | Amino-acid Position | HLA Alleles |
|---|---|---|---|---|---|
| 1.1 | Consensus | DGKMKDLSPRWYFYYL | - | 98–113 | |
| 1 | DGKMKDLSPRWYFY– | DGKMKDLSPRWYFY | 98–111 | A*30:02 | |
| 2 | -GKMKDLSPRWYFY– | GKMKDLSPRWYFY | 99–111 | A*30:02, A*29:02 | |
| 3 | –KMKDLSPRWYFYY- | KMKDLSPRWYFYY | 100–112 | A*30:02, A*29:02 | |
| 4 | –KMKDLSPRWYFY– | KMKDLSPRWYFY | 100–111 | A*30:02, A*29:02, A*30:01, A*31:01 | |
| 5 | –KMKDLSPRWY – - | KMKDLSPRWY | 100–109 | A*30:02, B*15:25, B*15:01 | |
| 6 | – MKDLSPRWYFY– | MKDLSPRWYFY | 101–111 | A*29:02, A*30:02 | |
| 7 | – -KDLSPRWYFY– | KDLSPRWYFY | 102–111 | A*30:02, A*03:01, A*29:02 | |
| 8 | – –DLSPRWYFYY- | DLSPRWYFYY | 103–112 | A*29:02 | |
| 9 | – –DLSPRWYFY– | DLSPRWYFY | 103–111 | A*29:02 | |
| 10 | – – LSPRWYFYY- | LSPRWYFYY | 104–112 | A*29:02, A*30:02 | |
| 11 | – – -SPRWYFYYL | SPRWYFYYL | 105–113 | B*07:02, B*08:01 | |
| 2.1 | Consensus | IAQFAPSASAFF | - | 304–315 | |
| 1 | IAQFAPSASAF- | IAQFAPSASAF | 304–314 | B*15:25 | |
| 2 | -AQFAPSASAFF | AQFAPSASAFF | 305–315 | B*15:01, B*15:25 | |
| 3 | -AQFAPSASAF- | AQFAPSASAF | 305–314 | B*15:25, B*15:01, B*15:02 | |
| 4 | –QFAPSASAFF | QFAPSASAFF | 306–315 | A*23:01 | |
| 5 | –QFAPSASAF- | QFAPSASAF | 306–314 | C*14:02 | |
| 6 | – FAPSASAFF | FAPSASAFF | 307–315 | C*12:03, B*35:01, C*03:03, C*03:04, C*03:02, C*14:02, C*16:01 |
|
| 3.1 | Consensus | MSRIGMEVTPSGTWLTY | - | 317–333 | |
| 1 | MSRIGMEVTPSGTW – | MSRIGMEVTPSGTW | 317–330 | B*58:01 | |
| 2 | – –MEVTPSGTWLTY | MEVTPSGTWLTY | 322–333 | B*35:01, B*18:01, B*44:03 | |
| 3 | – –MEVTPSGTW – | MEVTPSGTW | 322–330 | B*44:02 | |
| 4 | – – -VTPSGTWLTY | VTPSGTWLTY | 324–333 | A*29:02, B*35:01, A*30:02 | |
| 5 | – – –TPSGTWLTY | TPSGTWLTY | 325–333 | B*35:01, B*53:01 | |
| 4.1 | Consensus | NTNSSPDDQIGYY | - | 75–87 | |
| 1 | NTNSSPDDQIGYY | NTNSSPDDQIGYY | 75–87 | A*01:01 | |
| 2 | –NSSPDDQIGYY | NSSPDDQIGYY | 77–87 | A*01:01 | |
| 3 | – SSPDDQIGYY | SSPDDQIGYY | 78–87 | A*01:01 | |
| 4 | – -SPDDQIGYY | SPDDQIGYY | 79–87 | B*35:01 | |
| 5.1 | Consensus | FYYLGTGPEAGLPY | - | 110–123 | |
| 1 | FYYLGTGPEAGLPY | FYYLGTGPEAGLPY | 110–123 | A*29:02, C*14:02 | |
| 2 | -YYLGTGPEAGLPY | YYLGTGPEAGLPY | 111–123 | A*29:02 | |
| 6.1 | Consensus | LPQGTTLPKGFY | - | 161–172 | |
| 1 | LPQGTTLPKGFY | LPQGTTLPKGFY | 161–172 | B*35:01 | |
| 2 | – GTTLPKGFY | GTTLPKGFY | 164–172 | A*30:02 | |
| 7.1 | Consensus | ILLNKHIDAY | - | 351–360 | |
| 1 | ILLNKHIDAY | ILLNKHIDAY | 351–360 | B*15:25, B*15:01 | |
| 2 | -LLNKHIDAY | LLNKHIDAY | 352–360 | B*15:25, B*15:01, B*15:02 | |
| 8.1 | Consensus | KFPRGQGVPI | - | 65–74 | |
| 1 | KFPRGQGVPI | KFPRGQGVPI | 65–74 | B*07:02 | |
| 2 | -FPRGQGVPI | FPRGQGVPI | 66–74 | B*07:02 | |
| 9.1 | Singleton | NTASWFTAL | NTASWFTAL | 48–56 | A*68:02 |
| 10.1 | Singleton | RQKRTATKAY | RQKRTATKAY | 259–268 | B*15:01, B*15:25, A*30:02 |
| 11.1 | Singleton | KAYNVTQAF | KAYNVTQAF | 266–274 | C*03:02, B*15:25, C*12:03, A*32:01, C*16:01, C*03:03, C*03:04, B*15:01, C*14:02, B*58:01, C*12:02, B*15:02, B*35:01, C*02:09, C*02:02 |
| 12.1 | Singleton | LPAADLDDF | LPAADLDDF | 395–403 | B*35:01 |
| 13.1 | Singleton | LPNNTASWF | LPNNTASWF | 45–53 | B*35:01, B*53:01 |
| 14.1 | Singleton | LLLDRLNQL | LLLDRLNQL | 222–230 | A*02:01, A*02:06 |
| 15.1 | Singleton | IGYYRRATR | IGYYRRATR | 84–92 | A*31:01 |
| 16.1 | Singleton | NQRNAPRITF | NQRNAPRITF | 8–17 | B*15:01 |