Table 3.
Set of the SARS-CoV-derived spike (S) and nucleocapsid (N) protein T cell epitopes (obtained from positive MHC binding assays) that are identical in SARS-CoV-2 and that maximize estimated population coverage globally (87 distinct epitopes).
| Epitopes1 | MHC Allele Class | MHC Allele | Global Accumulated Population Coverage2 (%) | Accumulated Population Coverage in China (%) |
|---|---|---|---|---|
| FIAGLIAIV, GLIAIVMVTI, IITTDNTFV, ALNTLVKQL, LITGRLQSL, LLLQYGSFC, LQYGSFCT, NLNESLIDL, RLDKVEAEV, RLNEVAKNL, RLQSLQTYV, VLNDILSRL, VVFLHVTYV, ILLNKHID, FPRGQGVPI, LLLLDRLNQ, GMSRIGMEV, ILLNKHIDA, ALNTPKDHI, LALLLLDRL, LLLDRLNQL, LLLLDRLNQL, LQLPQGTTL, AQFAPSASA, TTLPKGFYA, VLQLPQGTTL | I | HLA-A*02:01 | 39.08 | 14.62 |
| GYQPYRVVVL, PYRVVVLSF, LSPRWYFYY | I | HLA-A*24:02 | 55.48 | 36.11 |
| DSFKEELDKY, LIDLQELGKY, PYRVVVLSF, GTTLPKGFY, VTPSGTWLTY | I | HLA-A*01:01 | 66.78 | 39.09 |
| GSFCTQLNR, GVVFLHVTY, AQALNTLVK, MTSCCSCLK, ASANLAATK, SLIDLQELGK, SVLNDILSR, TQNVLYENQK, CMTSCCSCLK, VQIDRLITGR, KTFPPTEPK, KTFPPTEPKK, LSPRWYFYY, ASAFFGMSR, ATEGALNTPK, QLPQGTTLPK, QQQGQTVTK, QQQQGQTVTK, SASAFFGMSR, SQASSRSSSR, TPSGTWLTY | I | HLA-A*03:01 | 76.14 | 41.68 |
| GSFCTQLNR, GVVFLHVTY, AQALNTLVK, MTSCCSCLK, ASANLAATK, SLIDLQELGK, SVLNDILSR, TQNVLYENQK, CMTSCCSCLK, VQIDRLITGR, KTFPPTEPK, KTFPPTEPKK, LSPRWYFYY, ASAFFGMSR, ATEGALNTPK, QLPQGTTLPK, QQQGQTVTK, QQQQGQTVTK, SASAFFGMSR, SQASSRSSSR, TPSGTWLTY | I | HLA-A*11:01 | 83.39 | 73.43 |
| GSFCTQLNR, GVVFLHVTY, AQALNTLVK, MTSCCSCLK, ASANLAATK, SLIDLQELGK, SVLNDILSR, TQNVLYENQK, CMTSCCSCLK, VQIDRLITGR, KTFPPTEPK, KTFPPTEPKK, LSPRWYFYY, ASAFFGMSR, ATEGALNTPK, QLPQGTTLPK, QQQGQTVTK, QQQQGQTVTK, SASAFFGMSR, SQASSRSSSR, TPSGTWLTY | I | HLA-A*68:01 | 85.71 | 74.25 |
| GYQPYRVVVL, PYRVVVLSF, LSPRWYFYY | I | HLA-A*23:01 | 87.72 | 74.87 |
| GSFCTQLNR, GVVFLHVTY, AQALNTLVK, MTSCCSCLK, ASANLAATK, SLIDLQELGK, SVLNDILSR, TQNVLYENQK, CMTSCCSCLK, VQIDRLITGR, KTFPPTEPK, KTFPPTEPKK, LSPRWYFYY, ASAFFGMSR, ATEGALNTPK, QLPQGTTLPK, QQQGQTVTK, QQQQGQTVTK, SASAFFGMSR, SQASSRSSSR, TPSGTWLTY | I | HLA-A*31:01 | 89.55 | 76.93 |
| FPNITNLCPF, APHGVVFLHV, FPRGQGVPI, APSASAFFGM | I | HLA-B*07:02 | 90.89 | 77.61 |
| GAALQIPFAMQMAYR, GWTFGAGAALQIPFA, IDRLITGRLQSLQTY, ISGINASVVNIQKEI, LDKYFKNHTSPDVDL, LGDISGINASVVNIQ, LGFIAGLIAIVMVTI, LNTLVKQLSSNFGAI, LQDVVNQNAQALNTL, LQSLQTYVTQQLIRA, LQTYVTQQLIRAAEI, AQKFNGLTVLPPLLT, PCSFGGVSVITPGTN, QIPFAMQMAYRFNGI, QQLIRAAEIRASANL, QTYVTQQLIRAAEIR, AYRFNGIGVTQNVLY, SSNFGAISSVLNDIL, TGRLQSLQTYVTQQL, WLGFIAGLIAIVMVT, CVNFNFNGLTGTGVL, DKYFKNHTSPDVDLG, IDAYKTFPPTEPKKD, MSRIGMEVTPSGTWL, NKHIDAYKTFPPTEP, VLQLPQGTTLPKGFY | II | HLA-DRB1*01:01 | 91.94 | 78.23 |
| FPRGQGVPI | I | HLA-B*08:01 | 92.85 | 78.41 |
| FPNITNLCPF, APHGVVFLHV, FPRGQGVPI, APSASAFFGM | I | HLA-B*35:01 | 93.53 | 79.23 |
| LQIPFAMQM, RVDFCGKGY | I | HLA-B*15:01 | 94.18 | 82.26 |
| FPNITNLCPF, APHGVVFLHV, FPRGQGVPI, APSASAFFGM | I | HLA-B*51:01 | 94.72 | 83.73 |
| YEQYIKWPWY | I | HLA-B*18:01 | 95.23 | 83.88 |
| GRLQSLQTY, RVDFCGKGY, VRFPNITNL | I | HLA-B*27:05 | 95.55 | 84 |
| MTSCCSCLK, SLIDLQELGK, CMTSCCSCLK, VQIDRLITGR, SASAFFGMSR, SQASSRSSSR | I | HLA-A*33:01 | 95.79 | 85.28 |
| LQIPFAMQM, RVDFCGKGY | I | HLA-B*58:01 | 95.99 | 86.45 |
| LQIPFAMQM, RVDFCGKGY | I | HLA-C*15:02 | 96.17 | 87.22 |
| VRFPNITNL | I | HLA-C*14:02 | 96.29 | 88.11 |
1 Multiple SARS-CoV-derived epitopes that were determined using MHC binding assays are shown for each allele. Epitopes that were also tested for positive T cell response (listed also in Table 2) are shown in bold. Epitopes that lie within the SARS-CoV receptor-binding motif are underlined. 2 Epitopes are ordered according to the estimated global accumulated population coverage.