Table 2.
Binding affinities of 120 VEPs from SARS-CoV-2 with HLA-A allotypes as detected by competitive peptide binding assays using transfected HMy2.CIR cell lines
| HLA-A | Epitope | Affinity | 5 μM inhibition (%) | 15 μM inhibition (%) | Epitope | Affinity | 5 μM inhibition (%) | 15 μM inhibition (%) |
|---|---|---|---|---|---|---|---|---|
| A0201 | R12 | High | 91.70 | 91.10 | R6 | No | 13.40 | 23.70 |
| R8 | High | 85.50 | 89.90 | D5 | Low | 10.00 | 37.80 | |
| B1 | High | 80 | 88.20 | A5 | No | 9.40 | 6.20 | |
| R10 | High | 75.80 | 92.80 | R13 | No | 8.66 | 28.90 | |
| R15 | High | 70.80 | 93.80 | D80 | No | 6.38 | 5.25 | |
| B3 | High | 66.10 | 74.40 | D42 | No | 5.93 | 6.72 | |
| R9 | High | 64.80 | 89.50 | D72 | No | 5.93 | 6.38 | |
| R5 | High | 58.70 | 89.10 | A4 | No | 4.80 | 4.00 | |
| R11 | Inter | 47.80 | 86.40 | R14 | No | 4.50 | 13.30 | |
| B2 | Inter | 42.10 | 83.70 | A1 | No | 3.30 | 2.90 | |
| R4 | Inter | 40.40 | 78.30 | A3 | No | 1.90 | 1.40 | |
| B6 | Inter | 33.00 | 65.90 | D13 | No | 0.70 | 1.20 | |
| D2 | Inter | 24.50 | 55.00 | C1 | No | 0 | 10.30 | |
| D12 | Low | 20.10 | 32.60 | C3 | No | 0 | 7.10 | |
| B4 | No | 16.70 | 20.70 | D6 | No | 0 | 2.10 | |
| A1101 | D38 | High | 80.70 | 87.70 | D48 | Low | 34.38 | 48.05 |
| D41 | High | 80.38 | 89.72 | D50 | Low | 32.38 | 43.38 | |
| R43 | High | 79.50 | 89.20 | B23 | Low | 32.30 | 41.00 | |
| R32 | High | 73.90 | 89.40 | R41 | Low | 31.90 | 46.20 | |
| R30 | High | 72.60 | 84.90 | B18 | Low | 21.55 | 34.38 | |
| D34 | High | 67.70 | 84.70 | D82 | Low | 20.72 | 38.22 | |
| B20 | High | 61.88 | 55.88 | A16 | No | 18.38 | 19.22 | |
| D72 | High | 58.05 | 76.05 | D77 | No | 15.72 | 29.38 | |
| D40 | High | 56.70 | 82.60 | D42 | Low | 14.70 | 47.80 | |
| D47 | High | 53.38 | 67.72 | A12 | No | 14.38 | 15.00 | |
| R42 | High | 50.20 | 75.20 | R38 | Low | 12.10 | 47.10 | |
| R44 | Inter | 47.60 | 81.4 | B21 | No | 10.55 | 29.38 | |
| C49 | Inter | 47.38 | 74.22 | D79 | No | 10.22 | 25.22 | |
| D81 | Inter | 0.4238 | 52.22 | R34 | No | 10.00 | 25.90 | |
| D46 | Inter | 34.38 | 52.22 | D80 | No | 4.22 | 5.55 | |
| R40 | Inter | 30.70 | 67.10 | A19 | No | 0.20 | 2.60 | |
| C27 | Inter | 28.00 | 54.40 | A18 | No | 0 | 4.00 | |
| R39 | Inter | 23.70 | 53.60 | |||||
| R35 | Inter | 22.50 | 52.30 | |||||
| A3303 | D80 | High | 86.40 | 97.40 | B23 | Low | 21.26 | 34.07 |
| D76 | High | 75.40 | 94.20 | B21 | Low | 20.36 | 46.43 | |
| R34 | High | 72.50 | 91.00 | R38 | Low | 18.79 | 42.61 | |
| D77 | High | 64.20 | 81.80 | D53 | Low | 14.94 | 35.87 | |
| R43 | High | 60.81 | 65.75 | D48 | Low | 13.39 | 43.28 | |
| D82 | High | 49.40 | 75.90 | C46 | Low | 10.90 | 42.80 | |
| B34 | Inter | 41.26 | 54.29 | A18 | No | 8.90 | 11.15 | |
| D79 | Inter | 33.10 | 62.70 | B35 | Low | 8.10 | 41.40 | |
| D81 | Inter | 16.00 | 74.00 | B20 | No | 7.10 | 14.74 | |
| C47 | Inter | 9.90 | 60.20 | A12 | No | 6.65 | 0.00 | |
| R41 | Inter | 8.00 | 51.15 | D78 | No | 3.30 | 20.30 | |
| A16 | Low | 42.61 | 46.43 | C45 | No | 0.00 | 29.10 | |
| A0203 | D30 | High | 82.80 | 91.80 | B16 | Low | 38.10 | 38.00 |
| R24 | High | 61.30 | 78.80 | D17 | Low | 21.83 | 43.31 | |
| B17 | High | 57.00 | 70.50 | C3 | No | 11.44 | 28.39 | |
| B15 | High | 50 | 54.00 | B6 | Low | 6.43 | 46.41 | |
| D5 | High | 70.87 | 83.76 | R6 | No | 5.84 | 8.10 | |
| R5 | High | 60.37 | 81.49 | A4 | No | 4.64 | 8.94 | |
| R9 | High | 59.30 | 81.61 | A5 | No | 5.24 | 11.09 | |
| D2 | High | 53.45 | 55.36 | D81 | No | 4.64 | 6.79 | |
| B2 | High | 51.90 | 68.84 | D78 | No | 3.93 | 3.21 | |
| D33 | Inter | 42.30 | 81.20 | D31 | No | 0 | 14.80 | |
| B1 | Inter | 37.82 | 57.74 | A10 | No | 0 | 0 | |
| R14 | Inter | 37.10 | 65.74 | D32 | No | 0 | 0 | |
| D13 | Inter | 25.29 | 55.48 | |||||
| C17 | Inter | 21.70 | 51.30 | |||||
| C1 | Inter | 20.39 | 54.54 | |||||
| A0206 | D26 | High | 52.30 | 68.10 | C10 | Low | 17.08 | 31.68 |
| R23 | Inter | 39.30 | 50.10 | D12 | No | 17.08 | 29.07 | |
| B3 | Inter | 42.63 | 57.11 | A1 | No | 16.30 | 16.95 | |
| D2 | Inter | 41.72 | 63.49 | C1 | No | 15.91 | 21.77 | |
| B1 | Inter | 41.20 | 60.37 | A6 | No | 15.51 | 13.30 | |
| B2 | Inter | 37.29 | 54.89 | R6 | No | 14.73 | 18.64 | |
| D33 | Inter | 35.72 | 68.19 | C16 | No | 12.65 | 13.69 | |
| R9 | Inter | 30.12 | 73.53 | C3 | No | 12.65 | 13.30 | |
| C12 | Low | 19.43 | 36.25 | D42 | No | 9.26 | 12.78 | |
| B4 | No | 18.77 | 14.34 | D78 | No | 8.47 | 8.34 | |
| B11 | Low | 18.30 | 43.40 | A9 | No | 0 | 10.20 | |
| B12 | Low | 17.00 | 32.60 | |||||
| A2402 | B30 | High | 88.65 | 91.49 | B28 | No | 18.00 | 28.20 |
| R47 | High | 88.50 | 88.70 | A22 | No | 10.70 | 29.30 | |
| B26 | High | 83.60 | 82.60 | D52 | No | 6.25 | 24.78 | |
| B31 | High | 81.10 | 86.30 | A1 | No | 5.60 | 7.20 | |
| D55 | High | 73.07 | 78.50 | A20 | No | 5.30 | 21.30 | |
| B29 | High | 70.10 | 74.90 | C35 | No | 2.80 | 10.10 | |
| D53 | High | 59.85 | 62.21 | A23 | No | 1.20 | 1.20 | |
| R48 | Inter | 40.10 | 51.00 | A19 | No | 0.00 | 0.00 | |
| D62 | Inter | 37.53 | 75.19 | A21 | No | 0.00 | 0.00 | |
| D64 | Inter | 35.05 | 69.41 | D79 | No | 0.00 | 0.00 | |
| D56 | Low | 30.21 | 45.80 | |||||
| A0207 | A7 | High | 68.52 | 69.58 | R6 | Low | 35.22 | 48.64 |
| B2 | High | 63.58 | 64.64 | D72 | Low | 32.87 | 41.69 | |
| R17 | High | 57.11 | 62.75 | D80 | Low | 20.64 | 47.93 | |
| B6 | High | 56.40 | 60.87 | D79 | No | 18.75 | 29.58 | |
| A6 | High | 54.99 | 62.05 | D17 | No | 16.40 | 21.11 | |
| B3 | High | 54.99 | 63.34 | D5 | Low | 11.46 | 44.64 | |
| A1 | Inter | 45.22 | 50.16 | B10 | No | 2.40 | 0.00 | |
| D6 | Low | 46.40 | 48.05 | D12 | No | 0.00 | 0.00 | |
| A4 | Low | 36.40 | 40.40 | |||||
| A3001 | D65 | High | 75.62 | 79.92 | D72 | Inter | 44.70 | 62.45 |
| D71 | High | 72.12 | 65.13 | R34 | Inter | 31.53 | 54.11 | |
| B40 | High | 63.52 | 72.12 | R40 | Low | 38.25 | 29.92 | |
| B41 | High | 60.30 | 60.30 | A26 | Low | 37.18 | 18.90 | |
| B36 | High | 60.03 | 73.20 | D40 | Low | 36.91 | 42.55 | |
| B37 | High | 54.11 | 60.03 | A25 | Low | 20.51 | 33.15 | |
| B38 | Inter | 49.54 | 61.91 | A18 | Low | 15.94 | 35.83 | |
| R39 | Inter | 46.05 | 55.46 |
Binding affinity of the epitope peptide with indicated HLA-A allotype was assessed by IC50 value, which is the concentration of unlabeled competitor peptide required to inhibit the binding of fluorescently labeled reference peptide by 50%. IC50 < 5 μM (5 μM inhibition >50%) means high binding affinity; 5 μM < IC50 < 15 μM (5 μM inhibition < 50% but 15 μM inhibition > 50%) means intermediate binding affinity; IC50 > 15 μM means low or no binding affinity (5 μM inhibition 20–50% or 15 μM inhibition 30–50% means low binding affinity and 5 μM inhibition < 20% or 15 μM inhibition < 30% means no binding affinity)