TABLE 2.
Binding affinities of predicted SARS-CoV-2 pp1a peptides to HLA-A*02:01
| Peptide namea | Sequence | BL50b | Namea | Sequence | BL50b |
|---|---|---|---|---|---|
| High binders | |||||
| pp1a-84 | VMVELVAEL | 6.8 ± 0.3 | pp1a-103 | TLGVLVPHV | 1.3 ± 0.2 |
| pp1a-214 | TLSEQLDFI | 2.0 ± 0.2 | pp1a-445 | GLNDNLLEI | 6.0 ± 0.2 |
| pp1a-597 | VMAYITGGV | 9.5 ± 0.9 | pp1a-619 | TVYEKLKPV | 5.6 ± 0.7 |
| pp1a-641 | FLRDGWEIV | 0.9 ± 0.1 | pp1a-1675 | YLATALLTL | 8.4 ± 0.2 |
| pp1a-2270 | YLNSTNVTI | 8.9 ± 0.3 | pp1a-2569 | ILLLDQALV | 9.6 ± 1.5 |
| pp1a-2785 | AIFYLITPV | 5.1 ± 1.6 | pp1a-2968 | YLEGSVRVV | 7.5 ± 0.1 |
| pp1a-3013 | SLPGVFCGV | 3.1 ± 0.2 | pp1a-3115 | YLTNDVSFL | 4.8 ± 0.3 |
| pp1a-3122 | FLAHIQWMV | 6.9 ± 0.4 | pp1a-3128 | WMVMFTPLV | 9.8 ± 1.1 |
| pp1a-3587 | ILTSLLVLV | 8.3 ± 0.9 | pp1a-3710 | TLMNVLTLV | 2.0 ± 0.4 |
| pp1a-3732 | SMWALIISV | 8.9 ± 0.4 | pp1a-4094 | ALWEIQQVV | 6.4 ± 0.4 |
| Medium binders | |||||
| pp1a-15 | QLSLPVLQV | 79.4 ± 4.4 | pp1a-38 | VLSEARQHL | 76.8 ± 6.8 |
| pp1a-52 | GLVEVEKGV | 14.5 ± 4.9 | pp1a-106 | VLVPHVGEI | 76.0 ± 2.0 |
| pp1a-468 | KLNEEIAII | 56.2 ± 4.8 | pp1a-600 | YITGGVVQL | 48.5 ± 7.9 |
| pp1a-685 | FLALCADSI | 10.2 ± 0.5 | pp1a-702 | ALNLGETFV | 40.7 ± 2.8 |
| pp1a-1109 | NLAKHCLHV | 38.5 ± 8.2 | pp1a-1114 | CLHVVGPNV | 62.9 ± 2.3 |
| pp1a-1161 | SLRVCVDTV | 85.7 ± 1.9 | pp1a-1312 | MLAKALRKV | 95.2 ± 0.7 |
| pp1a-2168 | YMPYFFTLL | 99.0 ± 2.4 | pp1a-2332 | ILFTRFFYV | 96.5 ± 14.0 |
| pp1a-2563 | QLMCQPILL | 11.1 ± 1.8 | pp1a-2884 | FLPRVFSAV | 29.3 ± 6.5 |
| pp1a-3047 | IVAGGIVAI | 50.5 ± 2.5 | pp1a-3083 | LLFLMSFTV | 39.4 ± 0.9 |
| pp1a-3183 | FLLNKEMYL | 12.9 ± 6.8 | pp1a-3403 | FLNGSCGSV | 18.7 ± 3.2 |
| pp1a-3467 | VLAWLYAAV | 45.0 ± 10.8 | pp1a-3475 | VINGDRWFL | 85.0 ± 5.4 |
| pp1a-3482 | FLNRFTTTL | 79.0 ± 9.6 | pp1a-3583 | LLLTILTSL | 63.8 ± 3.1 |
| pp1a-3639 | FLLPSLATV | 15.0 ± 4.4 | pp1a-3662 | RIMTWLDMV | 76.5 ± 7.1 |
| pp1a-3753 | FLARGIVFM | 71.2 ± 12.9 | pp1a-3798 | CLLNRYFRL | 81.6 ± 20.2 |
| pp1a-3807 | TLGVYDYLV | 61.7 ± 8.7 | pp1a-3871 | VLLSVLQQL | 44.9 ± 6.0 |
| pp1a-3886 | KLWAQCVQL | 27.2 ± 9.4 | pp1a-4183 | ALLSDLQDL | 42.4 ± 6.1 |
| pp1a-4266 | VLSFCAFAV | 20.1 ± 6.1 | pp1a-4283 | YLASGGQPI | 39.8 ± 6.2 |
| Low binders | |||||
| pp1a-572 | GISQYSLRL | ND | pp1a-589 | DLATNNLVV | ND |
| pp1a-692 | SIIIGGAKL | ND | pp1a-881 | KTLQPVSEL | 161.7 ± 28.3 |
| pp1a-1143 | VLLAPLLSA | ND | pp1a-1148 | LLSAGIFGA | ND |
| pp1a-1214 | FITESKPSV | 122.1 ± 31.7 | pp1a-1367 | ILGTVSWNL | 123.2 ± 11.3 |
| pp1a-1387 | KLMPVCVET | 174.2 ± 33.5 | pp1a-1433 | SLINTLNDL | 123.4 ± 11.0 |
| pp1a-1642 | FLGRYMSAL | 124.1 ± 1.9 | pp1a-1962 | DLNGDVVAI | ND |
| pp1a-2076 | ILKPANNSL | ND | pp1a-2226 | LINIIIWFL | ND |
| pp1a-2228 | NIIIWFLLL | ND | pp1a-2230 | IIWFLLLSV | 176.7 ± 6.3 |
| pp1a-2235 | LLSVCLGSL | ND | pp1a-2242 | SLIYSTAAL | 134.0 ± 7.6 |
| pp1a-2249 | ALGVLMSNL | ND | pp1a-2348 | QLFFSYFAV | 146.4 ± 19.7 |
| pp1a-2363 | WLMWLIINL | 102.7 ± 6.4 | pp1a-2364 | LMWLIINLV | 159.0 ± 42.8 |
| pp1a-2901 | KLIEYTDFA | 126.0 ± 2.5 | pp1a-3344 | SMQNCVLKL | 104.5 ± 2.2 |
| pp1a-3827 | GLLPPKNSI | ND | pp1a-3839 | KLNIKLLGV | 213.5 ± 85.7 |
| pp1a-3917 | VLLSMQGAV | 112.3 ± 7.2 | pp1a-4032 | MLFTMLRKL | 165.8 ± 21.7 |
a
The number within each peptide name shows the first amino acid position in the SARS-CoV-2 pp1a.
b
Data of peptide binding assays are shown as BL50, indicating a concentration (µM) of each peptide that yields the 50% relative binding, as described in the Materials and Methods. Experiments were performed in triplicate and repeated twice with similar results. Data are given as mean values ± SD. High binders, BL50 < 10 µM; medium binders, 10 µM ≤ BL50 < 100 µM; low binders, BL50 ≥ 100 µM or ND (not detected).