Table 2.
Best HLA-II candidate epitopes for South America in SARS-CoV-2 proteins.
| Best HLA-II candidate epitopes for South America | N° of alleles with WAF ≥ 0.05 covered by country | Coverage score | References | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Protein | Start | End | Peptide | Region | Experimental | IEDB ID | ARG | BOL | BRA | CHI | COL | ECU | PAR | PER | VEN | ||
| S | 1013 | 1027 | IRAAEIRASANLAAT | CH | LTM | 100428 | 5 | 5 | 5 | 4 | 5 | 7 | 4 | 7 | 4 | 8.148 | New |
| 1014 | 1028 | RAAEIRASANLAATK | 100428 | 6 | 5 | 7 | 4 | 5 | 7 | 5 | 7 | 5 | 9.000 | ||||
| 1152 | 1166 | LDKYFKNHTSPDVDL | HR2 | ML | 35205 | 4 | 4 | 4 | 3 | 4 | 5 | 5 | 6 | 3 | 6.760 | Ahmed et al. (66) | |
| 1153 | 1167 | DKYFKNHTSPDVDLG | 9006 | 4 | 4 | 4 | 3 | 4 | 5 | 5 | 6 | 3 | 6.760 | ||||
| S | 61 | 75 | NVTWFHAIHVSGTNG | NTD | - | - | 4 | 4 | 4 | 3 | 4 | 5 | 4 | 4 | 4 | 6.474 | New |
| 114 | 128 | TQSLLIVNNEATNVVI | 4 | 4 | 5 | 3 | 4 | 6 | 5 | 6 | 3 | 7.045 | |||||
| 115 | 129 | QSLLIVNNATNVVIK | 5 | 4 | 6 | 4 | 5 | 5 | 5 | 5 | 4 | 7.719 | |||||
| 116 | 130 | SLLIVNNATNVVIKV | 4 | 3 | 5 | 3 | 4 | 4 | 5 | 4 | 4 | 6.474 | |||||
| 206 | 220 | KHTPINLVRDLPQGF | 4 | 3 | 4 | 3 | 4 | 5 | 3 | 5 | 3 | 6.017 | |||||
| 207 | 221 | HTPINLVRDLPQGFS | 5 | 4 | 5 | 3 | 4 | 6 | 5 | 6 | 4 | 7.412 | |||||
| 208 | 222 | TPINLVRDLPQGFSA | 4 | 4 | 3 | 3 | 4 | 5 | 2 | 6 | 3 | 6.017 | |||||
| 216 | 230 | LPQGFSALEPLVDLP | 3 | 4 | 3 | 3 | 3 | 5 | 5 | 6 | 4 | 6.450 | |||||
| 217 | 231 | PQGFSALEPLVDLPI | 3 | 4 | 3 | 3 | 3 | 5 | 5 | 6 | 4 | 6.450 | |||||
| 308 | 322 | VEKGIYQTSNFRVQP | RBD | - | - | 4 | 5 | 5 | 3 | 4 | 7 | 5 | 7 | 3 | 7.531 | ||
| 309 | 323 | EKGIYQTSNFRVQPT | 5 | 5 | 6 | 4 | 5 | 7 | 5 | 7 | 4 | 8.490 | |||||
| 313 | 327 | YQTSNFRVQPTESIV | 3 | 5 | 3 | 3 | 3 | 6 | 5 | 6 | 3 | 6.593 | |||||
| 314 | 328 | QTSNFRVQPTESIVR | 6 | 5 | 7 | 4 | 5 | 6 | 5 | 6 | 5 | 8.714 | |||||
| 315 | 329 | TSNFRVQPTESIVRF | 6 | 5 | 7 | 4 | 5 | 7 | 5 | 7 | 5 | 9.000 | |||||
| 316 | 330 | SNFRVQPTESIVRFP | 3 | 4 | 5 | 3 | 3 | 5 | 5 | 5 | 4 | 6.593 | |||||
| 430 | 444 | TGCVIAWNSNNLDSK | 4 | 4 | 6 | 3 | 4 | 6 | 5 | 6 | 4 | 7.388 | |||||
| 689 | 703 | SQSIIAYTMSLGAEN | - | - | - | 3 | 5 | 3 | 3 | 4 | 7 | 4 | 7 | 3 | 6.879 | ||
| 690 | 704 | QSIIAYTMSLGAENS | 4 | 5 | 4 | 3 | 4 | 7 | 5 | 7 | 3 | 7.388 | |||||
| 785 | 799 | VKQIYKTPPIKDFGG | 3 | 5 | 2 | 3 | 3 | 5 | 4 | 6 | 3 | 6.107 | |||||
| 801 | 815 | NFSQILPDPSKPSKR | FP | - | - | 5 | 4 | 5 | 3 | 4 | 6 | 4 | 6 | 4 | 7.212 | ||
| 802 | 816 | FSQILPDPSKPSKRS | 5 | 4 | 5 | 3 | 4 | 6 | 5 | 6 | 4 | 7.412 | |||||
| 1059 | 1073 | GVVFLHVTYVPAQEK | BH | - | - | 3 | 5 | 3 | 3 | 3 | 7 | 5 | 7 | 4 | 7.079 | ||
| 1060 | 1074 | VVFLHVTYVPAQEKN | 3 | 4 | 2 | 3 | 3 | 5 | 4 | 6 | 4 | 6.107 | |||||
| 1098 | 1112 | NGTHWFVTQRNFYEP | SD3 | - | - | 4 | 4 | 4 | 3 | 3 | 5 | 5 | 5 | 4 | 6.617 | ||
| 1099 | 1113 | GTHWFVTQRNFYEPQ | 4 | 4 | 4 | 3 | 3 | 6 | 5 | 6 | 4 | 6.902 | |||||
| 1110 | 1124 | YEPQIITTDNTFVSG | 4 | 4 | 4 | 3 | 4 | 5 | 5 | 5 | 4 | 6.817 | |||||
| 1111 | 1125 | EPQIITTDNTFVSGN | 4 | 4 | 6 | 3 | 4 | 6 | 5 | 6 | 4 | 7.388 | |||||
| 1126 | 1140 | CDVVIGIVNNTVYDP | - | - | - | 4 | 3 | 5 | 3 | 4 | 4 | 5 | 4 | 4 | 6.474 | ||
| M | 7 | 21 | TITVEELKKLLEQWN | Virion Surface | - | - | 2 | 2 | 2 | 1 | 1 | 3 | 3 | 3 | 2 | 3.326 | New |
| E | 1 | 15 | MYSFVSEETGTLIVN | Virion Surface | - | - | 0 | 2 | 1 | 1 | 1 | 2 | 0 | 2 | 1 | 1.764 | New |
These candidate epitopes were selected from our prediction based on their scores (rank for NetMHC and IC50 for MHCflurry), Coverage Score (CS), and exposure (for Class-II only). Experimental evidence including the IEDB ID and experiment type (LTM: linearT_MHC, ML: MHC_ligand) is provided when available. Scientific articles already proposing these candidates are mentioned. Underlined residues indicate sites with predicted N-linked glycosylations. Residues in bold represent positive selection pressure sites.