Table 5 Binding affinity scores (as percentages) of Class II published epitopes and their variants were determined by the ProPred prediction program to common DRB1* alleles prevalent in the South African population
Epitope: | Sequence | HCV Genotype specificity | DRB1*0101 | *0102 | *0301 | *0401 | *0701 | *1101 | *1301 | *1501 |
|---|---|---|---|---|---|---|---|---|---|---|
Core 17–42 | RRPQDVKFPGGGQIVGGVYLLPRRGP | 1, 2, 5 & 3 var & 6 var |  |  |  |  |  |  |  |  |
| Â | VYLLPRRGP | 1, 2, 4, 5, 6 | 0.0% | 0.0% | 18.0% | 0.0% | 0.0% | 16.0% | 48.0% | 18.0% |
| Â | VGGVYLLPR | 1, 2, 4, 5, 6 | 0.0% | 0.0% | 17.0% | 0.0% | 9.0% | 9.0% | 10.0% | 20.0% |
NS3 1248–1261 | GYKVLVLNPSVAAT | 1, 2, 4, 5, 6 |  |  |  |  |  |  |  |  |
| Â | LVLNPSVAA | 1, 2, 3, 4, 5, 6 | 37.0% | 54.0% | 36.0% | 47.0% | 28.0% | 17.0% | 34.0% | 39.0% |
| Â | YKVLVLNPS | 1, 2, 4, 5, 6 | 5.0% | 0.0% | 0.0% | 30.0% | 9.0% | 31.0% | 27.0% | 17.0% |
NS4B 1781–1800 | LPGNPAIASLMAFTAAVTSP | 1a, 4 var |  |  |  |  |  |  |  |  |
| Â | LPGNPAVAS | 2,3, 5, 6 | 0.0% | 2.0% | 0.0% | 4.0% | 0.0% | 0.0% | 9.0% | 0.0% |
| Â | LPGNPAIAS | 1, 4 | 0.0% | 0.7% | 15.0% | 4.0% | 0.0% | 2.4% | 0.0% | 7.0% |
| Â | IASLMAFTA | 1 | 7.0% | 23.0% | 0.0% | 0.0% | 4.0% | 0.0% | 14.0% | 21.0% |
NS4B 1801–1820 | LTTSQTLLFNILGGWVAAQL | 1a, 1b var , |  |  |  |  |  |  |  |  |
| Â | LFNILGGWV | 1, 4, 5 | 0.0% | 0.0% | 16.0% | 0.0% | 24.0% | 0.0% | 16.0% | 28.0% |
| Â | FNILGGWVA | 1, 4, 5 | 47.0% | 47.0% | 0.0% | 2.0% | 16.0% | 28.0% | 16.0% | 31.0% |
| Â | ILGGWVASQ | 4, 5 | 0.0% | 0.0% | 28.0% | 0.0% | 0.0% | 2.4% | 8.0% | 0.0% |
| Â | LGGWVASQI | 4, 5 | 0.0% | 0.0% | 0.0% | 0.0% | 21.0% | 0.0% | 13.0% | 21.0% |
NS5B 2571–2590 | KGGRKPARLIVFPDLGVRVC | 1, 2 var & 6 var |  |  |  |  |  |  |  |  |
| Â | VFPDLGVRV | 1 | 0.0% | 0.0% | 34.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% |
| Â | VYPDLGVRV | 3, 5 | 0.0% | 0.0% | 35.0% | 0.0% | 14.0% | 0.0% | 0.0% | 19.0% |
| Â | IVYPDLGVR | 3, 5 | 0.0% | 0.0% | 28.0% | 0.0% | 0.0% | 0.0% | 7.0% | 0.0% |
| Â | LIVYPDLGV | 3, 5 | 0.0% | 0.0% | 0.0% | 0.0% | 12.0% | 0.0% | 3.0% | 60.0% |
NS5B 2661–2680 | QCCDLDPQARVAIKSLTERL | 5 var |  |  |  |  |  |  |  |  |
| Â | LAPEARQAI | 1b | 0.0% | 0.0% | 8.0% | 0.0% | 11.0% | 0.0% | 4.5% | 11.0% |
| Â | LDPQARVAI | 5 | 0.0% | 0.0% | 8.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% |
| Â | LQPEARAAI | 5var | 0.0% | 0.0% | 22.0% | 0.0% | 12.0% | 1.0% | 22.0% | 26.0% |