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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

From: Sequence-based in silico analysis of well studied Hepatitis C Virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds

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         
  VYLLPRRGP 1, 2, 4, 5, 6 0.0% 0.0% 18.0% 0.0% 0.0% 16.0% 48.0% 18.0%
  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         
  LVLNPSVAA 1, 2, 3, 4, 5, 6 37.0% 54.0% 36.0% 47.0% 28.0% 17.0% 34.0% 39.0%
  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         
  LPGNPAVAS 2,3, 5, 6 0.0% 2.0% 0.0% 4.0% 0.0% 0.0% 9.0% 0.0%
  LPGNPAIAS 1, 4 0.0% 0.7% 15.0% 4.0% 0.0% 2.4% 0.0% 7.0%
  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 ,         
  LFNILGGWV 1, 4, 5 0.0% 0.0% 16.0% 0.0% 24.0% 0.0% 16.0% 28.0%
  FNILGGWVA 1, 4, 5 47.0% 47.0% 0.0% 2.0% 16.0% 28.0% 16.0% 31.0%
  ILGGWVASQ 4, 5 0.0% 0.0% 28.0% 0.0% 0.0% 2.4% 8.0% 0.0%
  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         
  VFPDLGVRV 1 0.0% 0.0% 34.0% 0.0% 0.0% 0.0% 0.0% 0.0%
  VYPDLGVRV 3, 5 0.0% 0.0% 35.0% 0.0% 14.0% 0.0% 0.0% 19.0%
  IVYPDLGVR 3, 5 0.0% 0.0% 28.0% 0.0% 0.0% 0.0% 7.0% 0.0%
  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         
  LAPEARQAI 1b 0.0% 0.0% 8.0% 0.0% 11.0% 0.0% 4.5% 11.0%
  LDPQARVAI 5 0.0% 0.0% 8.0% 0.0% 0.0% 0.0% 0.0% 0.0%
  LQPEARAAI 5var 0.0% 0.0% 22.0% 0.0% 12.0% 1.0% 22.0% 26.0%