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Table 4 Binding affinity scores of predicted epitopes and their variants to common HLA I allele types prevalent in South Africa

From: Prediction of T-cell epitopes of hepatitis C virus genotype 5a

Gene

Epitope sequencea

Genotype of epitope

HLA I allele typesb

   

HLA-A

HLA-B

HLA-C

   

HLA-A*01:01

HLA-A*02:01

HLA-A*30:01

HLA-A*30:02

HLA-B*07:02

HLA-B*08:01

HLA-B*35:01

HLA-C*04:01

HLA-C*06:02

HLA-C*07:01

HLA-C*07:02

E2

684

ALSTGLIHL#[25–27]

1a, 1b, 3, 4,5a, 6

+

+++

+

+

+

+

+

+

+

+

+

 

ALSTGLLHL

2

+

+++

+

+

+

+

+

+

+

+

+

NS2

1025

LLAPITAYA

1a, 3, 4, 5a

+

+++

+

++

+

+

+

+

+

+

+

 

LLAPITAYT

2

+

+++

+

++

+

+

+

+

+

+

+

NS3

1032

YAQQTRGVL

5a

+

+

+

+

+++

+

+

+

+

+

+

 

YAQQTRGLL

1a, 2

+

+

+

+

++

+

+

+

+

+

+

 

YSQQTRGLL

1b

+

+

+

+

+

+

+

+

+

+

+

 

YAQQTRGLV

6

+

+

+

+

+

+

+

+

+

+

+

1242

AAYAAQGYK

1a, 1b, 4, 5a

+

+

+++

+

+

+

+

+

+

+

+

 

AAYASQGYK

2

+

+

+++

+

+

+

+

+

+

+

+

1264

FGAYMSKAY

5a

+

+

+

+

+

+

+++

+

+

+

+

 

FGAYMSKAH

1a, 1b, 2

+

+

+

+

+

+

+

+

+

+

+

1359

HPNIEEVAL#[28–31]

1a, 1b, 5a

+

+

+

+

++

+

+++

+

+

+

+

 

HSNIEEVAL

2, 3, 4

+

+

+

+

+

+

+

+

+

+

+

 

HPNITETAL

6

+

+

+

+

+++

+

+++

+

+

+

+

1367

LPSEGEIPF

5a

+

+

+

+

++

 

+++

+

+

+

+

 

LGHEGEIPF

2

+

+

+

+

+

+

++

+

+

+

+

 

LGSEGEIPF

3

+

+

+

+

+

+

++

+

+

+

+

 

LPTTGEIPF

4, 6

+

+

+

+

++

 

+++

+

+

+

+

1585

YLVAYQATV#[25, 39]

1a, 1b, 4, 5a, 6

+

+++

+

+

+

+

+

+

+

+

+

 

YLTAYQATV

2, 3

+

+++

+

+

+

+

+

+

+

+

+

NS5A

1927

NHVSPTHYV

1a, 1b, 3, 4,5a, 6

+

+

+

+

+

+

+

+

++

+++

+

 

NHVAPTHYV

2

+

+

+

+

+

+

+

+

+

++

+

2285

LPVWARPGY

5a

+

+

+

+

+

+

+++

+

+

+

+

 

LPIWARPDY

1a, 3, 4, 6

+

+

+

+

+

+

+++

+

+

+

+

 

LPAWARPDY

2

+

+

+

+

+

+

+++

+

+

+

+

NS5B

2696

YRRCRASGV

1a, 1b, 2, 3, 5a

+

+

+

+

+

++

+

+

++

+++

++

2763

MTRYSAPPG

1a, 1b, 2, 3, 4, 5a, 6

+

+

+++

+

+

+

+

+

+

+

+

2889

LSAFSLHSY#[40]

1a, 1b, 5a

+++

+

+

+++

+

+

++

+

+

+

+

 

LSAFTLHSY

3

+++

+

+

+++

+

+

++

+

+

+

+

 

LSAFTLHGY

4

+++

+

+

+++

+

+

+

+

+

+

+

  1. #-indicates that the epitope has been experimentally proven to be a true positive.
  2. a–italics indicates amino acid(s) variation in epitope in comparison to the predicted epitope.
  3. b+++ indicates high binding affinity (<50 IC50nm), ++ indicates medium binding affinity (>50 IC50nm, <500 IC50nm), + indicates poor binding affinity (>500 IC50nm).