Table 2 HLA Class II-associated HCV variations for genotypes 1A and 3A.

From: Evidence of CD4+ T cell-mediated immune pressure on the Hepatitis C virus genome

GT

Protein

Residue

HLA-DRB1*

Consensus

OR

p-value

1A

E2

524#

3:01

A

4.5

0.001

610

15:01

D

0.25

0.005

641^

3:01

E

0.15

0.005

NS2

923

11:04

A

29

<0.001

939

13:02

I

9.4

0.006

958

10:01

D

28

0.001

975

13:01

V

4.9

0.007

NS3

1044^

14:01

I

11

0.003

1115^

15:01

Q

10

0.007

1266^

11:01

A

13

0.009

1397#

3:01

K

13

0.002

1495

3:01

K

4.4

0.005

1636^

13:02

T

13

0.001

NS4B

1964^

4:01

I

4.4

0.005

NS5A

1980^

11:01

I

18

0.007

1984

3:01

I

16

0.003

2020

4:04

R

43

0.004

NS5B

2609^

4:01

S

6.9

0.002

2674^

13:01

K

2.3

0.002

2852

3:01

V

13

0.005

3A

E2

480

15:01

P

0.038

0.001

499

4:04

P

35

0.001

554

3:01

T

0.15

0.007

574

13:01

G

18

0.008

614

15:01

M

4

0.003

628

11:01

V

7.9

0.002

NS2

893

3:01

I

15

0.002

906

4:04

I

15

0.002

NS3

1278

1:01

I

11

0.007

1416#

15:01

A

14

0.001

1607^

15:01

T

3.1

0.01

1646#

3:01

M

8.4

0.004

NS4B

1740

3:01

T

6.9

0.006

NS5A

2283

1:01

P

12

0.006

2377

15:01

G

0.1

0.002

NS5B

2605

13:02

E

0.14

0.006

2753

13:01

R

6.2

0.003

2757

13:01

R

6.1

0.008

  1. The association is given as the amino acid residue within the polyprotein and the HLA restriction. Overall N = 215 for genotype 1A and N = 136 for genotype 3A. Breakdown of HCV sequence numbers for each protein is shown in Supplementary Table 4. ^Indicates adaptations that fall within published epitopes for genotype 1 and with the same HLA restriction (http://www.immuneepitope.org). #HLA class I-associated variation at same site likely due to LD between HLA class I and II alleles known to form haplotypes. GT = genotype, OR = odds ratio.
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