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Table 3 Predicted HLA I epitopes HCV Proteins of Pakistani origin and their conservancy in Genotype 1, 2 and 3 worldwide

From: Promiscuous prediction and conservancy analysis of CTL binding epitopes of HCV 3a viral proteome from Punjab Pakistan: an In Silico Approach

Epitope start Position

Predicted T-cell epitopes

HLA alleles

HCV genotype 1

HCV Genotype 2

HCV Genotype 3

Capsid

     

38

R RGPRLGVR

9

RRGPRLGVR

RRGPRLGVR

RRGPRLGVR

35

V LPRRGPRL

25

  

VLPRRGPRL

Core

     

55

P GCSFSIFL

8

PGCSFSIFL

PGCSFSIFL

PGCSFSIFL *

41

R ALEDGINF

20

 

RV LEDGV NF **

RALEDGINF *

7

V IDTLTCGF

15

VIDTLTCGF

VIDTI TCGF *

VIDTLTCGF *

35

A LAHGVRAL

24

ALAHGVRV L

ALAHGVRVL

ALAHGVRAL *

24

L VGAPVGGV

18

LVGAPL GGA *

 

LVGAPVGGV *

26

G APVGGVAR

9

GAPL GGA AR *

GAPL GGVAR

GAPVGGVAR *

E1

     

135

S PAVGMVVA

14

  

SPAM GMVVA *

86

G DVCGAVFL

19

GDL CGS VFLD

GDVCGAVMI

GDM CGAVFL *

144

H ILRLPQTL

22

  

HILRLPQTL *

156

I AGAHWGVL

27

IAGAHWGVL

 

IAGAHWGI L

64

A SIRGHVDL

25

  

ASIRS HVDLD

E2

     

285

P LLHSTTEL

11

 

PLLHSTTEWD

PLLHSTTEL

305

A LSTGLIHL

25

ALT TGLIHL

 

ALSTGLIHL

227

C SFTPMPA L

20

CSFTTL PALD *

 

CSFTPMPAL

71

Q QLQAHHFL

27

   

157

C GLLVVGGL

28

   

212

R GHIQPVRL

24

   

6

T AARGGQGL

25

   

157

C GLLVVGGL

28

   

NS2

     

172

V ITWGADTA

6

  

VITWGADTA *

75

F DIAKLLIA

12

FDIT KLLL AD

FDIT KLLL AD *

FDIT KLLIAD

70

Y PSL VFDIA

15

  

YPSLI FDITDD

57

G SRDGVILL

21

GG RDA VILLD **

GG RDA VILLD *

GSRDGVILL

60

D GVILLTSL

26

  

DGVILLTSL *

148

W AAAGLKDL

27

 

WAAS GLR DLDD**

WAAAGLKDL *

50

V PPLLARGS

11

  

VPPLLARGS *

46

L QVWVPPLL

28

LH VWVPPLNDD

LH VWVPPLNDD *

LQVWVPPLL *

117

V TGGKYFQM

16

  

VV GGKYFQMD *

65

L TSLLYPSL

23

  

LTSLLYPSL

6

T LGAGILVL

48

  

TLGAGV LVL *

73

L VFDIAKLL

31

LVFDIT KLLD

LVFDIT KLLD *

LI FDIT KLLD

145

M QHW AAAGL

26

  

MQHWAAAGL

178

D TAACGDIL

21

DTAACGDII

DTAACGDIID *

DTAACGDIL

NS3

     

119

G HVAGIFRA

8

GHAV GIFRA *

GHVV GL FRA *

 

27

Y HGAGSRTL

14

YHGAGT RTI

YHGAGNK TLD

 

128

A VCTRGVAK

8

AVCTRGVAK

AVCTRGVAK *

 

57

P APPGAKSL

11

PAPQ GAR SLDD *

PS PPGT KSLDD

 

98

L SPRPLACL

25

 

LSPRPLST LD

 

95

A SLL SPRPL

24

   

130

C TRGVAKAL

20

CTRGVAKAV

  

7

L STATQTFL

24

   

NS4a

     

3

W VL LGGVLA

11

WVLV GGVLA

WVLV GGVLA

WVLLGGVLA

23

V VIVGHIEL

21

VVIVGR II LDD

VVIVGR IV LDD

VVIVGHIEL

10

L AALAAYCL

24

LAALAAYCL *

LAALAAYCL

LAALAAYCL

5

L LGGVL AAL

27

LV GGVLAAL

LV GGVLAAL

LLGGVLAAL

NS4b

     

96

P QSSSAFVV

6

  

PQSSSAFVV

40

N FVSGIQ YL

30

NFI SGIQYL

NFI SGIQYL

NFVSGIQYL

81

F FNIL GGWV

13

  

FFNILGGWV

46

Q YLAGLSTL

17

QYLAGLSTL

QYLAGLSTL

QYLAGLSTL

102

FV VSGLAGA

9

 

FVGA GLAGAD

FVVSGLAGA

54

L PG NPAVAS

14

LPGNPAI AS

LPGNPAI AS

LPGNPAVAS

161

S PGALVVGV

14

SPGALVVGV

SPGALVVGV

SPGALVVGV

141

I MGGELPNA

7

  

IMGGEF PT AD *

164

A LVVGVICA

11

ALVVGVV CA

ALVVGVV CA

ALVVGVICA

117

L GRVLLDIL

22

LGK VLV DILD*

LGK VLV DILD

LGK VLLDILD *

59

A VASLMAFA

9

AI ASLMAFTD

AI ASLMAFTD

AVASLMAFTD

152

V VNLLPAIL

15

   

113

G IGLGRVLL

24

  

GIGLGK VLLD *

56

G NPAVASLM

12

GNPAI ASLM

GNPAI ASLM

GNPAVASLM

52

S TLPGNPAV

21

STLPGNPAI

STLPGNPAV

STLPGNPAV

85

L GGWVATHL

26

LGGWVAAQ LDD

LGGWVAAQ LDD

LGGWVATHL

145

E LPNAEDVV

11

   

99

S SAFVVSGL

22

  

SSAFVVSGL

NS5a_1a

     

33

H VKNGSMRL

16

HVKNGSMRI *

HVKNGSMRI **

HVKNGSMRL

NS5a_1b

     

49

V PAAEFFTE

6

VPAP EFFTE *

VPAP EFFTE **

VPAAEFFTE

79

T FVVGLNSY

10

TFQ VGLNQ YD *

TFT VGLNSFD *

TFT VGLNSYD *

76

D EITFVVGL

19

DEV TFQ VGLD *

DEV TFT VGLD*

DEITFM VGL *

  1. Bold amino acid residues in T-cell Epitope column indicates the anchor residues
  2. Bold individual amino acid residues in HCV Genotype 1, 2 and 3 columns indicated the variation in peptide in comparison to the predicted epitope
  3. *Indicates that one of the protein sequence selected for epitope conservancy either does not respond or have conservancy lower then 70%
  4. ** Indicates that only one of the protein sequence from selected sequences respond to epitope conservancy
  5. D Indicates that amino acid residue in case of single/double variation diverted their group compared to primary epitope using pI value
  6. DD Indicates that both amino acid residues in case of double variation diverted their group compared to primary epitope using pI value