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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