Selection of Conserved Epitopes from Hepatitis C Virus for Pan-Populational Stimulation of T-Cell Responses

Table 2

Selected conserved HCV-specific T-cell epitopes with predicted HLA I binding profiles.

Epitope	Ct	Region	N	3D	3D-N	PPC	HLA I binding profile
KTSERSQPR	G	CAPSID	71	NA	—	32.2%	A0301 A1101 A3101 A3301 A6801
LIFCHSKKK	C	HELICc	1391	2F55∣A	365–373	32.2%	A0301 A1101 A3101 A3301 A6801
LLPRRGPRL	G	CAPSID	36	1XCQ∣P	—	28.2%	A0201 A0203 A0205 A0206 C0102
LPGCSFSIF	L	CORE	169	NA	—	27.8%	B0702 B1502 B1508 B3501 B5301 B5401
DPRRRSRNL	G	CAPSID/CORE	101	NA	—	26.9%	B0702 B0801 B5101 B5102 B5103 B5301 B5401
GFADLMGYI	P	CORE	129	NA	—	6.3%	A0202 A0203 A0205 A6802 B3801
NLPGCSFSI	F	CORE	168	NA	—	5.9%	A0205 C0102
SFSIFLLAL	L	CORE	173	NA	—	5.5%	A2402
TYSTYGKFL	A	DEXDC	1292	2F55∣A	266–274	5.5%	A2402
ITYSTYGKF	L	DEXDC	1291	2F55∣A	265–273	2.7%	B1516 B1517 B5702 B5801
HSKKKCDEL	A	HELICc	1395	2F55∣A	369–377	2.5%	B0801
YLLPRRGPR	L	CAPSID	35	1XCQ∣P	—	1.4%	A3301 A6601 A6801
GQIVGGVYL	L	CAPSID	28	1XCQ∣P	—	0.4%	A0206 A0214 B1510 B4002
TIMAKNEVF	C	RNADP	2587	2BRK∣A	137–145	0	B1513 B5702
GPRLGVRAT	R	CAPSID	61	NA	—	0
RLGVRATRK	T	CAPSID	63	NA	—	0
STGLIHLHQ	N	NS1	686	NA	—	0

Epitope: amino acid sequence of the epitope; Ct: residue that flanks the C-terminal end of the epitope; Region: protein/domain in HCV polyprotein bearing the epitope; N: position in HCV polyprotein of the epitope N-terminal residue; 3D: PDB code with 3D structure of protein encompassing the epitope; 3D-N: location of the epitope in the 3D structure; PPC: population protection coverage; HLA I binding profile: HLA I molecules predicted to present the epitope. All epitope residues and c-terminal flanking residues have 𝐻≤0.5. PPC values equal to the lower value computed with the gene frequencies corresponding to 5 ethnic populations [33]. PDB 1XCQ∣P corresponds to a peptide from HCV capsid bound to an antibody Fab; hence we do not show the location of the epitope in the 3D structure. NA: PDB not available.