Table 1

T cell epitopes in genotype-3a infection

Protein	Amino acid	3a Peptide sequence used in T cell assays	Patient no	Patient viral sequence pre-treatment	HLA	Treatment outcome	Defining CD4:CD8 T cell subsets
Core	27–44	GGQIVGGVYVLPRRGPRL	362	GGQIVGGVYVLPRRGPRL	DRB1 0103, 0701	SVR	NA
	73–90	GRSWAQPGYPWPLYGNEG^*	416	GRSWAQPGYPWPLYGNEG	DRBI 0101, 0701 DQBI 0201, 0501	SVR	NA
	143–158	PVGGVARALAHGVRAL^*	110	PAGGVARALAHGVRAL	DRB1 0801, 1101	SVR	CD4
			331	PVGGVARALAHGVRAL	NA	SVR
			437	PVGGVARALAHGVRAL	DRB1 0103, 0501	SVR
NS3 helicase	1513–1529	RPSGMFDSVVL^* ^†	140	RPSGMFDSVVLCECYDA	A2402, A3002, B0702, B3501	SVR	CD8
			235	RPSGMFDSVVLCECYDA	A0301, A3002, B0702, B3501, C0401, C0702	SVR
			362	RPSGMFDSVVLCECYDA	A2402, B3501, B4402, C0401, C0409	SVR
NS4b	1791–1806	PAVASLMAFTASVTSPL^*	416	PAVASLMAFTASVTSPL	A0101, A0201, B0801, B5701, C0602, C0701 DRB1 0101, 0701	SVR	CD8
	1791–1806	PAVASLMAFTASVTSPL^*	437	NA	A0201, A2601, B3801, B2702, C1203, C0102 DRB1 0103, 0101	SVR	CD8
	1824–1841	THLAGPQSSSAFVVSGLA^*	437	NA	A0201, A2601, B3801, B2702, C1203, C0102 DRB1 0103, 0101	SVR	NA
	1918–1933	EGAVQWMNRLIAFASR^‡	410	EGAVQWMNRLIAFASR	A0101, A3001, B1302, B4402, C0602, C0501 DRB1 0701, DQB1 0201	NR	CD8
NS5a	2029–2046	GVMSTRCPCGASIAGHVK^*	129	GVMSTRCPCGASITGHVK	A1101, A7401, B4403, B38, C04, C0702	REL	CD8
NS5b	2946–2963	GKAKICGLYLFNWAVRTK^*	275	GKAKITGLYLFNWAVRTK	A1101, B0702, B4402, C0501, C0702 DRB1 0401, 0407	SVR	CD8
NS5b	2965–2975	KLTPLPAAGQL^* ^†	450	KLTPLPAAGLL	NA	REL	CD8

Peptide amino acid sequence and patient viral sequence from pre-treatment time point are shown (amino acid differences between these are shown in bold).
CD4:CD8 T cell subset analysis was assessed using PBMC in IFN-γ ELISpot assays following CD8 depletion.
↵* Epitopes where viral sequence is different between genotypes-3a and -1.
↵† Peptides restricted to 11 residues in ELISpot assays based on previously published epitope or the overlapping sequence between two adjacent immunogenic peptides.
↵‡ Epitopes where viral sequence is identical between genotypes-3a and -1a.
IFN, interferon; NA, not available (PCR amplification not possible or insufficient sample); PBMC, peripheral blood mononuclear cells; REL, relapse; SVR, sustained virological response; NR, non-responder.