Table 3. Variant peptides eliciting T... | Rockefeller University Press

Table 3.

Variant peptides eliciting T cell responses

JEV peptide sequence	Subject type	Viruses with identical sequence	Subset	Variant	Virus/BEI peptide location
CSAVPVDW	H	DENV1	CD8	CSSVPVDW	MVEV
MTTEDMLQVW	H		CD8	MTTEDMLRVW	JEV
				MTTEDMLSVW	DENV1
				MTTEDMLTVW	DENV2,3
				MTTEDMLKVW	DENV4
				MTTEDMLEVW	WNV, YFV
				MTTEDMLDVW	TBEV
ALRGLPVRY	H	ZIKV	CD8	ALRGLPIRY	WNV, DENV2,4
NLFVMDEAHFTDPASIEAHFTDPASIAARGYI	H	DENV2,3	CD8	NYNMIIMDEAHFTDPA	DENV1 NS3 p49
				IMDEAHFTDPASIARRG	DENV1 NS3 p50
				NYNLIIMDEAHFTDPASI	DENV2 NS3 p38
				NYNLIIMDEAHFTDPA	DENV3 NS3 p48
				PNYNLIVMDEAHFTD	DENV4 NS3 p49
				LIVMDEAHFTDPSSVAA	DENV4 NS3 p50
				AHFTDPSSVAARGYIST	DENV4 NS3 p51
TMAMTDTTPFGQQRVFK	H	WNV	CD4 + CD8	MVTQIAMTDTTPFGQQR^{^a}	DENV1 NS5 p60
				AMTDTTPFGQQRVFKEK^{^a}	DENV2 NS5 p61
				MVTQMAMTDTTPFGQQR^{^a}	DENV3 NS5 p60
				MVTQLAMTDTTPFGQQR^{^a}	DENV4 NS5 p60
GEAAAIFMT	H	WNV, DENV1,3,4, ZIKV	CD8	MGEAAAIFMTATPPGSV^{^b}	DENV1 NS3 p54, DENV3 NS3 p52
				VEMGEAAAIFMTATPPG^{^b}	DENV4 NS3 p54
TAVLAPTRVVAAEMAEAL	H	WNV	CD8	NVRTLILAPTRVVASEM	DENV1 NS3 p38
				LRTLILAPTRVVAAEM	DENV2 NS3 p30
				TLILAPTRVVAAEMEEA	DENV3 NS3 p38, DENV4 NS3 p39
DVMCHATL	D	WNV, MVEV, SLEV	CD8	DLMCHATF	DENV1–4, ZIKV
				DAMCHATL	YFV
AVHSDLSYWIESRYNDTW	JE		CD4	NLAIHSDLSYWIESRL	WNV NS1 p26
WIESRYNDTWKLERAVF	JE		CD4	RLNDTWKLERAVLGEVK	WNV NS1 p28
				IESEKNETWKLARASFI	DENV NS1 p36
KQSVVALGSQEGGLHQAL	JE		CD4	HATKQSVIALGSQEGALH	WNV E p34
				ALGSQEGALHQALAGAI	WNV E p35
				VVVLGSQEGAMHTALTG	DENV1 E p44
				HAKKQDVVVLGSQEGAMH	DENV2 E p34
				VLGSQEGAMHTALTGA	DENV2 E p35
				HAKKQEVVVLGSQEGAMH	DENV3 E p35, DENV1^{^b}
				VLGSQEGAMHTALTGA	DENV3 E p36,
				HAKRQDVTVLGSQEGAMH	DENV4 E p36
				VLGSQEGAMHSALAGA	DENV4 E p37
HGTVVIELSYSGSDGPCK	JE		CD4	HGTVVLELQYTGTDGPCK	WNV E p44
LGKAFSTTLKGAQRLAAL	JE		CD4	HKSGSSIGKAFTTTLKGA	WNV E p55
				KAFTTTLKGAQRLAAL	WNV E p56
WDFGSIGGVFNSIGKAV	JE		CD4	WDFGSVGGVFTSVGKAVH	WNV E p59
GVFNSIGKAVHQVFGGAF				VFTSVGKAVHQVFGGAFR	WNV E p60
AISGDDCVVKPLDDRFCVVKPLDDRFATALHFL	JE		CD4 + CD8	AVSGDDCVVKPLDDRFA	WNV NS5 p91+92^{^c}
				VVKPLDDRFATSLHFLNA
				ISGDDCVVKPIDDRFAT	DENV1 NS5 p115+116^{^c}
				VVKPIDDRFATALTALN
				ISGDDCVVKPLDDRFA	DENV2 NS5 p116+117^{^c}
				CVVKPLDDRFASALTAL
				MAISGDDCVVKPIDDRF	DENV3 NS5 p115+116^{^c}
				DCVVKPIDDRFANALLA
				MAISGDDCVVKPLDERF	DENV4 NS5 p116+117^{^c}
				DCVVKPLDERFSTSLLF

JEV peptide sequence	Subject type	Viruses with identical sequence	Subset	Variant	Virus/BEI peptide location
CSAVPVDW	H	DENV1	CD8	CSSVPVDW	MVEV
MTTEDMLQVW	H		CD8	MTTEDMLRVW	JEV
				MTTEDMLSVW	DENV1
				MTTEDMLTVW	DENV2,3
				MTTEDMLKVW	DENV4
				MTTEDMLEVW	WNV, YFV
				MTTEDMLDVW	TBEV
ALRGLPVRY	H	ZIKV	CD8	ALRGLPIRY	WNV, DENV2,4
NLFVMDEAHFTDPASIEAHFTDPASIAARGYI	H	DENV2,3	CD8	NYNMIIMDEAHFTDPA	DENV1 NS3 p49
				IMDEAHFTDPASIARRG	DENV1 NS3 p50
				NYNLIIMDEAHFTDPASI	DENV2 NS3 p38
				NYNLIIMDEAHFTDPA	DENV3 NS3 p48
				PNYNLIVMDEAHFTD	DENV4 NS3 p49
				LIVMDEAHFTDPSSVAA	DENV4 NS3 p50
				AHFTDPSSVAARGYIST	DENV4 NS3 p51
TMAMTDTTPFGQQRVFK	H	WNV	CD4 + CD8	MVTQIAMTDTTPFGQQR^a	DENV1 NS5 p60
				AMTDTTPFGQQRVFKEK^a	DENV2 NS5 p61
				MVTQMAMTDTTPFGQQR^a	DENV3 NS5 p60
				MVTQLAMTDTTPFGQQR^a	DENV4 NS5 p60
GEAAAIFMT	H	WNV, DENV1,3,4, ZIKV	CD8	MGEAAAIFMTATPPGSV^b	DENV1 NS3 p54, DENV3 NS3 p52
				VEMGEAAAIFMTATPPG^b	DENV4 NS3 p54
TAVLAPTRVVAAEMAEAL	H	WNV	CD8	NVRTLILAPTRVVASEM	DENV1 NS3 p38
				LRTLILAPTRVVAAEM	DENV2 NS3 p30
				TLILAPTRVVAAEMEEA	DENV3 NS3 p38, DENV4 NS3 p39
DVMCHATL	D	WNV, MVEV, SLEV	CD8	DLMCHATF	DENV1–4, ZIKV
				DAMCHATL	YFV
AVHSDLSYWIESRYNDTW	JE		CD4	NLAIHSDLSYWIESRL	WNV NS1 p26
WIESRYNDTWKLERAVF	JE		CD4	RLNDTWKLERAVLGEVK	WNV NS1 p28
				IESEKNETWKLARASFI	DENV NS1 p36
KQSVVALGSQEGGLHQAL	JE		CD4	HATKQSVIALGSQEGALH	WNV E p34
				ALGSQEGALHQALAGAI	WNV E p35
				VVVLGSQEGAMHTALTG	DENV1 E p44
				HAKKQDVVVLGSQEGAMH	DENV2 E p34
				VLGSQEGAMHTALTGA	DENV2 E p35
				HAKKQEVVVLGSQEGAMH	DENV3 E p35, DENV1^b
				VLGSQEGAMHTALTGA	DENV3 E p36,
				HAKRQDVTVLGSQEGAMH	DENV4 E p36
				VLGSQEGAMHSALAGA	DENV4 E p37
HGTVVIELSYSGSDGPCK	JE		CD4	HGTVVLELQYTGTDGPCK	WNV E p44
LGKAFSTTLKGAQRLAAL	JE		CD4	HKSGSSIGKAFTTTLKGA	WNV E p55
				KAFTTTLKGAQRLAAL	WNV E p56
WDFGSIGGVFNSIGKAV	JE		CD4	WDFGSVGGVFTSVGKAVH	WNV E p59
GVFNSIGKAVHQVFGGAF				VFTSVGKAVHQVFGGAFR	WNV E p60
AISGDDCVVKPLDDRFCVVKPLDDRFATALHFL	JE		CD4 + CD8	AVSGDDCVVKPLDDRFA	WNV NS5 p91+92^c
				VVKPLDDRFATSLHFLNA
				ISGDDCVVKPIDDRFAT	DENV1 NS5 p115+116^c
				VVKPIDDRFATALTALN
				ISGDDCVVKPLDDRFA	DENV2 NS5 p116+117^c
				CVVKPLDDRFASALTAL
				MAISGDDCVVKPIDDRF	DENV3 NS5 p115+116^c
				DCVVKPIDDRFANALLA
				MAISGDDCVVKPLDERF	DENV4 NS5 p116+117^c
				DCVVKPLDERFSTSLLF

JE, recovered JE patient; H, healthy JEV exposed; D, dengue exposed; MVEV, Murray Valley encephalitis virus; YFV, yellow fever virus; TBEV, tick-borne encephalitis virus; SLEV, St. Louis encephalitis virus; ZIKV, Zika virus. Variant peptides were synthesized or obtained from BEI resources; and their location within each peptide set (see Materials and methods) is given in the last column. Bold/underlined amino acids represent differences from the JEV sequence.

Likely to represent conserved epitope DTTPFGQQR (see Fig. 2 D).

Identical viral sequences, but corresponding peptides vary slightly.

Pairs of peptides tested together in the same assay.

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