Table 3. Variant peptides eliciting T cell responses
JEV peptide sequenceSubject typeViruses with identical sequenceSubsetVariantVirus/BEI peptide location
CSAVPVDWHDENV1CD8CSSVPVDWMVEV
MTTEDMLQVWHCD8MTTEDMLRVWJEV
MTTEDMLSVWDENV1
MTTEDMLTVWDENV2,3
MTTEDMLKVWDENV4
MTTEDMLEVWWNV, YFV
MTTEDMLDVWTBEV
ALRGLPVRYHZIKVCD8ALRGLPIRYWNV, DENV2,4
NLFVMDEAHFTDPASIEAHFTDPASIAARGYIHDENV2,3CD8NYNMIIMDEAHFTDPADENV1 NS3 p49
IMDEAHFTDPASIARRGDENV1 NS3 p50
NYNLIIMDEAHFTDPASIDENV2 NS3 p38
NYNLIIMDEAHFTDPADENV3 NS3 p48
PNYNLIVMDEAHFTDDENV4 NS3 p49
LIVMDEAHFTDPSSVAADENV4 NS3 p50
AHFTDPSSVAARGYISTDENV4 NS3 p51
TMAMTDTTPFGQQRVFKHWNVCD4 + CD8MVTQIAMTDTTPFGQQRaDENV1 NS5 p60
AMTDTTPFGQQRVFKEKaDENV2 NS5 p61
MVTQMAMTDTTPFGQQRaDENV3 NS5 p60
MVTQLAMTDTTPFGQQRaDENV4 NS5 p60
GEAAAIFMTHWNV, DENV1,3,4, ZIKVCD8MGEAAAIFMTATPPGSVbDENV1 NS3 p54, DENV3 NS3 p52
VEMGEAAAIFMTATPPGbDENV4 NS3 p54
TAVLAPTRVVAAEMAEALHWNVCD8NVRTLILAPTRVVASEMDENV1 NS3 p38
LRTLILAPTRVVAAEMDENV2 NS3 p30
TLILAPTRVVAAEMEEADENV3 NS3 p38, DENV4 NS3 p39
DVMCHATLDWNV, MVEV, SLEVCD8DLMCHATFDENV1–4, ZIKV
DAMCHATLYFV
AVHSDLSYWIESRYNDTWJECD4NLAIHSDLSYWIESRLWNV NS1 p26
WIESRYNDTWKLERAVFJECD4RLNDTWKLERAVLGEVKWNV NS1 p28
IESEKNETWKLARASFIDENV NS1 p36
KQSVVALGSQEGGLHQALJECD4HATKQSVIALGSQEGALHWNV E p34
ALGSQEGALHQALAGAIWNV E p35
VVVLGSQEGAMHTALTGDENV1 E p44
HAKKQDVVVLGSQEGAMHDENV2 E p34
VLGSQEGAMHTALTGADENV2 E p35
HAKKQEVVVLGSQEGAMHDENV3 E p35, DENV1b
VLGSQEGAMHTALTGADENV3 E p36,
HAKRQDVTVLGSQEGAMHDENV4 E p36
VLGSQEGAMHSALAGADENV4 E p37
HGTVVIELSYSGSDGPCKJECD4HGTVVLELQYTGTDGPCKWNV E p44
LGKAFSTTLKGAQRLAALJECD4HKSGSSIGKAFTTTLKGAWNV E p55
KAFTTTLKGAQRLAALWNV E p56
WDFGSIGGVFNSIGKAVJECD4WDFGSVGGVFTSVGKAVHWNV E p59
GVFNSIGKAVHQVFGGAFVFTSVGKAVHQVFGGAFRWNV E p60
AISGDDCVVKPLDDRFCVVKPLDDRFATALHFLJECD4 + CD8AVSGDDCVVKPLDDRFAWNV NS5 p91+92c
VVKPLDDRFATSLHFLNA
ISGDDCVVKPIDDRFATDENV1 NS5 p115+116c
VVKPIDDRFATALTALN
ISGDDCVVKPLDDRFADENV2 NS5 p116+117c
CVVKPLDDRFASALTAL
MAISGDDCVVKPIDDRFDENV3 NS5 p115+116c
DCVVKPIDDRFANALLA
MAISGDDCVVKPLDERFDENV4 NS5 p116+117c
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.

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

  • b Identical viral sequences, but corresponding peptides vary slightly.

  • c Pairs of peptides tested together in the same assay.