TABLE 3.

Confirmed peptide responses in Gag, Pol, Vif, Env and Nef pools

Peptide pool or peptide (aa)Confirmed peptide sequenceSFU/106 cellsSelection of subtype B epitopes found in the subtype C epitopic regionsa
PBMCCD8
Gag
    1-1119RGGKLDKWEKIRLRPGGK26158KIRLRPGGK, GELDRWEKI
    1-11117EKIRLRPGGKKHYMLKHL3427612KIRLRPGGKK, RLRPGGKKK
    1-11125GKKHYMLKHLVWASREL41160KYKLKHIVW
    1-11132KHLVWASRELERFAL46345WASRELERF
    1-11171TGTEELRSLYNTVATLY879819GTEELRSL, SLYNTVATLY, RSLYNTVATLY, TGTEELRSLY
    1-11178SLYNTVATLYCVHAGIEV9564930SLYNTVATLY, TLYCVHAG
    112-218155WVKVIEEKAFSPEVIPMF172623KAFSPEVIPMF
    112-218163AFSPEVIPMFTALSEGA179201EVIPMFSAL, VIPMFSAL
    112-218170PMFTALSEGATPQDLNTM187512SEGATPQDL, LSEGATPQDL
    112-218178GATPQDLNTMLNTVGGH194929TPQDLNTML
    219-322257PVGDIYKRWIILGLNKIV275949GDIYKRWII, DIYKRWII, IYKRWIIL, IYKRWIILGL, IYKRWIILGLNK
    219-322289GPKEPFRDYVDRFFKTLR3061,90125RDYVDRFFKTLR, RDYVDRFFKT
    219-322297YVDRFFKTLRAEQATQDV3143,07320DRFFKTLRA
    219-322305LRAEQATQDVKNWMTDTL322188RAEQASQEV, AEQASQDVKNW, QASQDVKNW
Pol
    1-17522PQITLWQRPLVSIKI351,070VTLWQRPLV
    176-354305ALYVGSDLEIGQHRAKI3211,48010DLEIGQHRTK
    355-533359TVQPIQLPEKDSWTVNDI376230PIVLPEKDSW, IVLPEKDSW, VLPEKDSW
    355-533381GKLNWTSQIYPGIKVRQL3984180KLNWASQIY, QIYPGIKVR
    355-533485KQLTEAVQKISLESIVTW502180KITTESIVIW
    355-533508FRLPIQKETWEIWWTDYW525270PIQKETWETW, TWETWWTEYW
    534-689552PIAGAETFYVDGAANR56780310IVGAETFYVDGAAN, GAETFYVDGA, AETFYVDGA, AETFYVDGAAN
    534-689558TFYVDGAANRETKIGKA5747200No previously described epitopes
Vif
    1-10271LQTGERDWHLGHGVSIEW8818920No previously described epitopes
    1-10278HLGHGVSIEWRLRRY9337710No previously described epitopes
    1-10284VSIEWRLRRYSTQVDPGL10116410No previously described epitopes
    103-192143SLYQYLALTALIKPKKIK159420No previously described epitopes
Env
    192-346197KVSFDPIPIHYCAPAGYA2141,1170VSFEPIPIHY, SFEPIPIHY
    192-346290GNNTRKSIRIGPGQAFY306290QRGPGRAFV, RIQRGPGRAF
    192-346297IRIGPGQAFYTBHIIGDI314350No previously described epitopes
    347-523414DGGTDNTTEIFRPGGGNM4313500No previously described epitopes
    347-523470RAVGIGAVLLGFLGAA4923800No previously described epitopes
    524-694575WSNKSQQAIWDNMTWMQW592780No previously described epitopes
    524-694583IWDNMTWMQWDREINNY599400No previously described epitopes
    524-694657RIIFAVLSIVNRVRQGY67310310AVLSIVNRV, IVNRVRQGY
    524-694664SIVNRVRQGYSPLSFQTL6817400IVNRVRQGY
    695-826740AARTVELLGRSSLRGLQR7571900No previously described epitopes
Nef
    1-5142ALTSSNTAHNNPDCA55965ALTSSNTAA
    52-9162EVGFPVRPQVPLRPM76491FPVTPQVPL, FPVTPQVPLR, PVTPQVIPLRPM, PQVPLRPM
    52-9169PVRPQVPLRPMTYKA83258VPLRFMTY, QVPLRPMTYK, PLRPMTYK
    52-9173QVPLRPMTYKAAFDL87992QVPLRPMTYK, RPMTYKAAV
    52-9177RPMTYKAAFDLSSFL919107MTYKAAVD, KAAVDLSHFL, AAVDLSHFL
    92-13181YKAAFDLSFFLKEKG9559315KAAVDLSHFL, AAVDLSHFLKEK, AVDLSHFL, DLSHFLKEK
    92-131101IHSKRRQDILDLWVY11566517HSQRRQDILDLWIY, RRQDILDLWI, RQDILDLWIY, DILDLWIF
    92-131113WVYHTQGYFPDWQNY12761220YHTQGYFPDWQ, HTQGYFPDWQ, TQGYFPDWQNY
    132-171129PGPGVRYPLTFGWCF1431,70415GPGVRYPLTFGWCY, RYPLTFGW, RYPLTFGWCF, YPLTFGWCY, TPLTFGWCF
    132-171133VRYPLTFGWCFKLVP1471,28930RYPLTFGW, RYPLTFGWCY, RYPLTFGWCF
    132-171157NKGENNCLLHPMSQH171443No previously described epitopes
  • a Previously described subtype B CTL epitopes (27) found within the subtype C peptide sequences are shown; bold letters denote amino acid variations from the subtype C epitopic sequence.