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. 2007 Feb 7;81(8):4199–4214. doi: 10.1128/JVI.01388-06

TABLE 3.

Clonotypic compositions of epitope-specific CD8+ T cells during early and chronic HIV-1 infections

Study person; epitope Primary HIV-1 infection
Chronic HIV-1 infection
Vβ clonotype CDR3 sequencea Jβ clonotype Frequency Vβ clonotype CDR3 sequencea Jβ clonotype Frequency
AC-46; B8-FL8 29.1 CSV, WGTGKTYEQY FG-2.7 19/75
29.1 CSV, WGEGRSYEQY FG-2.7 5/75
20.1 CSA, TILAGVPYGEQY FG-2.7 17/75 20.1 CSA, TILAGVPYGEQY FG-2.7 24/76
ACGATCCTAGCGGGAGTTCCCTATGGGGAGCAGTAC 17/17 ACGATCCTAGCGGGAGTTCCCTATGGGGAGCAGTAC 23/24
ACGATCCTAGCGGGAGTCCCCTATGGGGAGCAGTAC 1/24
20.1 CSA, TILAGVPYGGQH FG-2.7 1/75
20.1 CSA, SEGTSSYEQY FG-2.7 1/75
7.3 CASS, FDREVTGELF FG-2.2 7/75
7.3 CASS, PDGGNTEAF FG-1.2 2/75
19 CASS, VGAGTEAF FG-1.1 5/75
10.3 CAI, SESGYGGPPGANVLT FG-2.6 1/75
10.3 CTI, SESGYRGPPGANVLT FG-2.6 1/75
10.3 CAI, SEPGYRGPPGANVLT FG-2.6 1/75
10.3 CAI, SESGYRGPPGANVLT FG-2.6 1/75
28 CAS, RPTDRNTGELF FG-2.2 3/75
28 CASS, LAAGGPYEQY FG-2.7 1/75
7.9 CASS, PPSGSYEQY FG-2.7 1/75
7.9 CASS, LESGQRPYEQY FG-2.7 1/75
19 CASS, IGPLEGNEQF FG-2.1 2/75 19 CASS, IGPLEGNEQF FG-2.1 1/76
27 CASS, WGQGOLSYEQY FG-2.7 2/75 27 CASS, WGQGQLSYEQY FG-2.7 35/76
5.4 CASS, YRGQGNYGYT FG-1.2 1/75
6.3 CASS, YERGMNTEAF FG-1.1 1/75
6.5 CASS, MGQGATEAF FG-1.1 1/75
6.6 CASS, YPMGANEKLF FG-1.4 1/75
27 CAS, RIGQGTVGELF FG-2.2 3/76
29.1 CSV, DNSYEQY FG-2.7 3/76
29.1 CSV, VGLESSYEQY FG-2.7 2/76
29.1 CSV, GENTEAF FG-1.1 1/76
7.2 CASS, IFGSPFNQPQH FG-1.5 4/76
19 CAT, LREGPTTGELF FG-2.2 3/76
AC-14; B8-FL8 27 CASS, LGQGLANYGYT FG-1.2 17/40
20.1 CSA, RPMAASGLTYEQY FG-2.7 6/40
6.1 CASS, EYGAAVYEQY FG-2.7 8/40
7.3 CASS, LNLRGSSGNTIY FG-1.3 5/40
28 CASS, SNPGTSGGYSYEQY FG-2.7 3/40 28 CASS, SNPGTSGGYSYEQY FG-2.7 3/51
7.9 CASS, GSPGLAGEQT FG-2.1 1/40
6.3 CASS, LLGQYNEQF FG-2.1 22/51
6.3 CASS, LLGQCNEQF FG-2.1 1/51
6.3 CASS, FHPGQGASYSNQPQH FG-1.5 11/51
6.6 CASS, YERGGLPKNIQY FG-2.4 10/51
27 CASS, LGQGRSLGHEQY FG-2.7 3/51
28 CASS, PRDRVIEDTQY FG-2.1 1/51
AC-09; A2-IV9 20.1 CSA, RQYRTDMNTEAF FG-1.1 15/39
29.1 CSV, EVGAGETQY FG-2.5 7/39
29.1 CSV, EDLGNEQF FG-2.3 1/39
29.1 CSA, ETSDSYEQY FG-2.7 1/39
6.6 CASS, YEWGGLPKNIQY FG-2.4 7/39
27 CAS, RLVGIGNSPLH FG-1.6 5/39
10.3 CAI, SEDGGETQY FG-2.5 3/39 10.3 CAI, SEDGGETQY FG-2.5 29/47
10.3 CAI, SGDGGETQY FG-2.5 1/47
10.3 CTI, SEWGGETQY FG-2.5 1/47
28 CASS, FGGDEQH FG-1.5 4/47
28 CASS, LGGDTQY FG-2.1 3/47
28 CASS, LGGDEQY FG-2.7 1/47
28 CASS, FGGDTQY FG-2.1 1/47
28 CASS, LRDEQY FG-2.7 1/47
29.1 CSV, EDSGNEQF FG-2.1 2/47
29.1 CSV, EDRANEQY FG-2.7 1/47
29.1 CSV, RAPPMTSPTDEQY FG-2.7 1/47
6.2 CASS, LDGGETQY FG-2.5 1/47
6.2 CASS, QDGGETQY FG-2.5 1/47
AC-02; B8-FL8 7.2 CASS, EPALAEQYYEQY FG-2.7 39/46
7.2 CASS, FTPGTGAPYSNQPQH FG-1.5 4/46
29.1 CSV, EGGSAYEQY FG-2.7 3/46
7.3 CASS, FDREVTGELF FG-2.2 32/45
7.3 CASS, LDREVTGELF FG-2.2 1/45
20.1 CSA, HLYRAYGYT FG-1.2 5/45
19 CASS, MGQHSNQPQH FG-1.5 4/45
7.2 CASS, LAWGRAESSYNEQF FG-2.1 2/45
29.1 CSV, WGTGKTYEQY FG-2.7 1/45
AC-15; B8-FL8 6.1 CAS, KWDPGQGSHYSNQPQH FG-1.5 17/37 6.1 CAS, KWDPGQGSHYSNQPQH FG-1.5 2/41
29.1 CSV, EPSGRARTYNEQF FG-2.1 10/37
30 CAW, DVKDRRIGNEQF FG-2.1 5/37
20.1 CSA, RDSGRGIENYEQY FG-2.7 2/37
20.1 CSA, SSQRGGIYEQY FG-2.7 2/37
7.9 CASS, LVGVGTSDEQF FG-2.1 1/37
7.3 CASS, FDREVTGELF FG-2.2 18/41
27 CASS, LGQGLANYGYT FG-2.1 11/41
27 CASS, LSPGTSGSRANEQF FG-2.1 1/41
28 CASS, LELAGEDYEQY FG-2.7 4/41
28 CASS, LSSNEQF FG-2.1 2/41
9 CASS, TLTSGGARDEQF FG-2.7 3/41
AC-131; B8-EI8 29.1 CSV, RDGYEQY FG-2.7 23/46
7.2 CASS, PVRGRTEAF FG-1.1 4/46
7.2 CASS, LVGPGGREKLF FG-1.4 3/46
9 CASS, VLTGGRETQY FG-2.5 7/46
19 CASS, IIKGNQPQH FG-1.5 4/46
19 CASS, SGLPTNEKLF FG-1.4 3/46
6.1 CAS, PYMDARSEAF FG-1.1 2/46
9 CASS, VVGDFRETQY FG-2.5 48/48
AC-177; B8-EI8 6.6 CASS, YGGTEAF FG-1.1 23/49 6.6 CASS, YGGTEAF FG-1.1 18/46
TACGGAGGCACTGAAGCTTTC 14/23
TACGGGGGCACTGAAGCATTC 1/23
TACGGGGGCACTGAAGCTCTC 1/23
TACGGAGGGACTGAAGCTTTC 4/23
TACGGAGGAACTGAAGCTTTC 1/23 TACGGAGGAACTGAAGCTTTC 10/18
TATGGGGGGACTGAAGCTTTC 2/23
TACGGGGGCACTGAAGCTTTC 5/18
TACGGGGGGACTGAAGCTTTC 3/18
7.2 CASS, LPGQGRTPLH FG-1.6 4/49 7.2 CASS, LPGQGRTPLH FG-1.6 7/46
TTACCTGGACAGGGAAGGACACCCCTCCAC 4/4 TTACCTGGACAGGGAAGGACACCCCTCCAC 6/7
TTACCTGGACAGGGAAGGACGCCCCTCCAC 1/7
7.2 CASS, LETRNSPLH FG-1.6 1/49
7.2 CASS, FLPKNEQF FG-2.1 4/49
7.2 CASS, LVRDDRIEQY FG-2.7 2/49
7.2 CASS, FPGQGRTEAF FG-1.1 2/49
20.1 CSA, RLSYEQY FG-2.7 7/49
20.1 CSA, RDNYEQY FG-2.7 2/49
20.1 CSA, RDSYEQY FG-2.7 1/49
20.1 CSA, RLDYEQY FG-2.7 1/49
20.1 CSA, RYDYEQY FG-2.7 1/49
7.3 CASS, LIPSGGRNEQF FG-2.1 1/49
9 CASS, AITSGGARDEQF FG-2.1 11/46
9 CASS, VGGDHREEQH FG-2.7 3/46
9 CASS, AGDIQY FG-2.4 2/46
9 CASS, AGGIQY FG-2.4 1/46
10.3 CAT, IRTGFSSYEQY FG-2.7 4/46
AC-132; A3-OK10 6.6 CASS, YSRGSGNTIY FG-1.3 19/43 6.6 CASS, YSRGSGNTIY FG-1.3 7/42
TACTCTAGGGGATCTGGAAACACCATATAT 6/19 TACTCTAGGGGATCTGGAAACACCATATAT 5/7
TACTCTAGGGGCTCTGGAAACACCATATAT 13/19 TACTCTAGGGGCTCTGGAAACACCATATAT 2/7
6.6 CASS, PYRGPNTEAF FG-1.1 1/43 6.6 CASS, PYRGPNTEAF FG-1.1 1/42
10.3 CAI, SAGASFVTRSTDTQY FG-2.1 6/43 10.3 CAI, SAGASFVTRSTDTQY FG-2.1 1/42
10.3 CAI, RSTDTQY FG-2.1 1/43
6.1 CAS, RQQGFVFEAKNIQY FG-2.4 3/43
6.1 CASS, EEVEAF FG-1.1 1/43
20.1 CSA, PTSGSAAF FG-1.1 3/43
20.1 CSA, RDSIQFSSNQPQH FG-1.5 1/43
6.2 CASS, YSMTSGSFSDLGAKNIQY FG-2.4 1/43
6.2 CAS, RPGPVKNTGELF FG-2.2 1/43 6.2 CAS, RPGPVKNTGELF FG-2.2 7/42
9 CASS, LYHNTGELF FG-2.2 1/43
9 CASS, GGAHFSKIPLAGYNEQF FG-2.1 1/43 9 CASS, GGAHFSKIPLAGYNEQF FG-2.1 3/42
5.4 CASS, RTDFTAGELF FG-2.2 1/43
27 CASS, LTGHPYEQY FG-2.7 1/43 27 CASS, LTGHPYEQY FG-2.7 9/42
28 CASS, PGEKYEQY FG-2.1 1/43
29.1 CSV, EDRHYEQY FG-2.7 1/43 29.1 CSV, EDRHYEQY FG-2.7 5/42
6.6 CASS, YSRGAGNTIY FG-1.3 7/42
6.6 CAS, TRSGGFRDEQY FG-2.7 1/42
7.9 CASS, RRDHQETQY FG-2.5 1/42
AC-160; B27-KK10 5.4 CASS, LTAPDTEAF FG-1.1 30/45 5.4 CASS, LTAPDTEAF FG-1.1 8/53
5.4 CASS, GTAPAAEAF FG-1.1 1/45
5.4 CASS, STAPDTEAF FG-1.1 1/45
5.4 CASS, TAPGTEAF FG-1.1 1/45
27 CASS, RSTGELF FG-2.2 10/45 27 CASS, RSTGELF FG-2.2 27/53
20.1 CSA, RDQRDYQETQY FG-2.5 2/45 20.1 CSA, RDQRDYQETQY FG-2.5 1/53
27 CASS, VRTGELF FG-2.2 14/53
27 CASS, PRTGELF FG-2.2 3/53
AC-121; B57-KF11 19 CASS, GQGYGYT FG-1.2 24/46 19 CASS, GQGYGYT FG-1.2 25/45
GGACAGGGGTATGGCTACACG 28/24 GGACAGGGGTATGGCTACACC 22/25
GGGCAGGGGTATGGCTACACC 1/24
GGACAGGGATATGGCTACACC 3/25
19 CAS, TGGGYGYT FG-1.2 8/46
19 CASS, GQDYGYT FG-1.2 5/46 19 CASS, GQDYGYT FG-1.2 10/45
19 CASS, GQGYGYA FG-1.2 1/46
19 CAS, TGSGYGYT FG-1.2 1/46
19 CASS, GQEYGYT FG-1.2 1/46 19 CASS, GQDYGYT FG-1.2 1/45
6.1 CAS, TDSYGYT FG-1.2 6/46 6.1 CAS, TDSYGYT FG-1.2 5/45
ACTGACAGCTATGGCTACACC ACTGACAGCTATGGCTACACC 4/5
ACTGACAGCTATGGCTATACC 1/5
19 CASS, GGSYGYT FG-12 4/45
a

Nucleotide data are provided when multiple nucleotypes coding for identical CDR3 amino acid sequences were detected in clonotypes persisting between early and chronic infections. TCR clonotypes detected in both primary and secondary infection are shown in boldface type.