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T Helper/CD4+ Epitope Variants and Escape Mutations

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List of Mutation types

Data last updated at 2018-06-12 08:36:40-06
Epitope ID Epitope Name Variant ID Subtype Epitope Subtype Variant Subtype Protein HXB2 start HXB2 end Subprotein HXB2 DNA Contig HLA Epitope Variant Epitope Mutation (epitope) Mutation (protein) Mutation Type Code Mutation Type Description Methods Note References
201712 Gag 253-267 11 B, C B B Gag 253 267 p24(121-135) 1546..1590   NPPIPVGEIYKRWII NPPIPVGdIYKRWII E8D E260D DR, OV, SF diminished response, observed variant, susceptible form CD4 T-cell Elispot - IFNy, HLA binding Variant NPPIPVGdIYKRWII, Gag 253-26 E-D, is present in only 6.05% of clade B sequences; cross reacting with 3/6 (50%) of Gag 253-267-specific HTL cell lines. Castelli2013
201712 Gag 253-267 12 B, C B B Gag 253 267 p24(121-135) 1546..1590   NPPIPVGEIYKRWII NPPvPVGEIYKRWII I4V I256V DR, OV, SF diminished response, observed variant, susceptible form CD4 T-cell Elispot - IFNy, HLA binding Variant NPPvPVGEIYKRWII, Gag 253-267 I-V, is present in only 3.21% of clade B sequences; cross reacting with 5/6 (83%) of Gag 253-267-specific HTL cell lines. Castelli2013
201712 Gag 253-267 13 B, C B B Gag 253 267 p24(121-135) 1546..1590   NPPIPVGEIYKRWII NPaIPVGEIYKRWII P3A P255A DR, OV, SF diminished response, observed variant, susceptible form CD4 T-cell Elispot - IFNy, HLA binding Variant NPaIPVGEIYKRWII, Gag 253-267 P-A, is present in only 3.12% of clade B sequences; cross reacting with 5/6 (83%) of Gag 253-267-specific HTL cell lines. Castelli2013
201713 Gag 259-273 14 B, C B B Gag 259 273 p24(127-141) 1564..1608   GEIYKRWIILGLNKI GdIYKRWIILGLNKI E2D E260D DR, OV, SF diminished response, observed variant, susceptible form CD4 T-cell Elispot - IFNy, HLA binding Variant GdIYKRWIILGLNKI, Gag 259-273 E-D, is present in only 4.06% of clade B sequences; cross reacting with 1/2 (50%) of Gag 259-273-specific HTL cell lines. Castelli2013
201713 Gag 259-273 15 B, C B B Gag 259 273 p24(127-141) 1564..1608   GEIYKRWIILGLNKI GdIYKRWIImGLNKI L10M, E2D L268M, E260D DR, OV, SF diminished response, observed variant, susceptible form CD4 T-cell Elispot - IFNy, HLA binding Variant GdIYKRWIImGLNKI, Gag 259-273 E-D/L-M, is present in only 1.51% of clade B sequences; cross reacting with 1/2 (50%) of Gag 259-273-specific HTL cell lines. Castelli2013
201714 Gag 270-284 16 B, C B B Gag 270 284 p24(138-152) 1597..1641   LNKIVRMYSPTSILD LNKIVRMYSPvSILD T11V T280V DR, OV, SF diminished response, observed variant, susceptible form CD4 T-cell Elispot - IFNy, HLA binding Variant LNKIVRMYSPvSILD, Gag 270-284 T-V, is present in 20.42% of clade B sequences; cross reacting with 8/15 (53%) of Gag 270-284-specific HTL cell lines. Castelli2013
201714 Gag 270-284 17 B, C B B Gag 270 284 p24(138-152) 1597..1641   LNKIVRMYSPTSILD LNKIVRMYSPsSILD T11S T280S DR, OV, SF diminished response, observed variant, susceptible form CD4 T-cell Elispot - IFNy, HLA binding Variant LNKIVRMYSPvSILD, Gag 270-284 T-S, is present in only 3.59% of clade B sequences; cross reacting with 14/15 (93%) of Gag 270-284-specific HTL cell lines. Castelli2013
201714 Gag 270-284 18 B, C B B Gag 270 284 p24(138-152) 1597..1641   LNKIVRMYSPTSILD LNKIVRMYSPiSILD T11I T280I DR, OV, SF diminished response, observed variant, susceptible form CD4 T-cell Elispot - IFNy, HLA binding Variant LNKIVRMYSPiSILD, Gag 270-284 T-I, is present in only 2.93% of clade B sequences; cross reacting with 12/15 (67%) of Gag 270-284-specific HTL cell lines. Castelli2013
201417   36       Gag 293 303 p24(161-171) 1666..1710 DQA1*01, DQB1*05 FRDYVDRFYKT FRDYVDqFYKT R7Q R299Q E escape documented in this paper Flow cytometric T-cell cytokine assay, Intracellular cytokine staining, Tetramer binding The variant FRDYVDqFYKT was present at 5 and 7 months postinfection. It failed to elicit a response as measured by IL-2 production, degranulation (CD107a staining) or INF-γ production, thus constituting an escape variant. This escape mutant did not antagonize responses to the index peptide and mutations flanking the epitope did not impact recognition. Jones2009
201197   4 B, C, F, BF B, BF, C, F BF gp160 108 119 gp120(108-119) 6546..6581   IISLWDQSLKPC vISLWDQSLKPC I1V I108V OV observed variant Sequence Variant vISLWDQSLKPC was seen only in 2/19 HIV B/F recombinant sequences. Queiroz2007
201722   19 B B CRF01_AE gp160 167 181 gp120(167-181) 6723..6767 DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 DKMQKEYALLYKLDI DKkQKvhALfYKLDI L10F, K12R, M3K, E6V, Y7H L176F, K178R, M169K, E172V, Y173H A, DHB, SNSF, SSF HLA association, diminished HLA binding or increased off-rate, subtype-specific non-susceptible form, subtype-specific susceptible form CD4 T-cell Elispot - IFNy, HLA binding Subtype CRF01_AE-specific variant DKkQKvhALfYKLDI, from either strains 92TH023 or A244, bound HLA-DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, with IC50 = 39312 nM, 10 nM, 71 nM, 371 nM respectively but did not bind HLAs -DRB3*0202 or -DRB5*0101 appreciably. Gartland2014
201722   20 B B CRF01_AE gp160 167 181 gp120(167-181) 6723..6767 DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 DKMQKEYALLYKLDI DKkQKvhALfYrLDI L10F, K12R, M3K, E6V, Y7H L176F, K178R, M169K, E172V, Y173H A, DHB, SNSF, SSF HLA association, diminished HLA binding or increased off-rate, subtype-specific non-susceptible form, subtype-specific susceptible form CD4 T-cell Elispot - IFNy, HLA binding Subtype CRF01_AE-specific variant DKkQKvhALfYrLDI, from either strains 92TH023 or A244, bound HLA-DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 with IC50 = 26963 nM, 6.7 nM, 60 nM, 486 nM, 189896 nM respectively but did not bind HLA-DRB3*0202 appreciably. This variant was isolated from an RV144 placebo CRF01_AE-infected subject. Gartland2014
201722   21 B B CRF01_AE gp160 167 181 gp120(167-181) 6723..6767 DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 DKMQKEYALLYKLDI DKqQKvhALfYrLDI L10F, K12R, M3Q, E6V, Y7H L176F, K178R, M169Q, E172V, Y173H A, DHB, SNSF, SSF HLA association, diminished HLA binding or increased off-rate, subtype-specific non-susceptible form, subtype-specific susceptible form CD4 T-cell Elispot - IFNy, HLA binding Subtype CRF01_AE-specific variant DKqQKvhALfYrLDI, from either strains 92TH023 or A244, bound DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 with IC50 = 16 nM, 324 nM, 697 nM, 23743 nM respectively but did not bind HLAs -DRB1*0301, -DRB3*0202 appreciably. This variant was isolated from an RV144 vaccinated CRF01_AE-infected subject. Gartland2014
201722   22 B B CRF01_AE gp160 167 181 gp120(167-181) 6723..6767 DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 DKMQKEYALLYKLDI DKqhKvhALfYkLDI L10F, M3Q, Q4H, E6V, Y7H L176F, M169Q, Q170H, E172V, Y173H A, DHB, SNSF, SSF HLA association, diminished HLA binding or increased off-rate, subtype-specific non-susceptible form, subtype-specific susceptible form CD4 T-cell Elispot - IFNy, HLA binding Subtype CRF01_AE-specific variant DKqhKvhALfYkLDI, from either strains 92TH023 or A244, bound DRB1*1201, DRB1*1501, DRB4*0101 with IC50 = 11 nM, 366 nM, 222 nM respectively but did not bind HLAs -DRB1*0301, -DRB3*0202, -DRB5*0101 appreciably. This variant was isolated from an RV144 vaccinated CRF01_AE-infected subject. Gartland2014
201722   23 B B CRF01_AE gp160 167 181 gp120(167-181) 6723..6767 DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 DKMQKEYALLYKLDI DKrrmvhALfYrLDI L10F, K12R, M3R, Q4R, K5M, E6V, Y7H L176F, K178R, M169R, Q170R, K171M, E172V, Y173H A, DHB, SNSF, SSF HLA association, diminished HLA binding or increased off-rate, subtype-specific non-susceptible form, subtype-specific susceptible form CD4 T-cell Elispot - IFNy, HLA binding Subtype CRF01_AE-specific variant DKrrmvhALfYrLDI, from either strains 92TH023 or A244, bound DRB1*0301, DRB1*1201, DRB1*1501, DRB3*0202, DRB4*0101, DRB5*0101 with IC50 = 16654 nM, 5.3 nM, 15 nM, 42166 nM, 72 nM, 235 nM respectively. This variant was isolated from an RV144 vaccinated CRF01_AE-infected subject. Gartland2014
201722   24 B B CRF01_AE gp160 167 181 gp120(167-181) 6723..6767 DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 DKMQKEYALLYKLDI DKkQvvrALfYKLDI L10F, M3K, K5V, E6V, Y7R L176F, M169K, K171V, E172V, Y173R A, DHB, SNSF, SSF HLA association, diminished HLA binding or increased off-rate, subtype-specific non-susceptible form, subtype-specific susceptible form CD4 T-cell Elispot - IFNy, HLA binding Subtype CRF01_AE-specific variant DKkQvvrALfYKLDI, from either strains 92TH023 or A244, bound DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 with IC50 = 3.6 nM, 20 nM, 303 nM, 958 nM respectively but did not bind HLAs -DRB1*0301 and -DRB3*0202 appreciably. This variant was isolated from an RV144 placebo CRF01_AE-infected subject. Gartland2014
201722   25 B B CRF01_AE gp160 167 181 gp120(167-181) 6723..6767 DRB1*0301, DRB1*1201, DRB1*1501, DRB4*0101, DRB5*0101 DKMQKEYALLYKLDI DKqQKvYALfnKLDI L10F, Y11N, M3Q, E6V L176F, Y177N, M169Q, E172V A, DHB, SNSF, SSF HLA association, diminished HLA binding or increased off-rate, subtype-specific non-susceptible form, subtype-specific susceptible form CD4 T-cell Elispot - IFNy, HLA binding Subtype CRF01_AE-specific variant DKqQKvYALfnKLDI, from either strains 92TH023 or A244, bound DRB1*0301 DRB1*1201, DRB1*1501, DRB3*0202, DRB4*0101, DRB5*0101 with IC50 = 64 nM, 47 nM, 3964 nM, 21290, 18920, 13113 nM respectively. This variant was isolated from an RV144 placebo CRF01_AE-infected subject. Gartland2014
201783 peptide 32, pep 32 26 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDlVqIEDNK I10L, P12Q I181L, P183Q E, NSF escape documented in this paper, non-susceptible form CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDlVqIEDNK, completely abrogated CTL response in all 4 previously vaccinated subjects from RV144 that were tested. Ratto-Kim2015
201783 peptide 32, pep 32 27 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDlVPIgDNK I10L, E14G I181L, E185G DR diminished response CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDlVPIgDNK, reduced CTL response by 50% in all 1/4 and reduced response 3x in 1/4 previously vaccinated subjects from RV144 that were tested. Ratto-Kim2015
201783 peptide 32, pep 32 28 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDIVqIEDNK P12Q P183Q E, NSF escape documented in this paper, non-susceptible form CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDIVqIEDNK, completely abrogated CTL response in all 4 previously vaccinated subjects from RV144 that were tested. Ratto-Kim2015
201783 peptide 32, pep 32 29 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDIVPtEDNK I13T I184T SF susceptible form CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDIVPtEDNK, did not affect immune response in the 4 RV144 subjects tested. Ratto-Kim2015
201783 peptide 32, pep 32 30 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDIVPIgDNK E14G E185G SF susceptible form CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDIVPIgDNK, did not affect immune response in the 4 RV144 subjects tested. Ratto-Kim2015
201783 peptide 32, pep 32 31 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDIVPmEDNK I13M I184M SF susceptible form CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDIVPmEDNK, did not affect immune response in the 4 RV144 subjects tested. Ratto-Kim2015
201783 peptide 32, pep 32 32 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDlVPIEDNK I10L I181L DR diminished response CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDlVPIEDNK, reduced CTL response by 3x in 2/4 previously vaccinated subjects from RV144 that were tested. Ratto-Kim2015
201783 peptide 32, pep 32 33 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDlVPtEDNK I10L, I13T I181L, I184T DR, E, NSF diminished response, escape documented in this paper, non-susceptible form CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDlVPtEDNK, reduced CTL response by 50% in 2/4 and abrogated response in 2/4 previously vaccinated subjects from RV144 that were tested. Ratto-Kim2015
201783 peptide 32, pep 32 35 B, CRF01_AE B, CRF01_AE B, CRF01_AE gp160 172 188 gp120(172-188) 6738..6788   VHALFYKLDIVPIEDNK VHALFYKLDlVPmEDNK I10L, I13M I181L, I184M DR, E, NSF diminished response, escape documented in this paper, non-susceptible form CD8 T-cell Elispot - IFNy Peptide 32 variant VHALFYKLDlVPmEDNK, reduced CTL response by 50% in 1/4 and by 3x in 1/4, while the other 2/4 previously vaccinated subjects from RV144 that were tested were unaffected. Ratto-Kim2015
50524   1 B A A gp160 311 319 gp120(311-319) 7155..7181   RGPGRAFVT RGPGRAFVv T9V T319V A HLA association Assay for Class I down-regulation by Nef 2222222222222 Barouch2002
50524   2 B A A gp160 311 319 gp120(311-319) 7155..7181   RGPGRAFVT RGPGRAFVv T9V T319V A HLA association Assay for Class I down-regulation by Nef 2222222222222 Barouch2002
201196   3 B B, BF, F B, BF, C gp160 562 576 gp41(51-65) 7908..7952   QQHLLQLTVWGIKQL QQHmLQLTVWGIKQL L4M L565M OV observed variant Sequence Variant QQHmLQLTVWGIKQL was seen 4/7 subtype B sequences, all 13 subtype C sequences and in 6/19 B/F recombinant HIV sequences. Queiroz2007
201198   5 B, C, BF B, BF, C BF, F gp160 593 604 gp41(82-93) 8001..8036   LGIWGCSGKLIC LGlWGCSGKLIC I3L I595L OV observed variant Sequence Variant LGlWGCSGKLIC was seen in all 11 HIV subtype F sequences, and 9/19 HIV B/F recombinants. Queiroz2007
201198   6 B, C, BF B, BF, C F gp160 593 604 gp41(82-93) 8001..8036   LGIWGCSGKLIC LGlWGCSGrLIC I3L, K9R I595L, K601R OV observed variant Sequence Variant LGlWGCSGrLIC was seen only in 2/19 HIV B/F recombinants. Queiroz2007
201201   9 B, C, BF B, BF, C BF, F gp160 594 603 gp41(83-92) 8004..8033   GIWGCSGKLI GlWGCSGKLI I2L I595L OV observed variant Sequence Variant GlWGCSGKLI was seen in all 11 HIV subtype F sequences, and 9/19 HIV B/F recombinants. Queiroz2007
201201   10 B, C, BF B, BF, C BF gp160 594 603 gp41(83-92) 8004..8033   GIWGCSGKLI GlWGCSGrLI I2L, K8R I595L, K601R OV observed variant Sequence Variant GlWGCSGrLI was seen only in 2/19 HIV B/F recombinants. Queiroz2007
201200   7 B, C, BF B, BF, C BF, F gp160 594 604 gp41(83-93) 8004..8036   GIWGCSGKLIC GlWGCSGKLIC I2L I595L OV observed variant Sequence Variant GlWGCSGKLIC was seen in all 11 HIV subtype F sequences, and 9/19 HIV B/F recombinants. Queiroz2007
201200   8 B, C, BF B, BF, C BF gp160 594 604 gp41(83-93) 8004..8036   GIWGCSGKLIC GlWGCSGrLIC I2L, K8R I595L, K601R OV observed variant Sequence Variant GlWGCSGrLIC was seen only in 2/19 HIV B/F recombinants. Queiroz2007
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