Found 23 matching records:
HXB2 Location | Gag(147-155) | Gag Epitope Map
View variants at this location |
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Epitope |
ISPRTLNAW
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Epitope Alignment | ||||
Variants |
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Epitope Name | IW9 | |||||
Species (MHC/HLA) | human(B*57:01) |
Showing all: 1 variant(s).
Variant ID. | 1980 |
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Epitope Seq. | ISPRTLNAW |
Variant Seq. | lSPRTLNAW |
Mutations | I/L |
Epitope Location | I1L |
HXB2 Location | I147L |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | A simple but atypical pattern of escape was seen with this variant in one patient, CH77 where the variant completely replaced the index epitope. In patient CH58, no significant change with respect to selection in this epitope was detected. For CH58, positive ELISpot from the full proteome scan but with not statistical evidence for selection for change was seen. For CH77, known T cell response from the full proteome scan with evidence for variation and escape by positive ELISpot was seen. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Gag(240-249) | Gag Epitope Map
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Epitope |
TSTLQEQIGW
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Epitope Alignment | |||||||
Variants |
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Species (MHC/HLA) | human(B*57:01) |
Showing all: 2 variant(s).
Variant ID. | 2128 |
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Epitope Seq. | TSTLQEQIGW |
Variant Seq. | TnTLQEQIGW |
Mutations | S/N |
Epitope Location | S2N |
HXB2 Location | S241N |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH58 carried this mutant. By day 85, two mutants, TnTLQEQIGW (22%) and TSTLQEQIeW (67%) dominated; pooled mutants were reactive to the same extent as the transmitted form. |
Variant ID. | 2129 |
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Epitope Seq. | TSTLQEQIGW |
Variant Seq. | TSTLQEQIeW |
Mutations | G/E |
Epitope Location | G9E |
HXB2 Location | G248E |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH58 carried this mutant. By day 85, two mutants, TnTLQEQIGW (22%) and TSTLQEQIeW (67%) dominated; pooled mutants were reactive to the same extent as the transmitted form. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Gag(240-249) | Gag Epitope Map
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Epitope |
TSTLQEQVGW
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Epitope Alignment | ||||||||||
Variants |
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Epitope Name | TW10 | |||||||||||
Species (MHC/HLA) | human(B*57:01) |
Showing all: 3 variant(s).
Variant ID. | 1987 |
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Epitope Seq. | TSTLQEQVGW |
Variant Seq. | TSTLQEQiGW |
Mutations | V/I |
Epitope Location | V8I |
HXB2 Location | V247I |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | In patient 77 at day 159, the transmitted epitope disappeared and was substituted by two variants, TSTLQEQiGW (89%) and TSTLQEQVeW (11%). At the same time, response was high. |
Variant ID. | 1988 |
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Epitope Seq. | TSTLQEQVGW |
Variant Seq. | TSTLQEQVeW |
Mutations | G/E |
Epitope Location | G9E |
HXB2 Location | G248E |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | In patient 77 at day 159, the transmitted epitope disappeared and was substituted by two variants, TSTLQEQiGW (89%) and TSTLQEQVeW (11%). At the same time, response was high. |
Variant ID. | 2332 |
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Epitope Seq. | TSTLQEQVGW |
Variant Seq. | TSnLQEQiaW |
Mutations | T/N V/I G/A |
Epitope Location | T3N V8I G9A |
HXB2 Location | T242N V247I G248A |
Mutation Type | IE: inferred escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining |
Note | In patient CH77 at 592 days, this variant predominated and the authors infer escape. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Gag(395-403) | Gag Epitope Map
View variants at this location |
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Epitope |
CGKEGHIAR
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Epitope Alignment | |||||||
Variants |
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Species (MHC/HLA) | human(A*31:01) |
Showing all: 2 variant(s).
Variant ID. | 2004 |
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Epitope Seq. | CGKEGHIAR |
Variant Seq. | CGKEGHIAk |
Mutations | R/K |
Epitope Location | R9K |
HXB2 Location | R403K |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | CGKEGHIAR was strongly recognized by T cells, whereas CGKEGHIAk was not. |
Variant ID. | 2005 |
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Epitope Seq. | CGKEGHIAR |
Variant Seq. | CGKEGHlAR |
Mutations | I/L |
Epitope Location | I7L |
HXB2 Location | I401L |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | CGKEGHIAR was strongly recognized by T cells, whereas the mutant was not. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Gag(481-498) | Gag Epitope Map
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Epitope |
KELYPLASLRSLFGNDPS
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Epitope Alignment | ||||
Variants |
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Species (MHC/HLA) | human |
Showing all: 1 variant(s).
Variant ID. | 2081 |
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Epitope Seq. | KELYPLASLRSLFGNDPS |
Variant Seq. | qELYPLASLRSLFGNDPS |
Mutations | K/Q |
Epitope Location | K1Q |
HXB2 Location | K481Q |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant in Patient CH40 gave a positive ELISpot from the full proteome scan but was not associated with statistical evidence of positive selection. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Pol(81-98) | Pol Epitope Map
View variants at this location |
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Epitope |
DTGADDTVLEEMNLPGRW
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Epitope Alignment | ||||
Variants |
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Species (MHC/HLA) | human |
Showing all: 1 variant(s).
Variant ID. | 2330 |
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Epitope Seq. | {KEALL}DTGADDTVLEEMNLPGRW |
Variant Seq. | {rEALL}DTGADDTVLEEMNLPGRW |
Mutations | K/R |
Epitope Location | K-5R |
HXB2 Location | K76R |
Mutation Type | CE: calculated escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining |
Note | The mutation seen proximal to DTGADDTVLEEMNLPGRW was {GQLrEAL}DTGADDTVLEEMNLPGRW where K/R, and it was predicted to be a processing escape. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Vif(119-127) | Vif Epitope Map
View variants at this location |
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Epitope |
AIRKAILGR
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Epitope Alignment | ||||||||||||||||
Variants |
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Species (MHC/HLA) | human |
Showing all: 5 variant(s).
Variant ID. | 2083 |
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Epitope Seq. | AIRKAILGR |
Variant Seq. | AIRKAlLGR |
Mutations | I/L |
Epitope Location | I6L |
HXB2 Location | I124L |
Mutation Type | IE: inferred escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH40 carried this mutant, and at the same time lost response to the original epitope. |
Variant ID. | 2084 |
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Epitope Seq. | AIRKAILGR |
Variant Seq. | AIRKAIvGR |
Mutations | L/V |
Epitope Location | L7V |
HXB2 Location | L125V |
Mutation Type | IE: inferred escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH40 carried this mutant, and at the same time lost response to the original epitope. |
Variant ID. | 2085 |
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Epitope Seq. | AIRKAILGR |
Variant Seq. | AIRtAILGR |
Mutations | K/T |
Epitope Location | K4T |
HXB2 Location | K122T |
Mutation Type | IE: inferred escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH40 carried this mutant, and at the same time lost response to the original epitope. |
Variant ID. | 2086 |
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Epitope Seq. | AIRKAILGR |
Variant Seq. | AIReAILGR |
Mutations | K/E |
Epitope Location | K4E |
HXB2 Location | K122E |
Mutation Type | IE: inferred escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH40 carried this mutant, and at the same time lost response to the original epitope. |
Variant ID. | 2329 |
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Epitope Seq. | {ES}AIRKAILGR |
Variant Seq. | {dS}AIReAILGR |
Mutations | E/D K/E |
Epitope Location | E-2D K4E |
HXB2 Location | E117D K122E |
Mutation Type | IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH40 carried this mutant, and at the same time lost response to the original epitope. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Vpr(73-90) | Vpr Epitope Map
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Epitope |
RIGCQHSRIGISQRRRAR
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Epitope Alignment | ||||||||||||||||
Variants |
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Species (MHC/HLA) | human |
Showing all: 5 variant(s).
Variant ID. | 1998 |
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Epitope Seq. | RIGCQHSRIGISQRRRAR |
Variant Seq. | RIGCQHSRIGIrQRRRAR |
Mutations | S/R |
Epitope Location | S12R |
HXB2 Location | S84R |
Mutation Type | R: reversion |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This S84R substitution to the Clade B consensus persisted and was inferred to be a case of reversion. While there was no ELISpot evidence, there was evidence for positive selection. |
Variant ID. | 1999 |
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Epitope Seq. | RIGCQHSRIGISQRRRAR |
Variant Seq. | RIGCQrSRIGIrQRRRAR |
Mutations | S/R H/R |
Epitope Location | S12R H6R |
HXB2 Location | S84R H78R |
Mutation Type | CE: calculated escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Substitution seen in Patient CH40. While there was no ELISpot evidence, there was evidence for positive selection. |
Variant ID. | 2000 |
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Epitope Seq. | RIGCQHSRIGISQRRRAR |
Variant Seq. | RIGCQHSRIGIrhRRRAR |
Mutations | S/R Q/H |
Epitope Location | S12R Q13H |
HXB2 Location | S84R Q85H |
Mutation Type | CE: calculated escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Substitution seen in Patient CH40. While there was no ELISpot evidence, there was evidence for positive selection. |
Variant ID. | 2001 |
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Epitope Seq. | RIGCQHSRIGISQRRRAR |
Variant Seq. | RIGCQHSRIGIgQRRRAR |
Mutations | S/G |
Epitope Location | S12G |
HXB2 Location | S84G |
Mutation Type | CE: calculated escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Substitution seen in Patient CH40. While there was no ELISpot evidence, there was evidence for positive selection. |
Variant ID. | 2002 |
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Epitope Seq. | RIGCQHSRIGISQRRRAR |
Variant Seq. | RIGCQHSRIGlgQRRRAR |
Mutations | I/L S/G |
Epitope Location | I11L S12G |
HXB2 Location | I83L S84G |
Mutation Type | CE: calculated escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Substitution seen in Patient CH40. While there was no ELISpot evidence, there was evidence for positive selection. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Rev(9-26) | Rev Epitope Map
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Epitope |
DEDLLKTVRLIKRLYQSS
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Epitope Alignment | ||||||||||||||||||||||
Variants |
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Species (MHC/HLA) | human |
Showing all: 7 variant(s).
Variant ID. | 2050 |
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Epitope Seq. | DEDLLKTVRLIKRLYQSS |
Variant Seq. | DEnLLKTVRLIKRLYQSS |
Mutations | D/N |
Epitope Location | D3N |
HXB2 Location | D11N |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant seen in Patient CH77. Response not measured. |
Variant ID. | 2051 |
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Epitope Seq. | DEDLLKTVRLIKRLYQSS |
Variant Seq. | DEDLLKaVRLIKRLYQSS |
Mutations | T/A |
Epitope Location | T7A |
HXB2 Location | T15A |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant seen in Patient CH77. Response not measured. |
Variant ID. | 2052 |
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Epitope Seq. | DEDLLKTVRLIKRLYQSS |
Variant Seq. | DEDLLKiVRLIKRLYQSS |
Mutations | T/I |
Epitope Location | T7I |
HXB2 Location | T15I |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant seen in Patient CH77. Response not measured. |
Variant ID. | 2053 |
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Epitope Seq. | DEDLLKTVRLIKRLYQSS |
Variant Seq. | DEDLLKTVgiIKRLYQSS |
Mutations | L/I R/G |
Epitope Location | L10I R9G |
HXB2 Location | L18I R17G |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant seen in Patient CH77. Response not measured. |
Variant ID. | 2054 |
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Epitope Seq. | DEDLLKTVRLIKRLYQSS |
Variant Seq. | DEDLLKTVRvIKRLYQSS |
Mutations | L/V |
Epitope Location | L10V |
HXB2 Location | L18V |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant seen in Patient CH77. Response not measured. |
Variant ID. | 2055 |
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Epitope Seq. | DEDLLKTVRLIKRLYQSS |
Variant Seq. | DEDLLKTVRiIKRLYQSS |
Mutations | L/I |
Epitope Location | L10I |
HXB2 Location | L18I |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant seen in Patient CH77. Response not measured. |
Variant ID. | 2056 |
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Epitope Seq. | DEDLLKTVRLIKRLYQSS |
Variant Seq. | DEDLLrTVRLIKRLYQSS |
Mutations | K/R |
Epitope Location | K6R |
HXB2 Location | K14R |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant seen in Patient CH77. Response not measured. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Rev(47-55) | Rev Epitope Map
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Epitope |
QRQRQIQSL
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Epitope Alignment | ||||||||||||||||
Variants |
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Species (MHC/HLA) | human |
Showing all: 5 variant(s).
Variant ID. | 1990 |
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Epitope Seq. | QRQRQIQSL |
Variant Seq. | QkQRQIQSL |
Mutations | R/K |
Epitope Location | R2K |
HXB2 Location | R48K |
Mutation Type | DR: diminished response |
Method | CD8 T-cell Elispot - IFNy, Sequence |
Note | Patient SUMA0874 developed this nonsynonymous substitution that diminished CTL response measured by ELISpot. |
Variant ID. | 1991 |
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Epitope Seq. | QRQRQIQSL |
Variant Seq. | QRQRhIQSL |
Mutations | Q/H |
Epitope Location | Q5H |
HXB2 Location | Q51H |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Sequence |
Note | Patient SUMA0874 developed this nonsynonymous substitution that abrogated ELISpot response. |
Variant ID. | 1992 |
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Epitope Seq. | QRQRQIQSL |
Variant Seq. | QRQRQIrSL |
Mutations | Q/R |
Epitope Location | Q7R |
HXB2 Location | Q53R |
Mutation Type | DR: diminished response |
Method | CD8 T-cell Elispot - IFNy, Sequence |
Note | Patient SUMA0874 developed this nonsynonymous substitution that diminished CTL response measured by ELISpot. |
Variant ID. | 1993 |
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Epitope Seq. | QRQRQIQSL |
Variant Seq. | QRQRQIQSi |
Mutations | L/I |
Epitope Location | L9I |
HXB2 Location | L55I |
Mutation Type | DR: diminished response SF: susceptible form |
Method | CD8 T-cell Elispot - IFNy, Sequence |
Note | Patient SUMA0874 developed this nonsynonymous substitution that had a robust EliSpot response, but somewhat diminished. |
Variant ID. | 2207 |
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Epitope Seq. | QRQRQIQSL |
Variant Seq. | QRQRQIQlL |
Mutations | S/L |
Epitope Location | S8L |
HXB2 Location | S54L |
Mutation Type | DR: diminished response E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Sequence |
Note | Patient SUMA0874 developed this nonsynonymous substitution that severely diminished CTL response measured by ELISpot. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Rev(49-66) | Rev Epitope Map
View variants at this location |
||||
---|---|---|---|---|---|---|
Epitope |
QRQIRSISERILSTYLER
|
Epitope Alignment | ||||
Variants |
|
|||||
Species (MHC/HLA) | human |
Showing all: 1 variant(s).
Variant ID. | 2088 |
---|---|
Epitope Seq. | QRQIRSISERILSTYLER |
Variant Seq. | QRQIRSISERILnTYLER |
Mutations | S/N |
Epitope Location | S13N |
HXB2 Location | S61N |
Mutation Type | IE: inferred escape |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH40 responded to the epitope until day 412 when this mutant dominated the sequenced population. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Env(334-351) | Env Epitope Map
View variants at this location |
||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Epitope |
SGEDWNKTLSHVVDKLRE
|
Epitope Alignment | ||||||||||||||||
Variants |
|
|||||||||||||||||
Species (MHC/HLA) | human |
Showing all: 5 variant(s).
Variant ID. | 2061 |
---|---|
Epitope Seq. | SGEDWNKTLSHVVDKLRE |
Variant Seq. | SGEDWNKTLSyVVDKLRE |
Mutations | H/Y |
Epitope Location | H11Y |
HXB2 Location | H344Y |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant sequence was observed but not documented as an escape mutant. |
Variant ID. | 2062 |
---|---|
Epitope Seq. | SGEDWNKTLSHVVDKLRE |
Variant Seq. | SGEDWNKTLSHVVnKLRE |
Mutations | D/N |
Epitope Location | D14N |
HXB2 Location | D347N |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant sequence was observed but not documented as an escape mutant. |
Variant ID. | 2064 |
---|---|
Epitope Seq. | SGEDWNKTLSHVVDKLRE |
Variant Seq. | SGEDWNKTLnHVVDKLRE |
Mutations | S/N |
Epitope Location | S10N |
HXB2 Location | S343N |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant sequence was observed but not documented as an escape mutant. |
Variant ID. | 2065 |
---|---|
Epitope Seq. | SGEDWNKTLSHVVDKLRE |
Variant Seq. | SGEDWNKTLSHVVaKLRE |
Mutations | D/A |
Epitope Location | D14A |
HXB2 Location | D347A |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant sequence was observed but not documented as an escape mutant. |
Variant ID. | 2273 |
---|---|
Epitope Seq. | SGEDWNKTLSHVVDKLRE |
Variant Seq. | SGEDWNKTLgHVVDKLRE |
Mutations | S/G |
Epitope Location | S10G |
HXB2 Location | S343G |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant sequence was observed but not documented as an escape mutant. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Env(352-361) | Env Epitope Map
View variants at this location |
|||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Epitope |
QFRNKTIVF
|
Epitope Alignment | |||||||||||||||||||
Variants |
|
||||||||||||||||||||
Species (MHC/HLA) | human |
Showing all: 6 variant(s).
Variant ID. | 2033 |
---|---|
Epitope Seq. | QFRNKTIVF |
Variant Seq. | QFkNKTIVF |
Mutations | R/K |
Epitope Location | R3K |
HXB2 Location | R354K |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly described epitope showed escape early on in Patient CH77. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2034 |
---|---|
Epitope Seq. | QFRNKTIVF |
Variant Seq. | QFsNKTIVF |
Mutations | R/S |
Epitope Location | R3S |
HXB2 Location | R354S |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly described epitope showed escape early on in Patient CH77. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2035 |
---|---|
Epitope Seq. | QFRNKTIVF |
Variant Seq. | QFnNKTIVF |
Mutations | R/N |
Epitope Location | R3N |
HXB2 Location | R354N |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly described epitope showed escape early on in Patient CH77. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2036 |
---|---|
Epitope Seq. | QFRNKTIVF |
Variant Seq. | QFRNKaIVF |
Mutations | T/A |
Epitope Location | T6A |
HXB2 Location | T357A |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly described epitope showed escape early on in Patient CH77. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2037 |
---|---|
Epitope Seq. | QFRNKTIVF |
Variant Seq. | QFkNKaIVF |
Mutations | R/K T/A |
Epitope Location | R3K T6A |
HXB2 Location | R354K T357A |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly described epitope showed escape early on in Patient CH77. There was no response to the R3K mutant; R3K, T6A was not tested. |
Variant ID. | 2038 |
---|---|
Epitope Seq. | QFRNKTIVF |
Variant Seq. | QFkdKTIVF |
Mutations | R/K N/D |
Epitope Location | R3K N4D |
HXB2 Location | R354K N355D |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly described epitope showed escape early on in Patient CH77. There was no response to the R3K mutant; R3K, N4D was not tested. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Env(584-592) | Env Epitope Map
View variants at this location |
|||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Epitope |
ERYLRDQQL
|
Epitope Alignment | |||||||||||||
Variants |
|
||||||||||||||
Species (MHC/HLA) | human(B*14:01) |
Showing all: 4 variant(s).
Variant ID. | 2066 |
---|---|
Epitope Seq. | ERYLRDQQL |
Variant Seq. | ERYLgDQQL |
Mutations | R/G |
Epitope Location | R5G |
HXB2 Location | R588G |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant arose in longitudinal study of Patient CH58, but loss of response not documented. |
Variant ID. | 2067 |
---|---|
Epitope Seq. | ERYLRDQQL |
Variant Seq. | ERhLRDQQL |
Mutations | Y/H |
Epitope Location | Y3H |
HXB2 Location | Y586H |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Decrease in response to this epitope was documented in Patient CH58. |
Variant ID. | 2068 |
---|---|
Epitope Seq. | ERYLRDQQL |
Variant Seq. | ERYLkDQQL |
Mutations | R/K |
Epitope Location | R5K |
HXB2 Location | R588K |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant arose in longitudinal study of Patient CH58, but loss of response not documented. |
Variant ID. | 2069 |
---|---|
Epitope Seq. | ERYLRDQQL |
Variant Seq. | ERYLsDQQL |
Mutations | R/S |
Epitope Location | R5S |
HXB2 Location | R588S |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Decrease in response to this epitope was documented in Patient CH58. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Env(597-622) | Env Epitope Map
View variants at this location |
|||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Epitope |
GCSGRVICTTTVPWNVSWSNKSLNEI
|
Epitope Alignment | |||||||||||||
Variants |
|
||||||||||||||
Species (MHC/HLA) | human(B*57:01) |
Showing all: 4 variant(s).
Variant ID. | 2057 |
---|---|
Epitope Seq. | GCSGRVICTTTVPWNVSWSNKSLNEI |
Variant Seq. | dCSGRVICTTTVPWNVSWSNKSLNEI |
Mutations | G/D |
Epitope Location | G1D |
HXB2 Location | G597D |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | The peptide containing epitope TTVPWNVSW showed this variant in Patient CH77. |
Variant ID. | 2058 |
---|---|
Epitope Seq. | GCSGRVICTTTVPWNVSWSNKSLNEI |
Variant Seq. | GCSGRVICTTTVPWNsSWSNKSLNEI |
Mutations | V/S |
Epitope Location | V16S |
HXB2 Location | V612S |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | The peptide containing epitope TTVPWNVSW showed this variant in Patient CH77. |
Variant ID. | 2059 |
---|---|
Epitope Seq. | GCSGRVICTTTVPWNVSWSNKSLNEI |
Variant Seq. | GCSGRVICTTTVPWNtSWSNKSLsEI |
Mutations | V/T N/S |
Epitope Location | V16T N24S |
HXB2 Location | V612T N620S |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | The peptide containing epitope TTVPWNVSW showed this variant in Patient CH77. |
Variant ID. | 2060 |
---|---|
Epitope Seq. | GCSGRVICTTTVPWNVSWSNKSLNEI |
Variant Seq. | GCSGRVICTTTVPWNtSWSNKSLNEI |
Mutations | V/T |
Epitope Location | V16T |
HXB2 Location | V612T |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | The peptide containing epitope TTVPWNVSW showed this variant in Patient CH77. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Env(765-782) | Env Epitope Map
View variants at this location |
||||
---|---|---|---|---|---|---|
Epitope |
LFSYHRLRDLLLIVTRIV
|
Epitope Alignment | ||||
Variants |
|
|||||
Species (MHC/HLA) | human |
Showing all: 1 variant(s).
Variant ID. | 2082 |
---|---|
Epitope Seq. | LFSYHRLRDLLLIVTRIV |
Variant Seq. | LFrYHRLRDLLLIVTRIV |
Mutations | S/R |
Epitope Location | S3R |
HXB2 Location | S767R |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This variant in Patient CH40 gave a positive ELISpot from the full proteome scan but was not associated with statistical evidence of positive selection. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Env(822-836) | Env Epitope Map
View variants at this location |
|||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Epitope |
VAEGTDRVIEELQRA
|
Epitope Alignment | |||||||||||||||||||||||||||||||
Variants |
|
||||||||||||||||||||||||||||||||
Species (MHC/HLA) | human |
Showing all: 10 variant(s).
Variant ID. | 2130 |
---|---|
Epitope Seq. | VAEGTDRVIEELQRA |
Variant Seq. | VAEGTgRVIEgLQRA |
Mutations | E/G D/G |
Epitope Location | E11G D6G |
HXB2 Location | E832G D827G |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this variant. |
Variant ID. | 2131 |
---|---|
Epitope Seq. | VAEGTDRVIEELQRA |
Variant Seq. | VAEGTDRVIEgLQRA |
Mutations | E/G |
Epitope Location | E11G |
HXB2 Location | E832G |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this variant. |
Variant ID. | 2132 |
---|---|
Epitope Seq. | VAEGTDRVIEELQRA |
Variant Seq. | VAEGTDRVIEEsQRA |
Mutations | L/S |
Epitope Location | L12S |
HXB2 Location | L833S |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this variant. |
Variant ID. | 2133 |
---|---|
Epitope Seq. | VAEGTDRVIEELQRA |
Variant Seq. | VAEGTDRiIEEsQRA |
Mutations | L/S V/I |
Epitope Location | L12S V8I |
HXB2 Location | L833S V829I |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this variant. |
Variant ID. | 2134 |
---|---|
Epitope Seq. | VAEGTDRVIEELQRA |
Variant Seq. | VAEGTDRVIEaLQRA |
Mutations | E/A |
Epitope Location | E11A |
HXB2 Location | E832A |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this variant. |
Variant ID. | 2318 |
---|---|
Epitope Seq. | {A}VAEGTDRVIEELQRA |
Variant Seq. | {t}VAEGTDRVIEELQRA |
Mutations | A/T |
Epitope Location | A-1T |
HXB2 Location | A821T |
Mutation Type | CM: compensatory mutation IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2319 |
---|---|
Epitope Seq. | {A}VAEGTDRVIEELQRA |
Variant Seq. | {t}VAEGTDRVIEgLQRA |
Mutations | A/T E/G |
Epitope Location | A-1T E11G |
HXB2 Location | A821T E832G |
Mutation Type | CM: compensatory mutation IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2320 |
---|---|
Epitope Seq. | {A}VAEGTDRVIEELQRA |
Variant Seq. | {t}VAEGTDRiIEgLQRA |
Mutations | A/T E/G V/I |
Epitope Location | A-1T E11G V8I |
HXB2 Location | A821T E832G V829I |
Mutation Type | CM: compensatory mutation IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2321 |
---|---|
Epitope Seq. | {A}VAEGTDRVIEELQRA |
Variant Seq. | {v}VAEGTDRiIEgLQRv |
Mutations | A/V E/G A/V V/I |
Epitope Location | A-1V E11G A15V V8I |
HXB2 Location | A821V E832G A836V V829I |
Mutation Type | CM: compensatory mutation IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2322 |
---|---|
Epitope Seq. | {A}VAEGTDRVIEELQRA |
Variant Seq. | {v}VAEGTDRiIEgLQRA |
Mutations | A/V E/G V/I |
Epitope Location | A-1V E11G V8I |
HXB2 Location | A821V E832G V829I |
Mutation Type | CM: compensatory mutation IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation . |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Env(830-847) | Env Epitope Map
View variants at this location |
|||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Epitope |
IEVVQRACRAILHIPRRI
|
Epitope Alignment | |||||||||||||
Variants |
|
||||||||||||||
Species (MHC/HLA) | human |
Showing all: 4 variant(s).
Variant ID. | 2090 |
---|---|
Epitope Seq. | IEVVQRACRAILHIPRRI |
Variant Seq. | IEVVQRACRAILHIPRkI |
Mutations | R/K |
Epitope Location | R17K |
HXB2 Location | R846K |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | The authors suggested this as an escape mutation by statistical evidence, but the variant was transient, infrequent, and there was no loss of EliSpot response to the original epitope. |
Variant ID. | 2091 |
---|---|
Epitope Seq. | IEVVQRACRAILHIPRRI |
Variant Seq. | IEiVQRACRAILHIPRRI |
Mutations | V/I |
Epitope Location | V3I |
HXB2 Location | V832I |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | The authors suggested this as an escape mutation by statistical evidence, but the variant was transient, infrequent, and there was no loss of EliSpot response to the original epitope. |
Variant ID. | 2092 |
---|---|
Epitope Seq. | IEVVQRACRAILHIPRRI |
Variant Seq. | IEVVQRACRAIcHIPRRI |
Mutations | L/C |
Epitope Location | L12C |
HXB2 Location | L841C |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | The authors suggested this as an escape mutation by statistical evidence, but the variant was transient, infrequent, and there was no loss of EliSpot response to the original epitope. |
Variant ID. | 2093 |
---|---|
Epitope Seq. | IEVVQRACRAILHIPRRI |
Variant Seq. | IEVVQRACRAIrHIPRRI |
Mutations | L/R |
Epitope Location | L12R |
HXB2 Location | L841R |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | The authors suggested this as an escape mutation by statistical evidence, but the variant was transient, infrequent, and there was no loss of EliSpot response to the original epitope. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Env(838-855) | Env Epitope Map
View variants at this location |
||||
---|---|---|---|---|---|---|
Epitope |
RAVLNIPTRIRQGLERAL
|
Epitope Alignment | ||||
Variants |
|
|||||
Species (MHC/HLA) | human |
Showing all: 1 variant(s).
Variant ID. | 2135 |
---|---|
Epitope Seq. | RAVLNIPTRIRQGLERAL |
Variant Seq. | RAVLNvPTRIRQGLERAL |
Mutations | I/V |
Epitope Location | I6V |
HXB2 Location | I843V |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This transmitted peptide sequence RAVLNIPTRIRQGLERAL was recognized in patient CH77 by week 24. A mutation was seen at RAVLNvPTRIRQGLERAL. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Nef(17-34) | Nef Epitope Map
View variants at this location |
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Epitope |
RERRRRDEPAAVGVGPAS
|
Epitope Alignment | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Variants |
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Species (MHC/HLA) | human |
Showing all: 21 variant(s).
Variant ID. | 2006 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRRnEPAAVGVGPAS |
Mutations | D/N |
Epitope Location | D7N |
HXB2 Location | D23N |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. Variant occurred at day 14, when pooled mutants were negative for response. |
Variant ID. | 2007 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRRnEPAAVGVGsAS |
Mutations | P/S D/N |
Epitope Location | P16S D7N |
HXB2 Location | P32S D23N |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Variant ID. | 2008 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRkDEPAAVGVGPAS |
Mutations | R/K |
Epitope Location | R6K |
HXB2 Location | R22K |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 14. Loss of response to this specific variant was clearly documented. |
Variant ID. | 2009 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRkDEPAAVGVGPvS |
Mutations | A/V R/K |
Epitope Location | A17V R6K |
HXB2 Location | A33V R22K |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Variant ID. | 2010 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRkRDEPAAVGVGPAS |
Mutations | R/K |
Epitope Location | R5K |
HXB2 Location | R21K |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at several time points, and loss of response was clearly documented. |
Variant ID. | 2011 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERgkRDEPAAVGVGPAS |
Mutations | R/G R/K |
Epitope Location | R4G R5K |
HXB2 Location | R20G R21K |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 592. |
Variant ID. | 2012 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERR....PAAVGVGPAS |
Mutations | R/. R/. D/. E/. |
Epitope Location | R5. R6. D7. E8. |
HXB2 Location | R21. R22. D23. E24. |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 32. |
Variant ID. | 2013 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRReEPAAVGVGPAS |
Mutations | D/E |
Epitope Location | D7E |
HXB2 Location | D23E |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at several time points and lack of response to variant was clearly demonstrated. |
Variant ID. | 2014 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | kERRRReEPAAVGVGPAS |
Mutations | R/K D/E |
Epitope Location | R1K D7E |
HXB2 Location | R17K D23E |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159, when patient response had been lost. |
Variant ID. | 2015 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRReEPAAVGVGPvS |
Mutations | A/V D/E |
Epitope Location | A17V D7E |
HXB2 Location | A33V D23E |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Variant ID. | 2016 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRgDEPAAVGVGPAS |
Mutations | R/G |
Epitope Location | R6G |
HXB2 Location | R22G |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Variant ID. | 2017 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRgDEPAAVGVGtAS |
Mutations | P/T R/G |
Epitope Location | P16T R6G |
HXB2 Location | P32T R22G |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Variant ID. | 2018 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRtDEPAAVGVGPAS |
Mutations | R/T |
Epitope Location | R6T |
HXB2 Location | R22T |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Variant ID. | 2019 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRgRDEPAAVGVGPAS |
Mutations | R/G |
Epitope Location | R5G |
HXB2 Location | R21G |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159. |
Variant ID. | 2020 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRRDEsAAVGVGPAS |
Mutations | P/S |
Epitope Location | P9S |
HXB2 Location | P25S |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 32 when patient response was unknown. |
Variant ID. | 2021 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | REgaRerrPAAVGVGPAS |
Mutations | R/G R/A R/E D/R E/R |
Epitope Location | R3G R4A R6E D7R E8R |
HXB2 Location | R19G R20A R22E D23R E24R |
Mutation Type | OV: observed variant |
Method | Sequence |
Note | This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant was found at day 32. |
Variant ID. | 2024 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRgRDEPAAVGVGPAS|r |
Mutations | Q/R R/G |
Epitope Location | Q19R R5G |
HXB2 Location | Q35R R21G |
Mutation Type | E: escape documented in this paper |
Method | Sequence |
Note | This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Variant ID. | 2025 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRgkDEPAAVGVGPAS|r |
Mutations | Q/R R/G R/K |
Epitope Location | Q19R R5G R6K |
HXB2 Location | Q35R R21G R22K |
Mutation Type | OV: observed variant |
Method | Sequence |
Note | This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 592. |
Variant ID. | 2026 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRtDEPAAVGVGPAS|r |
Mutations | S/R R/T |
Epitope Location | S18R R6T |
HXB2 Location | S34R R22T |
Mutation Type | E: escape documented in this paper |
Method | Sequence |
Note | This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Variant ID. | 2272 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRReEPAAVGVGPAS |
Mutations | R/E |
Epitope Location | R6E |
HXB2 Location | R22E |
Mutation Type | OV: observed variant |
Method | Sequence |
Note | This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 32; escape was not documented. |
Variant ID. | 2334 |
---|---|
Epitope Seq. | RERRRRDEPAAVGVGPAS |
Variant Seq. | RERRRgDEPA.......S |
Mutations | A/. V/. G/. V/. G/. P/. A/. R/G |
Epitope Location | A11. V12. G13. V14. G15. P16. A17. R6G |
HXB2 Location | A27. V28. G29. V30. G31. P32. A33. R22G |
Mutation Type | E: escape documented in this paper |
Method | Sequence |
Note | This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Nef(82-90) | Nef Epitope Map
View variants at this location |
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Epitope |
KAALDLSHF
|
Epitope Alignment | ||||||||||||||||||||||||||||
Variants |
|
|||||||||||||||||||||||||||||
Species (MHC/HLA) | human(B*57:01) |
Showing all: 9 variant(s).
Variant ID. | 1981 |
---|---|
Epitope Seq. | KAALDLSHF |
Variant Seq. | KgALDLSHF |
Mutations | A/G |
Epitope Location | A2G |
HXB2 Location | A83G |
Mutation Type | DR: diminished response |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Documented reduced response to this variant. |
Variant ID. | 1982 |
---|---|
Epitope Seq. | KAALDLSHF |
Variant Seq. | qAALDLSHF |
Mutations | K/Q |
Epitope Location | K1Q |
HXB2 Location | K82Q |
Mutation Type | DR: diminished response |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Documented reduced response to this variant. |
Variant ID. | 1983 |
---|---|
Epitope Seq. | KAALDLSHF |
Variant Seq. | tAALDLSHF |
Mutations | K/T |
Epitope Location | K1T |
HXB2 Location | K82T |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant arose on day 32; response unknown. |
Variant ID. | 1984 |
---|---|
Epitope Seq. | KAALDLSHF |
Variant Seq. | pAALDLSHF |
Mutations | K/P |
Epitope Location | K1P |
HXB2 Location | K82P |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant arose on day 32; response unknown. |
Variant ID. | 1985 |
---|---|
Epitope Seq. | KAALDLSHF |
Variant Seq. | KAAhDLSHF |
Mutations | L/H |
Epitope Location | L4H |
HXB2 Location | L85H |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant arose on day 32; response unknown. |
Variant ID. | 1986 |
---|---|
Epitope Seq. | KAALDLSHF |
Variant Seq. | KAALDiSHF |
Mutations | L/I |
Epitope Location | L6I |
HXB2 Location | L87I |
Mutation Type | OV: observed variant |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | Variant arose on day 32; response unknown. |
Variant ID. | 2326 |
---|---|
Epitope Seq. | {V*****}KAALDLSHF |
Variant Seq. | {l*****}qAALDLSHF |
Mutations | K/Q V/L |
Epitope Location | K1Q V-6L |
HXB2 Location | K82Q V76L |
Mutation Type | CM: compensatory mutation IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This flanking substitution is predicted to be either a processing escape or a compensatory mutation. |
Variant ID. | 2327 |
---|---|
Epitope Seq. | {V*****}KAALDLSHF |
Variant Seq. | {*****}KgALDLSHF |
Mutations | A/G V/L |
Epitope Location | A2G V-6L |
HXB2 Location | A83G V76L |
Mutation Type | CM: compensatory mutation IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This flanking substitution is predicted to be either a processing escape or a compensatory mutation. |
Variant ID. | 2328 |
---|---|
Epitope Seq. | {M**}KAALDLSHF |
Variant Seq. | {**}KAALDLSHF |
Mutations | M/I |
Epitope Location | M-3I |
HXB2 Location | M79I |
Mutation Type | CM: compensatory mutation IE: inferred escape P: processing |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This flanking substitution is predicted to be either a processing escape or a compensatory mutation. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Nef(105-115) | Nef Epitope Map
View variants at this location |
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Epitope |
KRQDILDLWVY
|
Epitope Alignment | |||||||
Variants |
|
||||||||
Species (MHC/HLA) | human(C*07:01) |
Showing all: 2 variant(s).
Variant ID. | 2070 |
---|---|
Epitope Seq. | KRQDILDLWVY |
Variant Seq. | rRQDILDLWVY |
Mutations | K/R |
Epitope Location | K1R |
HXB2 Location | K105R |
Mutation Type | DR: diminished response |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This nonsynonymous change, K110R showed 50% CTL response compared to index epitope sequence in Patient CH58. It could also affect processing of the downstream epitope HTQGYFPDWQ. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Variant ID. | 2071 |
---|---|
Epitope Seq. | KRQDILDLWVY |
Variant Seq. | KRQeILDLWVY |
Mutations | D/E |
Epitope Location | D4E |
HXB2 Location | D108E |
Mutation Type | DR: diminished response |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This nonsynonymous change, K110R showed 50% CTL response compared to wild index epitope in Patient CH58. It could also affect processing of the downstream epitope HTQGYFPDWQ. Known T cell response from the full proteome scan with evidence for variation and escape was seen. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
HXB2 Location | Nef(188-196) | Nef Epitope Map
View variants at this location |
|||||||
---|---|---|---|---|---|---|---|---|---|
Epitope |
SLAFRHVAR
|
Epitope Alignment | |||||||
Variants |
|
||||||||
Species (MHC/HLA) | human(A*31:01) |
Showing all: 2 variant(s).
Variant ID. | 1997 |
---|---|
Epitope Seq. | SLAFRHVAR |
Variant Seq. | nLAFRHVAR |
Mutations | S/N |
Epitope Location | S1N |
HXB2 Location | S188N |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This S188N substitution was a dominating variant in Patient CH40. The variant was not recognized by EliSpot. |
Variant ID. | 2271 |
---|---|
Epitope Seq. | SLAFRHVAR |
Variant Seq. | SLAFRHVAq |
Mutations | R/Q |
Epitope Location | R9Q |
HXB2 Location | R196Q |
Mutation Type | E: escape documented in this paper |
Method | CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence |
Note | This R196Q substitution was a dominating variant in Patient CH40. The variant was not recognized by EliSpot. |
Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.
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