HIV molecular immunology database
Found 16 matching records:
| HXB2 Location | Pol(173-181) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
GPKVKQWPL
|
Epitope Alignment | ||||||||||
| Variants |
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| Species (MHC/HLA) | human(B8) | |||||||||||
Showing all: 3 variant(s).
| Variant ID. | 1238 |
|---|---|
| Epitope Seq. | GPKVKQWPL |
| Variant Seq. | sPKVKQWPL |
| Mutations | G/S |
| Epitope Location | G1S |
| HXB2 Location | G173S |
| Mutation Type | SF: susceptible form |
| Method | Chromium-release assay |
| Note | This longitudinally studied natural variant was functional, with normal activity of RT. Both mutant and wild-type index epitopes showed antagonism, inducing anergy in effector CTL against either epitope form (i.e. index or variant epitope) when previously exposed to the other form. |
| Variant ID. | 1240 |
|---|---|
| Epitope Seq. | GPKVKQWPL |
| Variant Seq. | GPrVKQWPL |
| Mutations | K/R |
| Epitope Location | K3R |
| HXB2 Location | K175R |
| Mutation Type | SF: susceptible form |
| Method | Chromium-release assay |
| Note | This longitudinally studied natural variant was functional, with normal activity of RT. Both mutant and wild-type index epitopes showed antagonism, inducing anergy in effector CTL against either form when previously exposed to the other form. |
| Variant ID. | 2216 |
|---|---|
| Epitope Seq. | GPKVKQWPL |
| Variant Seq. | GPeVKQWPL |
| Mutations | K/E |
| Epitope Location | K3E |
| HXB2 Location | K175E |
| Mutation Type | CHB: calculated diminished HLA binding |
| Method | Structural prediction |
| Note | This variant is suggested to have abrogated binding to HLA-B8 based on structural information of closely related species. The substitution is at an anchor residue. |
Meier1995 U.-C. Meier, P. Klenerman, P. Griffin, W. James, B. Koppe, B. Larder, R. E. Phillips, A. J. McMichael, and R. E. Phillips. Cytotoxic T Lymphocyte Lysis Inhibited by Viable HIV Mutants. Science, 270:1360-1362, 1995. HIV bearing mutations in epitope allowed transactive inhibition of specific CTL mediated lysis. Therefore, mutations in epitopes may not only allow escape from specific CTL, but enhance the ability of wildtype virus to persist. PubMed ID: 7481824. Show all entries for this paper.
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
| HXB2 Location | Pol(173-181) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
GPKVKQWPL
|
Epitope Alignment | ||||||||||
| Variants |
|
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| Species (MHC/HLA) | human(B8) | |||||||||||
Showing all: 3 variant(s).
| Variant ID. | 1239 |
|---|---|
| Epitope Seq. | GPKVKQWPL |
| Variant Seq. | sPKVKQWPL |
| Mutations | G/S |
| Epitope Location | G1S |
| HXB2 Location | G173S |
| Mutation Type | SF: susceptible form |
| Method | Chromium-release assay |
| Note | This longitudinally studied natural variant was functional, with normal activity of RT. Both mutant and wild-type index epitopes showed antagonism, inducing anergy in effector CTL against either epitope form (i.e. index or variant epitope) when previously exposed to the other form. |
| Variant ID. | 1241 |
|---|---|
| Epitope Seq. | GPKVKQWPL |
| Variant Seq. | GPrVKQWPL |
| Mutations | K/R |
| Epitope Location | K3R |
| HXB2 Location | K175R |
| Mutation Type | SF: susceptible form |
| Method | Chromium-release assay |
| Note | This longitudinally studied natural variant was functional, with normal activity of RT. Both mutant and wild-type index epitopes showed antagonism, inducing anergy in effector CTL against either form when previously exposed to the other form. |
| Variant ID. | 2217 |
|---|---|
| Epitope Seq. | GPKVKQWPL |
| Variant Seq. | GPeVKQWPL |
| Mutations | K/E |
| Epitope Location | K3E |
| HXB2 Location | K175E |
| Mutation Type | CHB: calculated diminished HLA binding |
| Method | Structural prediction |
| Note | This variant is suggested to have abrogated binding to HLA-B8 based on structural information of closely related species. The substitution is at an anchor residue. |
Goulder1997c P. J. R. Goulder, S. W. Reid, D. A. Price, C. A. O'Callaghan, A. J. McMichael, R. E. Phillips, and E. Y. Jones. Combined Structural and Immunological Refinement of HIV-1 HLA-B8 Restricted Cytotoxic T Lymphocyte Epitopes. Eur. J. Immunol., 27:1515-1521, 1997. PubMed ID: 9209505. Show all entries for this paper.
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
| HXB2 Location | Pol(273-282) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|
| Epitope |
VPLDKDFRKY
|
Epitope Alignment | ||||
| Variants |
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| Species (MHC/HLA) | human(B*35:01) | |||||
Showing all: 1 variant(s).
| Variant ID. | 1252 |
|---|---|
| Epitope Seq. | VPLDEDFRKY |
| Variant Seq. | VPLDkDFRKY |
| Mutations | E/K |
| Epitope Location | E5K |
| HXB2 Location | E277K |
| Mutation Type | SF: susceptible form |
| Method | Chromium-release assay, HLA binding |
| Note | This Lys-122 variant was not recognized by CTL specific to the Glu-122 index epitope though it was recognized by Lys-122-specific CTL. Glu-122 epitope was also unrecognized by Lys-122-specific CTL. Both index epitope and variant, however, were able to bind HLA-B35. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
Tomiyama1997 H. Tomiyama, K. Miwa, H. Shiga, Y. I. Moore, S. Oka, A. Iwamoto, Y. Kaneko, and M. Takiguchi. Evidence of Presentation of Multiple HIV-1 Cytotoxic T Lymphocyte Epitopes by HLA-B*3501 Molecules That Are Associated with the Accelerated Progression of AIDS. J. Immunol., 158:5026-5034, 1997. PubMed ID: 9144523. Show all entries for this paper.
| HXB2 Location | Pol(283-290) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
TAFTIPSI
|
Epitope Alignment | |||||||||||||||||||
| Variants |
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| Species (MHC/HLA) | human(B51) | ||||||||||||||||||||
Showing all: 6 variant(s).
| Variant ID. | 1254 |
|---|---|
| Epitope Seq. | TAFTIPSI |
| Variant Seq. | TAFTIPSt |
| Mutations | I/T |
| Epitope Location | I8T |
| HXB2 Location | I290T |
| Mutation Type | SF: susceptible form |
| Method | Chromium-release assay |
| Note | This variant has slightly altered CTL recognition and lysis, but 100x higher peptide concentration was required for 50% half maximum lysis. [Menendez-Arias1998]. |
| Variant ID. | 1255 |
|---|---|
| Epitope Seq. | TAFTIPSI |
| Variant Seq. | TAFTIPSv |
| Mutations | I/V |
| Epitope Location | I8V |
| HXB2 Location | I290V |
| Mutation Type | SF: susceptible form |
| Method | Chromium-release assay |
| Note | This variant has slightly altered CTL recognition and lysis, but 10x higher peptide concentration was required for 50% half maximum lysis. [Menendez-Arias1998]. |
| Variant ID. | 1256 |
|---|---|
| Epitope Seq. | TAFTIPSI |
| Variant Seq. | TvFTIPSI |
| Mutations | A/V |
| Epitope Location | A2V |
| HXB2 Location | A284V |
| Mutation Type | NSF: non-susceptible form |
| Method | Chromium-release assay |
| Note | CTL recognition of this highly conserved Ala-129 is almost abrogated. |
| Variant ID. | 1619 |
|---|---|
| Epitope Seq. | TAFTIPSI |
| Variant Seq. | TAFTIPSt |
| Mutations | I/T |
| Epitope Location | I8T |
| HXB2 Location | I290T |
| Mutation Type | DR: diminished response |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Chromium-release assay |
| Note | This naturally occurring, strain CAMI variant, was poorly recognized by a Patient LWS CTL clone. [Sipsas1997]. |
| Variant ID. | 1620 |
|---|---|
| Epitope Seq. | TAFTIPSI |
| Variant Seq. | TAFTIPSv |
| Mutations | I/V |
| Epitope Location | I8V |
| HXB2 Location | I290V |
| Mutation Type | DR: diminished response |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Chromium-release assay |
| Note | This naturally occurring, strain CAMI variant, was not well recognized by a Patient LWS CTL clone. [Sipsas1997]. |
| Variant ID. | 1621 |
|---|---|
| Epitope Seq. | TAFTIPSI |
| Variant Seq. | TvFTIPSt |
| Mutations | A/V I/T |
| Epitope Location | A2V I8T |
| HXB2 Location | A284V I290T |
| Mutation Type | DR: diminished response |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Chromium-release assay |
| Note | This naturally occurring, strain MANC variant, was very poorly recognized by a Patient LWS CTL clone. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
Sipsas1997 N. V. Sipsas, S. A. Kalams, A. Trocha, S. He, W. A. Blattner, B. D. Walker, and R. P. Johnson. Identification of Type-Specific Cytotoxic T Lymphocyte Responses to Homologous Viral Proteins in Laboratory Workers Accidentally Infected with HIV-1. J. Clin. Invest., 99:752-762, 1997. To examine a situation where the autologous strain and the reference reagents would be the same, the CTL response of three lab workers accidentally infected with HIV IIIB was studied. Both group specific and type specific epitopes were targets for CTL clones. One subject had a broadening of CTL response over time, using a broad range of restricting HLA class I alleles. Characterization of the cytotoxic T lymphocyte (CTL) response against HIV-1 has been limited by the use of target cells expressing viral proteins from laboratory isolates of HIV-1. This approach has favored identification of group-specific CTL responses and precluded assessment of the extent of type-specific CTL responses directed against HIV-1. Using cells expressing viral proteins from the HIV-1 IIIB strain, we performed a detailed characterization of HIV-1-specific CTL response in three laboratory workers accidentally infected with HIV-1 IIIB. Eight of the epitopes identified were group specific, lying in relatively conserved regions of Gag, reverse transcriptase, and envelope. Three type-specific epitopes were identified, two of them in highly variable regions of envelope. In longitudinal studies in one subject, seven different epitopes and five different restricting HLA class I alleles were identified, with a progressive increase in the number of CTL epitopes recognized by this subject over time. Our data demonstrate that type-specific CTL responses make up a significant proportion of the host cellular immune response against HIV-1 and that a broadening of epitope specificity may occur. PubMed ID: 9045880. Show all entries for this paper.
| HXB2 Location | Pol(313-321) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
AIFQSSMTK
|
Epitope Alignment | |||||||||||||||||||
| Variants |
|
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| Species (MHC/HLA) | human(A*03:01, A*11:01, A*68:01, A3) | ||||||||||||||||||||
Showing all: 6 variant(s).
| Variant ID. | 1257 |
|---|---|
| Epitope Seq. | AIFQSSMTK |
| Variant Seq. | AIFQcSMTK |
| Mutations | S/C |
| Epitope Location | S5C |
| HXB2 Location | S317C |
| Mutation Type | SF: susceptible form |
| Note | Binding and recognition of this natural variant to HLA-A*0301, -A*1101 and -A*6801-positive CTL was high. |
| Variant ID. | 1258 |
|---|---|
| Epitope Seq. | AIFQSSMTK |
| Variant Seq. | AIFQSSMTt |
| Mutations | K/T |
| Epitope Location | K9T |
| HXB2 Location | K321T |
| Mutation Type | DHB: diminished HLA binding or increased off-rate NSF: non-susceptible form |
| Note | Binding of this natural variant to HLA-A*0301, -A*1101 and -A*6801-positive CTL was abrogated. |
| Variant ID. | 1259 |
|---|---|
| Epitope Seq. | AIFQSSMTK |
| Variant Seq. | AIFQrSMTr |
| Mutations | S/R K/R |
| Epitope Location | S5R K9R |
| HXB2 Location | S317R K321R |
| Mutation Type | DHB: diminished HLA binding or increased off-rate SF: susceptible form |
| Note | Binding and recognition of this natural variant to HLA-A*0301, -A*1101 and -A*6801-positive CTL was high. |
| Variant ID. | 1260 |
|---|---|
| Epitope Seq. | AIFQSSMTK |
| Variant Seq. | AIlQSSMTr |
| Mutations | F/L K/R |
| Epitope Location | F3L K9R |
| HXB2 Location | F315L K321R |
| Mutation Type | DR: diminished response SF: susceptible form |
| Note | Binding and recognition of this natural variant to HLA-A*0301, and -A*6801-positive CTL was diminished but to HLA-A*1101-CTL was still high. |
| Variant ID. | 1261 |
|---|---|
| Epitope Seq. | AIFQSSMTK |
| Variant Seq. | AIFQSSMTr |
| Mutations | K/R |
| Epitope Location | K9R |
| HXB2 Location | K321R |
| Mutation Type | SF: susceptible form |
| Note | Binding of this K166R natural variant to HLA-A*0301, -A*1101 and -A*6801-positive CTL was high. CTL recognition and lysis was similar to that elicited by the index epitope sequence. |
| Variant ID. | 1262 |
|---|---|
| Epitope Seq. | AIFQSSMTK |
| Variant Seq. | sIFQSSMTK |
| Mutations | A/S |
| Epitope Location | A1S |
| HXB2 Location | A313S |
| Mutation Type | SF: susceptible form |
| Note | Binding of this A158S natural variant to HLA-A*0301, -A*1101 and -A*6801-positive CTL was high. CTL recognition and lysis was similar to that elicited by the index epitope sequence. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
Threlkeld1997 S. C. Threlkeld, P. A. Wentworth, S. A. Kalams, B. M. Wilkes, D. J. Ruhl, E. Kepgh, J. Sidney, S. Southwood, B. D. Walker, and A. Sette. Degenerate and Promiscuous Recognition by CTL of Peptides Presented by the MHC Class I A3-Like Superfamily. J. Immunol., 159(4):1648-1657, 1997. Similarities in peptide binding across A3-like superfamily results in similar peptide-MHC complex structures engaged by T-cell receptors. PubMed ID: 9257824. Show all entries for this paper.
| HXB2 Location | Pol(330-338) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
NPDIVIYQY
|
Epitope Alignment | ||||||||||||||||
| Variants |
|
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| Species (MHC/HLA) | human(B35) | |||||||||||||||||
Showing all: 5 variant(s).
| Variant ID. | 1266 |
|---|---|
| Epitope Seq. | NPDIVIYQY |
| Variant Seq. | hPDIVIYQY |
| Mutations | N/H |
| Epitope Location | N1H |
| HXB2 Location | N330H |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Variant Subtype | A |
| Note | This variant is the HIV-1 Clade A consensus and obtained by a Medline database search in August 1998. |
| Variant ID. | 1267 |
|---|---|
| Epitope Seq. | NPDIVIYQY |
| Variant Seq. | hPDIlIYQY |
| Mutations | N/H V/L |
| Epitope Location | N1H V5L |
| HXB2 Location | N330H V334L |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Note | This HIV-2 homologous epitope is recognized by NPDIVIYQY-specific clones. |
| Variant ID. | 1629 |
|---|---|
| Epitope Seq. | NPDIVIYQY |
| Variant Seq. | NPDIiIYQY |
| Mutations | V/I |
| Epitope Location | V5I |
| HXB2 Location | V334I |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Chromium-release assay |
| Note | This naturally occurring, strain JRCSF variant, was recognized by a Patient LWF CTL clone. |
| Variant ID. | 1630 |
|---|---|
| Epitope Seq. | NPDIVIYQY |
| Variant Seq. | NPeIVIYQY |
| Mutations | D/E |
| Epitope Location | D3E |
| HXB2 Location | D332E |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Chromium-release assay |
| Note | This naturally occurring, strain JRU2RF variant, was recognized by a Patient LWF CTL clone. |
| Variant ID. | 1631 |
|---|---|
| Epitope Seq. | NPDIVIYQY |
| Variant Seq. | NPDlVIYQY |
| Mutations | I/L |
| Epitope Location | I4L |
| HXB2 Location | I333L |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Chromium-release assay |
| Note | This naturally occurring variant was recognized by a Patient LWF CTL clone. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
Sipsas1997 N. V. Sipsas, S. A. Kalams, A. Trocha, S. He, W. A. Blattner, B. D. Walker, and R. P. Johnson. Identification of Type-Specific Cytotoxic T Lymphocyte Responses to Homologous Viral Proteins in Laboratory Workers Accidentally Infected with HIV-1. J. Clin. Invest., 99:752-762, 1997. To examine a situation where the autologous strain and the reference reagents would be the same, the CTL response of three lab workers accidentally infected with HIV IIIB was studied. Both group specific and type specific epitopes were targets for CTL clones. One subject had a broadening of CTL response over time, using a broad range of restricting HLA class I alleles. Characterization of the cytotoxic T lymphocyte (CTL) response against HIV-1 has been limited by the use of target cells expressing viral proteins from laboratory isolates of HIV-1. This approach has favored identification of group-specific CTL responses and precluded assessment of the extent of type-specific CTL responses directed against HIV-1. Using cells expressing viral proteins from the HIV-1 IIIB strain, we performed a detailed characterization of HIV-1-specific CTL response in three laboratory workers accidentally infected with HIV-1 IIIB. Eight of the epitopes identified were group specific, lying in relatively conserved regions of Gag, reverse transcriptase, and envelope. Three type-specific epitopes were identified, two of them in highly variable regions of envelope. In longitudinal studies in one subject, seven different epitopes and five different restricting HLA class I alleles were identified, with a progressive increase in the number of CTL epitopes recognized by this subject over time. Our data demonstrate that type-specific CTL responses make up a significant proportion of the host cellular immune response against HIV-1 and that a broadening of epitope specificity may occur. PubMed ID: 9045880. Show all entries for this paper.
| HXB2 Location | Pol(330-338) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
NPDIVIYQY
|
Epitope Alignment | ||||||||||
| Variants |
|
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| Species (MHC/HLA) | human(B35) | |||||||||||
Showing all: 3 variant(s).
| Variant ID. | 1263 |
|---|---|
| Epitope Seq. | NPDIVIYQY |
| Variant Seq. | NPeIVIYQY |
| Mutations | D/E |
| Epitope Location | D3E |
| HXB2 Location | D332E |
| Mutation Type | DHB: diminished HLA binding or increased off-rate SF: susceptible form |
| Epitope Subtype | B |
| Variant Subtype | D |
| Method | Chromium-release assay, HLA binding |
| Note | This D177E natural variant which is the consensus for clade D, displayed CTL cross-reactivity with the consensus, index epitope, NPDIVIYQY. Binding to HLA-B35 was diminished. |
| Variant ID. | 1264 |
|---|---|
| Epitope Seq. | NPDIVIYQY |
| Variant Seq. | NPDlVIYQY |
| Mutations | I/L |
| Epitope Location | I4L |
| HXB2 Location | I333L |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Method | Chromium-release assay |
| Note | This I178L natural variant displayed CTL cross-reactivity with the consensus, index epitope. |
| Variant ID. | 1265 |
|---|---|
| Epitope Seq. | NPDIVIYQY |
| Variant Seq. | NPDIiIYQY |
| Mutations | V/I |
| Epitope Location | V5I |
| HXB2 Location | V334I |
| Mutation Type | DHB: diminished HLA binding or increased off-rate SF: susceptible form |
| Epitope Subtype | B |
| Method | Chromium-release assay, HLA binding |
| Note | This V179I natural variant displayed CTL cross-reactivity with the consensus, index epitope. Binding to HLA-B35 was diminished. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
RowlandJones1998b S. Rowland-Jones, T. Dong, P. Krausa, J. Sutton, H. Newell, K. Ariyoshi, F. Gotch, S. Sabally, T. Corrah, J. Kimani, K. MacDonald, F. Plummer, J. Ndinya-Achola, H. Whittle, and A. McMichael. The Role of Cytotoxic T Cells in HIV Infection. Dev. Biol. Stand., 92:209-214, 1998. In this paper CTL response to previously defined conserved epitopes was found in exposed but uninfected prostitutes in Nairobi. Subtypes A and D are circulating in this regions, and the reactive epitopes tended to be conserved. Similarly previous studies in the Gambia showed that exposed but uninfected prostitutes tended to have B35 presented CTL epitopes conserved between HIV-1 and HIV-2. It was suggested that what was special about B35 is simply that it presents epitopes found both in HIV-1 and HIV-2. PubMed ID: 9554277. Show all entries for this paper.
| HXB2 Location | Pol(334-342) | Pol Epitope Map
View variants at this location |
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| Epitope |
VIYQYMDDL
|
Epitope Alignment | ||||||||||||||||
| Variants |
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| Species (MHC/HLA) | human(A*02:01) | |||||||||||||||||
Showing all: 5 variant(s).
| Variant ID. | 1242 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | tIYQYMDDL |
| Mutations | V/T |
| Epitope Location | V1T |
| HXB2 Location | V334T |
| Mutation Type | DI: drug induced SF: susceptible form |
| Note | There was no change in CTL-mediated lysis of target cells presenting this RT inhibitor induced-variant. |
| Variant ID. | 1244 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | iIYQYMDDL |
| Mutations | V/I |
| Epitope Location | V1I |
| HXB2 Location | V334I |
| Mutation Type | DI: drug induced SF: susceptible form |
| Note | There was no change in CTL-mediated lysis of target cells presenting this RT inhibitor induced-variant. |
| Variant ID. | 1246 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | eIYQYMDDL |
| Mutations | V/E |
| Epitope Location | V1E |
| HXB2 Location | V334E |
| Mutation Type | DI: drug induced E: escape documented in this paper |
| Note | CTL recognition was abolished by this V179E amino acid replacement. |
| Variant ID. | 1248 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | VIYQYvDDL |
| Mutations | M/V |
| Epitope Location | M6V |
| HXB2 Location | M339V |
| Mutation Type | DI: drug induced E: escape documented in this paper |
| Note | CTL recognition was abolished by this M184V amino acid replacement. This variant confers high-level resistance to lamivudine (3TC). |
| Variant ID. | 1250 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | VIcQYMDDL |
| Mutations | Y/C |
| Epitope Location | Y3C |
| HXB2 Location | Y336C |
| Mutation Type | DI: drug induced DR: diminished response |
| Note | CTL recognition was strongly reduced by this Y181C amino acid replacement. This variant is associated with resistance to nevirapine and other NNRTIs. |
Harrer1996 E. Harrer, T. Harrer, P. Barbosa, M. Feinberg, R. P. Johnson, S. Buchbinder, and B. D. Walker. Recognition of the Highly Conserved YMDD Region in the Human Immunodeficiency Virus Type 1 Reverse Transcriptase by HLA-A2-Restricted Cytotoxic T Lymphocytes from an Asymptomatic Long-Term Nonprogresser. J. Infect. Dis., 173:476-479, 1996. The amino acid stretch YMDD is a critical functional domain of reverse transcriptase, and is highly conserved. This sequence is also part of an HLA-A2-restricted epitope. The substitution YMDD to YVDD confers drug resistance to FTC and dideoxyinosine, and also abolishes the CTL specific response. PubMed ID: 8568316. Show all entries for this paper.
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
| HXB2 Location | Pol(334-342) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
VIYQYMDDL
|
Epitope Alignment | ||||||||||||||||
| Variants |
|
|||||||||||||||||
| Species (MHC/HLA) | human(A*02:01) | |||||||||||||||||
Showing all: 5 variant(s).
| Variant ID. | 95 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | VIYQYvDDL |
| Mutations | M/V |
| Epitope Location | M6V |
| HXB2 Location | M339V |
| Mutation Type | DI: drug induced E: escape documented in this paper |
| Note | CTL recognition was abolished by this M184V amino acid replacement. This variant confers high-level resistance to lamivudine (3TC). |
| Variant ID. | 1243 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | tIYQYMDDL |
| Mutations | V/T |
| Epitope Location | V1T |
| HXB2 Location | V334T |
| Mutation Type | DI: drug induced SF: susceptible form |
| Note | There was no change in CTL-mediated lysis of target cells presenting this RT inhibitor induced-variant. |
| Variant ID. | 1245 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | iIYQYMDDL |
| Mutations | V/I |
| Epitope Location | V1I |
| HXB2 Location | V334I |
| Mutation Type | DI: drug induced SF: susceptible form |
| Note | There was no change in CTL-mediated lysis of target cells presenting this RT inhibitor induced-variant. |
| Variant ID. | 1247 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | eIYQYMDDL |
| Mutations | V/E |
| Epitope Location | V1E |
| HXB2 Location | V334E |
| Mutation Type | DI: drug induced E: escape documented in this paper |
| Note | CTL recognition was abolished by this V179E amino acid replacement. |
| Variant ID. | 1251 |
|---|---|
| Epitope Seq. | VIYQYMDDL |
| Variant Seq. | VIcQYMDDL |
| Mutations | Y/C |
| Epitope Location | Y3C |
| HXB2 Location | Y336C |
| Mutation Type | DI: drug induced DR: diminished response |
| Note | CTL recognition was strongly reduced by this Y181C amino acid replacement. This variant is associated with resistance to nevirapine and other NNRTIs. |
Brander1998 Christian Brander, Kelly E. Hartman, Alicja K. Trocha, Norman G. Jones, R. Paul Johnson, Bette Korber, Peggy Wentworth, Susan P. Buchbinder, Steve Wolinsky, Bruce D. Walker, and Spyros A. Kalams. Lack of Strong Immune Selection Pressure by the Immunodominant, HLA-A*0201-Restricted Cytotoxic T Lymphocyte Response in Chronic Human Immunodeficiency Virus-1 Infection. J. Clin. Invest., 101(11):2559-2566, 1 Jun 1998. PubMed ID: 9616227. Show all entries for this paper.
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
| HXB2 Location | Pol(399-407) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
IVLPEKDSW
|
Epitope Alignment | ||||||||||
| Variants |
|
|||||||||||
| Species (MHC/HLA) | human(B*57:01) | |||||||||||
Showing all: 3 variant(s).
| Variant ID. | 1268 |
|---|---|
| Epitope Seq. | IVLPEKDSW |
| Variant Seq. | ImLPEKDSW |
| Mutations | V/M |
| Epitope Location | V2M |
| HXB2 Location | V400M |
| Mutation Type | SF: susceptible form |
| Note | Cross-recognition of the variant by index epitope-specific CTL is seen even though binding of the variant to HLA-B*5701 is diminished. |
| Variant ID. | 1269 |
|---|---|
| Epitope Seq. | IVLPEKDSW |
| Variant Seq. | ItLPEKgSW |
| Mutations | V/T D/G |
| Epitope Location | V2T D7G |
| HXB2 Location | V400T D405G |
| Mutation Type | NSF: non-susceptible form |
| Note | This variant binds HLA-B*5701 with similar affinity as the index peptide does, but it is not recognized by index peptide-specific CTL. |
| Variant ID. | 1270 |
|---|---|
| Epitope Seq. | IVLPEKDSW |
| Variant Seq. | IeLPEKDSW |
| Mutations | V/E |
| Epitope Location | V2E |
| HXB2 Location | V400E |
| Mutation Type | SF: susceptible form |
| Note | This variant binds HLA-B*5701 with reduced affinity, but it is recognized by index peptide-specific CTL. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
vanderBurg1997 S. H. van der Burg, M. R. Klein, O. Pontesilli, A. M. Holwerda, J. Drijfhout, W. M. Kast, F. Miedema, and C. J. M. Melief. HIV-1 Reverse Transcriptase-Specific CTL against Conserved Epitopes Do Not Protect against Progression to AIDS. J. Immunol., 159:3648-3654, 1997. PubMed ID: 9317165. Show all entries for this paper.
| HXB2 Location | Pol(464-472) | Pol Epitope Map
View variants at this location |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
ILKEPVHGV
|
Epitope Alignment | |||||||||||||
| Variants |
|
||||||||||||||
| Species (MHC/HLA) | human(A2) | ||||||||||||||
Showing all: 4 variant(s).
| Variant ID. | 1271 |
|---|---|
| Epitope Seq. | ILKEPVHGV |
| Variant Seq. | ILKdPVHGV |
| Mutations | E/D |
| Epitope Location | E4D |
| HXB2 Location | E467D |
| Mutation Type | DR: diminished response |
| Note | A large reduction in CTL-mediated lysis is seen in this subtype A U455 isolate. |
| Variant ID. | 1272 |
|---|---|
| Epitope Seq. | ILKEPVHGV |
| Variant Seq. | ILKdPVHeV |
| Mutations | E/D G/E |
| Epitope Location | E4D G8E |
| HXB2 Location | E467D G471E |
| Mutation Type | DR: diminished response |
| Note | A large reduction in CTL-mediated lysis is seen in this subtype B SF2 isolate. |
| Variant ID. | 1273 |
|---|---|
| Epitope Seq. | ILKEPVHGV |
| Variant Seq. | yLKEPVHGV |
| Mutations | I/Y |
| Epitope Location | I1Y |
| HXB2 Location | I464Y |
| Mutation Type | SF: susceptible form |
| Note | This variant bound HLA-A2 more stably, strongly stimulating a response by index epitope-specific CTL. |
| Variant ID. | 1274 |
|---|---|
| Epitope Seq. | ILKEPVHGV |
| Variant Seq. | fLKEPVHGV |
| Mutations | I/F |
| Epitope Location | I1F |
| HXB2 Location | I464F |
| Mutation Type | SF: susceptible form |
| Note | This variant bound HLA-A2 more stably than the index epitope did. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
Tsomides1994 T. J. Tsomides, A. Aldovini, R. P. Johnson, B. D. Walker, R. A. Young, and H. N. Eisen. Naturally Processed Viral Peptides Recognized by Cytotoxic T Lymphocytes on Cells Chronically Infected by Human Immunodeficiency Virus Type 1. J. Exp. Med., 180:1283-1293, 1994. Naturally processed peptides can be purified from trifluoroacetic acid lysates of HIV-1 infected cells. A gag and RT epitope were compared; both synthetic peptides are optimally active in CTL assays. The naturally processed gag peptide was more abundant than the RT peptide in HIV-1 infected HLA-A2 positive cells, and the gag specific CTL more effective, suggesting surface density of peptides may influence efficiency of CTL killing. PubMed ID: 7523570. Show all entries for this paper.
| HXB2 Location | Pol(464-472) | Pol Epitope Map
View variants at this location |
||||
|---|---|---|---|---|---|---|
| Epitope |
ILKEPVHGV
|
Epitope Alignment | ||||
| Variants |
|
|||||
| Species (MHC/HLA) | human(A2) | |||||
Showing all: 1 variant(s).
| Variant ID. | 109 |
|---|---|
| Epitope Seq. | ILKEPVHGV |
| Variant Seq. | ILKdPVHGV |
| Mutations | E/D |
| Epitope Location | E4D |
| HXB2 Location | E467D |
| Mutation Type | SNSF: subtype-specific non-susceptible form |
| Epitope Subtype | A, B, D |
| Variant Subtype | A |
| Method | Chromium-release assay |
| Note | The consensus peptides of B and D clade viruses and some As have the sequence ILKEPVHGV. The consensus peptide of a subset of A clade viruses, ILKDPVHGV, is not cross-reactive. |
Cao1997a H. Cao, P. Kanki, J. L. Sankale, A. Dieng-Sarr, Gail P. Mazzara, S. Kalams, B. Korber, S. M'Boup, and B. D. Walker. CTL Cross-Reactivity among Different HIV-1 Clades: Implications for Vaccine Development. J. Virol., 71:8615-8623, 1997. PubMed ID: 9343219. Show all entries for this paper.
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
| HXB2 Location | Pol(547-556) | Pol Epitope Map
View variants at this location |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Epitope |
PIQKETWETW
|
Epitope Alignment | ||||||||||
| Variants |
|
|||||||||||
| Species (MHC/HLA) | human(A*32:01) | |||||||||||
Showing all: 3 variant(s).
| Variant ID. | 1275 |
|---|---|
| Epitope Seq. | PIQKETWETW |
| Variant Seq. | PIQKETWEaW |
| Mutations | T/A |
| Epitope Location | T9A |
| HXB2 Location | T555A |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Other |
| Note | Variant epitope PIQKETWEaW was able to elicit a lytic response from Subject 15160's CTL and it was found in 6/7 samples of subject's autologous viral sequences. |
| Variant ID. | 4356 |
|---|---|
| Epitope Seq. | PIQKETWETW |
| Variant Seq. | PIQKEaWETW |
| Mutations | T/A |
| Epitope Location | T6A |
| HXB2 Location | T552A |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Other |
| Note | This variant, PIQKEaWETW, was detected in a mother-infant transmission study. The variant was recognized by index epitope-specific CTL clones. |
| Variant ID. | 4357 |
|---|---|
| Epitope Seq. | PIQKETWETW |
| Variant Seq. | PIQKETWdaW |
| Mutations | E/D T/A |
| Epitope Location | E8D T9A |
| HXB2 Location | E554D T555A |
| Mutation Type | SF: susceptible form |
| Epitope Subtype | B |
| Variant Subtype | B |
| Method | Other |
| Note | Variant epitope PIQKETWdaW was able to elicit a lytic response from Subject 15160's CTL though it was not found in the subject's autologous viral sequences. |
Harrer1996b T. Harrer, E. Harrer, S. A. Kalams, P. Barbosa, A. Trocha, R. P. Johnson, T. Elbeik, M. B. Feinberg, S. P. Buchbinder, and B. D. Walker. Cytotoxic T Lymphocytes in Asymptomatic Long-Term Nonprogressing HIV-1 Infection. Breadth and Specificity of the Response and Relation to In Vivo Viral Quasispecies in a Person with Prolonged Infection and Low Viral Load. J. Immunol., 156:2616-2623, 1996. PubMed ID: 8786327. Show all entries for this paper.
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
| HXB2 Location | Pol(587-595) | Pol Epitope Map
View variants at this location |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Epitope |
EPIVGAETF
|
Epitope Alignment | |||||||
| Variants |
|
||||||||
| Species (MHC/HLA) | human(B*35:01) | ||||||||
Showing all: 2 variant(s).
| Variant ID. | 1276 |
|---|---|
| Epitope Seq. | EPIVGAETF |
| Variant Seq. | dPIVGAETF |
| Mutations | E/D |
| Epitope Location | E1D |
| HXB2 Location | E587D |
| Mutation Type | DR: diminished response |
| Note | The E432D variant did not affect HLA-B35 binding though CTL-mediated lysis was reduced. |
| Variant ID. | 1277 |
|---|---|
| Epitope Seq. | EPIVGAETF |
| Variant Seq. | EPIiGAETF |
| Mutations | V/I |
| Epitope Location | V4I |
| HXB2 Location | V590I |
| Mutation Type | DR: diminished response |
| Note | The V435I variant did not affect HLA-B35 binding though CTL-mediated lysis was reduced. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
Tomiyama1997 H. Tomiyama, K. Miwa, H. Shiga, Y. I. Moore, S. Oka, A. Iwamoto, Y. Kaneko, and M. Takiguchi. Evidence of Presentation of Multiple HIV-1 Cytotoxic T Lymphocyte Epitopes by HLA-B*3501 Molecules That Are Associated with the Accelerated Progression of AIDS. J. Immunol., 158:5026-5034, 1997. PubMed ID: 9144523. Show all entries for this paper.
| HXB2 Location | Pol(591-600) | Pol Epitope Map
View variants at this location |
||||
|---|---|---|---|---|---|---|
| Epitope |
GAETFYVDGA
|
Epitope Alignment | ||||
| Variants |
|
|||||
| Species (MHC/HLA) | human(B45) | |||||
Showing all: 1 variant(s).
| Variant ID. | 1279 |
|---|---|
| Epitope Seq. | GAETFYVDGA |
| Variant Seq. | GvETFYVDGA |
| Mutations | A/V |
| Epitope Location | A2V |
| HXB2 Location | A592V |
| Mutation Type | SF: susceptible form |
| Note | RT-specific CTL clones from an HLA-B45 subject recognized both index epitope and its natural variant. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.
| HXB2 Location | Pol(593-603) | Pol Epitope Map
View variants at this location |
||||
|---|---|---|---|---|---|---|
| Epitope |
ETFYVDGAANR
|
Epitope Alignment | ||||
| Variants |
|
|||||
| Species (MHC/HLA) | human(A26) | |||||
Showing all: 1 variant(s).
| Variant ID. | 1278 |
|---|---|
| Epitope Seq. | ETFYVDGAANR |
| Variant Seq. | ETyYVDGAANR |
| Mutations | F/Y |
| Epitope Location | F3Y |
| HXB2 Location | F595Y |
| Mutation Type | SF: susceptible form |
| Note | This natural variant is cross-recognized by index epitope-specific CTL. |
Menendez-Arias1998 L. Menendez-Arias, A. Mas, and E. Domingo. Cytotoxic T-Lymphocyte Responses to HIV-1 Reverse Transcriptase. Viral Immunol., 11:167-181, 1998. PubMed ID: 10189185. Show all entries for this paper.