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Found 16 matching records:

Displaying record number 403

HXB2 Location  Pol(173-181)   Pol Epitope Map
View variants at this location
Epitope GPKVKQWPL   Epitope Alignment
Variants
sPKVKQWPL   susceptible form
GPrVKQWPL   susceptible form
GPeVKQWPL   calculated diminished HLA binding
Species (MHC/HLA human(B8)

Variant Details

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.

References

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.


Displaying record number 404

HXB2 Location  Pol(173-181)   Pol Epitope Map
View variants at this location
Epitope GPKVKQWPL   Epitope Alignment
Variants
sPKVKQWPL   susceptible form
GPrVKQWPL   susceptible form
GPeVKQWPL   calculated diminished HLA binding
Species (MHC/HLA human(B8)

Variant Details

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.

References

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.


Displaying record number 429

HXB2 Location  Pol(273-282)   Pol Epitope Map
View variants at this location
Epitope VPLDKDFRKY   Epitope Alignment
Variants
VPLDkDFRKY   susceptible form
Species (MHC/HLA human(B*35:01)

Variant Details

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.

References

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.


Displaying record number 434

HXB2 Location  Pol(283-290)   Pol Epitope Map
View variants at this location
Epitope TAFTIPSI   Epitope Alignment
Variants
TAFTIPSt   susceptible form
TAFTIPSv   susceptible form
TvFTIPSI   non-susceptible form
TAFTIPSt   diminished response
TAFTIPSv   diminished response
TvFTIPSt   diminished response
Species (MHC/HLA human(B51)

Variant Details

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.

References

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.


Displaying record number 446

HXB2 Location  Pol(313-321)   Pol Epitope Map
View variants at this location
Epitope AIFQSSMTK   Epitope Alignment
Variants
AIFQcSMTK   susceptible form
AIFQSSMTt   diminished HLA binding or increased off-rate; non-susceptible form
AIFQrSMTr   diminished HLA binding or increased off-rate; susceptible form
AIlQSSMTr   diminished response; susceptible form
AIFQSSMTr   susceptible form
sIFQSSMTK   susceptible form
Species (MHC/HLA human(A*03:01, A*11:01, A*68:01, A3)

Variant Details

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.

References

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.


Displaying record number 461

HXB2 Location  Pol(330-338)   Pol Epitope Map
View variants at this location
Epitope NPDIVIYQY   Epitope Alignment
Variants
hPDIVIYQY   susceptible form
hPDIlIYQY   susceptible form
NPDIiIYQY   susceptible form
NPeIVIYQY   susceptible form
NPDlVIYQY   susceptible form
Species (MHC/HLA human(B35)

Variant Details

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.

References

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.


Displaying record number 463

HXB2 Location  Pol(330-338)   Pol Epitope Map
View variants at this location
Epitope NPDIVIYQY   Epitope Alignment
Variants
NPeIVIYQY   diminished HLA binding or increased off-rate; susceptible form
NPDlVIYQY   susceptible form
NPDIiIYQY   diminished HLA binding or increased off-rate; susceptible form
Species (MHC/HLA human(B35)

Variant Details

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.

References

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.


Displaying record number 473

HXB2 Location  Pol(334-342)   Pol Epitope Map
View variants at this location
Epitope VIYQYMDDL   Epitope Alignment
Variants
tIYQYMDDL   drug induced; susceptible form
iIYQYMDDL   drug induced; susceptible form
eIYQYMDDL   drug induced; escape documented in this paper
VIYQYvDDL   drug induced; escape documented in this paper
VIcQYMDDL   drug induced; diminished response
Species (MHC/HLA human(A*02:01)

Variant Details

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.

References

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.


Displaying record number 477

HXB2 Location  Pol(334-342)   Pol Epitope Map
View variants at this location
Epitope VIYQYMDDL   Epitope Alignment
Variants
VIYQYvDDL   drug induced; escape documented in this paper
tIYQYMDDL   drug induced; susceptible form
iIYQYMDDL   drug induced; susceptible form
eIYQYMDDL   drug induced; escape documented in this paper
VIcQYMDDL   drug induced; diminished response
Species (MHC/HLA human(A*02:01)

Variant Details

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.

References

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.


Displaying record number 485

HXB2 Location  Pol(399-407)   Pol Epitope Map
View variants at this location
Epitope IVLPEKDSW   Epitope Alignment
Variants
ImLPEKDSW   susceptible form
ItLPEKgSW   non-susceptible form
IeLPEKDSW   susceptible form
Species (MHC/HLA human(B*57:01)

Variant Details

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.

References

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.


Displaying record number 515

HXB2 Location  Pol(464-472)   Pol Epitope Map
View variants at this location
Epitope ILKEPVHGV   Epitope Alignment
Variants
ILKdPVHGV   diminished response
ILKdPVHeV   diminished response
yLKEPVHGV   susceptible form
fLKEPVHGV   susceptible form
Species (MHC/HLA human(A2)

Variant Details

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.

References

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.


Displaying record number 518

HXB2 Location  Pol(464-472)   Pol Epitope Map
View variants at this location
Epitope ILKEPVHGV   Epitope Alignment
Variants
ILKdPVHGV   subtype-specific non-susceptible form
Species (MHC/HLA human(A2)

Variant Details

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.

References

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.


Displaying record number 551

HXB2 Location  Pol(547-556)   Pol Epitope Map
View variants at this location
Epitope PIQKETWETW   Epitope Alignment
Variants
PIQKETWEaW   susceptible form
PIQKEaWETW   susceptible form
PIQKETWdaW   susceptible form
Species (MHC/HLA human(A*32:01)

Variant Details

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.

References

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.


Displaying record number 554

HXB2 Location  Pol(587-595)   Pol Epitope Map
View variants at this location
Epitope EPIVGAETF   Epitope Alignment
Variants
dPIVGAETF   diminished response
EPIiGAETF   diminished response
Species (MHC/HLA human(B*35:01)

Variant Details

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.

References

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.


Displaying record number 561

HXB2 Location  Pol(591-600)   Pol Epitope Map
View variants at this location
Epitope GAETFYVDGA   Epitope Alignment
Variants
GvETFYVDGA   susceptible form
Species (MHC/HLA human(B45)

Variant Details

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.

References

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.


Displaying record number 564

HXB2 Location  Pol(593-603)   Pol Epitope Map
View variants at this location
Epitope ETFYVDGAANR   Epitope Alignment
Variants
ETyYVDGAANR   susceptible form
Species (MHC/HLA human(A26)

Variant Details

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.

References

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.


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