Search CTL/CD8+ T-Cell Epitope Database

Found 59 matching records:

Displaying record number 404

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HXB2 Location	Pol(173-181) RT(18-26) DNA(2601..2627)	Pol Epitope Map
Author Location	RT(173-181)
Epitope	`GPKVKQWPL`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B8)
Immunogen
Experimental methods
Keywords

Notes

Included in a study of the B*08 binding motif.
Article reviewed in Menendez-Arias1998, with a discussion of antagonism.

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 403

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HXB2 Location	Pol(173-181) RT(18-26) DNA(2601..2627)	Pol Epitope Map
Author Location	RT(18-26)
Epitope	`GPKVKQWPL`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

HIV proteins with mutations in this epitope allowed transactive inhibition of specific {CTL}-mediated lysis.
Article reviewed in Menendez-Arias1998, with a discussion of antagonism.

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.

Displaying record number 407

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HXB2 Location	Pol(173-181) RT(18-26) DNA(2601..2627)	Pol Epitope Map
Author Location	RT(185-193 LAI)
Epitope	`GPKVKQWPL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Naturally occurring antagonist GPRVKQWPL found in viral PBMC DNA and RNA.
Article reviewed in Menendez-Arias1998 with a discussion of antagonism.

References

Klenerman1995 P. Klenerman, U.-C. Meier, R. E. Phillips, and A. J. McMichael. The Effects of Natural Altered Peptide Ligands on the Whole Blood Cytotoxic T Lymphocyte Response to Human Immunodeficiency Virus. Eur. J. Immunol., 25:1927-1931, 1995. This paper explores naturally occurring altered peptide ligands and their ability to sustain CTL, serve as antagonists to CTL specific for other variants, and to allow cell killing. The authors propose that a CTL response may be sustained in vivo that fails to recognize viral variants as they arise, proposing a mechanism for T-cell original antigenic sin. PubMed ID: 7542596. Show all entries for this paper.

Displaying record number 412

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HXB2 Location	Pol(193-207) RT(38-52) DNA(2661..2705)	Pol Epitope Map
Author Location	RT(205-219 BRU)
Epitope	`CTEMEKEGKISKIGP`	Epitope Alignment
Species (MHC/HLA)	mouse(H-2^k)
Immunogen	vaccine
Experimental methods
Keywords	review

Vaccine Details

Vaccine type	protein
Vaccine strain	B clade BRU
Vaccine component	RT

Notes

Murine and human helper and CTL epitope.
Epitope noted in a review by Menendez-Arias1998 to be located in the "fingers" domain of RT and is a helper and CTL epitope.

References

DeGroot1991 A. S. De Groot, M. Clerici, A. Hosmalin, S. H. Hughes, D. Barnd, C. W. Hendrix, R. Houghten, G. M. Shearer, and J. A. Berzofsky. Human Immunodeficiency Virus Reverse Transcriptase T-Helper Epitopes Identified in Mice and Humans: Correlation with a Cytotoxic T Cell Epitope. J. Infect. Dis., 164:1058-1065, 1991. This peptide stimulates both murine helper and cytotoxic T-cells and was able to stimulate IL-2 producing T-cells from 9 out of 17 HIV seropositive humans. RT epitope: CTEMEKEGKISKIGP. PubMed ID: 1720151. Show all entries for this paper.

Displaying record number 413

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HXB2 Location	Pol(193-207) RT(38-52) DNA(2661..2705)	Pol Epitope Map
Author Location	RT(205-219)
Epitope	`CTEMEKEGKISKIGP`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

Murine and human helper and CTL epitope.
Epitope noted in a review by Menendez-Arias1998 to be located in the "fingers" domain of RT and is a helper and CTL epitope.

References

Hosmalin1990 A. Hosmalin, M. Clerici, R. Houghten, C. D. Pendleton, C. Flexner, D. R. Lucey, B. Moss, R. N. Germain, G. M. Shearer, and J. A. Berzofsky. An Epitope in Human Immunodeficiency Virus 1 Reverse Transcriptase Recognized by Both Mouse and Human Cytotoxic T Lymphocytes. Proc. Natl. Acad. Sci. U.S.A., 87:2344-2348, 1990. PubMed ID: 1690429. Show all entries for this paper.

Displaying record number 420

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HXB2 Location	Pol(262-270) RT(107-115) DNA(2868..2894)	Pol Epitope Map
Author Location	RT(262-270 IIIB)
Epitope	`TVLDVGDAY`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review, responses in children, mother-to-infant transmission

Notes

Epitope defined in the context of the Pediatric AIDS Foundation ARIEL Project, a mother-infant HIV transmission study.
TVLDMGDAC is a naturally occurring variant that is less reactive.
Menendez-Arias1998, in a review, notes that this epitope includes a catalytic residue (Asp-110) in the active site of RT.

References

Walkerpercom1996 C. Wilson, B. Wilkes, D. Ruhl, and B. Walker. Personal communication, 1996. Defined in the context of the Pediatric AIDS Foundation ARIEL Project, a mother-infant HIV transmission study. Personal communication. Show all entries for this paper.

Displaying record number 429

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HXB2 Location	Pol(273-282) RT(118-127) DNA(2901..2930)	Pol Epitope Map
Author Location	RT(273-282 SF2)
Epitope	`VPLDKDFRKY`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

A CTL clone responsive to this epitope was obtained.
4/7 B*35-positive individuals had a CTL response to this epitope.
A K to E substitution at position 5 abrogates specific lysis, and reduces binding to B*3501.
Menendez-Arias1998, in a review, notes that a Glu to Lys (E to K) change abrogates CTL activity, but that both VPLDEDFRKY and VPLDKDFRKY can serve as HLA-B*35 epitopes, so the change must alter T cell receptor binding -- residues in this epitope may be important for polymerase activity.

References

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

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HXB2 Location	Pol(283-290) RT(128-135) DNA(2931..2954)	Pol Epitope Map
Author Location	RT(295-302 IIIB)
Epitope	`TAFTIPSI`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B51)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

HIV IIIB proteins were used to define the range of CTL epitopes recognized by 3 lab workers accidentally infected with HIV-1 IIIB.
TAFTIPST, a variant found in HIV-1 CAM1, was also recognized but 100-fold more peptide was needed.
TAFTIPSV, a variant found in HIV-1 VE1RT, was also recognized, but 10-fold more peptide was needed.
TVFTIPSI, a variant found in HIV-1 MANC, was also recognized.
Menendez-Arias1998, in a review, notes that this epitope includes a region near the active site of RT -- the substitution of the position two conservative change from A to V decreases CTL recognition.

References

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 440

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HXB2 Location	Pol(311-319) RT(156-164) DNA(3015..3041)	Pol Epitope Map
Author Location	RT(311-319 SF2)
Epitope	`SPAIFQSSM`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

Binds HLA-B*3501.
Menendez-Arias1998, in a review, notes that this epitope includes catalytic residues in the active site of RT.

References

Shiga1996 H. Shiga, T. Shioda, H. Tomiyama, Y. Takamiya, S. Oka, S. Kimura, Y. Yamaguchi, T. Gojoubori, H. G. Rammensee, K. Miwa, and M. Takiguchi. Identification of Multiple HIV-1 Cytotoxic T Cell Epitopes Presented by Human Leukocyte Antigen B35 Molecule. AIDS, 10:1075-1083, 1996. PubMed ID: 8874623. Show all entries for this paper.

Displaying record number 441

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HXB2 Location	Pol(311-319) RT(156-164) DNA(3015..3041)	Pol Epitope Map
Author Location	RT(311-319 SF2)
Epitope	`SPAIFQSSM`	Epitope Alignment
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

A CTL clone responsive to this epitope was obtained.
Only 1/7 B35-positive individuals had a CTL response to this epitope.
Menendez-Arias1998, in a review, notes that this epitope is near the active site of RT.

References

Displaying record number 443

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HXB2 Location	Pol(311-320) RT(156-165) DNA(3015..3044)	Pol Epitope Map
Author Location	RT(311-319 SF2)
Epitope	`SPAIFQSSMT`	Epitope Alignment
Species (MHC/HLA)	human(B7)
Immunogen
Experimental methods
Keywords	review

Notes

Pers. comm. from C. Hey and D. Ruhl to C. Brander and B. Walker.
Menendez-Arias1998, in a review, notes that this epitope includes catalytic residues in the active site of RT.

References

Brander1997 Christian Brander and Bruce Walker. Systematic Identification of Optimal HIV-1 CTL Epitopes. In Systematic Identification of Optimal HIV-1 CTL Epitopes. pages IV--1--IV--11. Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, 1997. URL: http://hiv-web.lanl.gov/immunology. Show all entries for this paper.

Displaying record number 446

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HXB2 Location	Pol(313-321) RT(158-166) DNA(3021..3047)	Pol Epitope Map
Author Location	RT(325-333)
Epitope	`AIFQSSMTK`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A03:01, A11:01, A*68:01, A3)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Study of the fine specificity of an A3-like super-type epitope (the A3 super-type includes A*0301, A*1101, A*3101, A*3301, and A*6801)
A3 super-type is characterized by a hydrophobic or hydroxyl containing anchor residue at position 2, and a positive charge in the C-term position.
While most lines were specific, promiscuous cloned CTL lines were also derived from HIV+ donors that could recognize epitope presented by either A3 or A11 or A*6801.
Alanine substitutions throughout the epitope and natural variants indicate that the same amino acid positions are critical for presentation by either MHC molecule, A*03 or* A11.
AIFQSSMTK is presented by three members of the A3 superfamily: A*0301, A*1101, and A*6801, and the naturally occurring variants A1S and K9R are recognized with similar efficiency to wild type epitope -- AIFQRSMTR can also bind to two additional members of the A3 superfamily, A*3101 and A*3301.

References

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 449

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HXB2 Location	Pol(313-321) RT(158-166) DNA(3021..3047)	Pol Epitope Map
Author Location	RT(325-333 LAI)
Epitope	`AIFQSSMTK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A11)
Immunogen	peptide-HLA interaction
Experimental methods
Keywords

Notes

Exploration of A11 binding motif, based on Nixon et al. 1991.

References

Zhang1993 Q.-I. Zhang, R. Gavioli, G. Klein, and M. G. Masucci. An HLA-A11-Specific Motif in Nonamer Peptides Derived from Viral And Cellular Proteins. Proc. Natl. Acad. Sci. U.S.A., 90:2217-2221, 1993. PubMed ID: 8384718. Show all entries for this paper.

Displaying record number 461

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HXB2 Location	Pol(330-338) RT(175-183) DNA(3072..3098)	Pol Epitope Map
Author Location	RT(328-336 IIIB)
Epitope	`NPDIVIYQY`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review, escape

Notes

HIV IIIB proteins were used to define the range of CTL epitopes recognized by 3 lab workers accidentally infected with HIV-1 IIIB.
NPDIIIYQY, a variant found in HIV-1 JRCSF, was also recognized.
NPEIVIYQY, was also recognized.
NPDLVIYQY, was also recognized.
Menendez-Arias1998, in a review, notes that the YXDD motif, highly conserved among polymerases, overlaps this epitope -- CTL activity to this epitope was originally detected in a long-term survivor, however it has since been found in normal progressors -- it is cross-reactive with HIV-2 (HPDILIYQY), but D3E and V5I substitutions reduce binding.

References

Displaying record number 459

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HXB2 Location	Pol(330-338) RT(175-183) DNA(3072..3098)	Pol Epitope Map
Author Location	RT(328-336 IIIB)
Epitope	`NPDIVIYQY`	Epitope Alignment
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Binds HLA-B*3501.
CTL activity to this epitope was originally detected in a long-term survivor, however it has since been found in normal progressors -- it is cross-reactive with HIV-2 (HPDILIYQY), but D3E and V5I substitutions reduce binding Menendez-Arias1998

References

Displaying record number 463

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HXB2 Location	Pol(330-338) RT(175-183) DNA(3072..3098)	Pol Epitope Map
Author Location	RT
Epitope	`NPDIVIYQY`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B35)
Immunogen	HIV-1 exposed seronegative
Experimental methods
Keywords	review, subtype comparisons, HIV exposed persistently seronegative (HEPS)

Notes

A CTL response was found in exposed but uninfected prostitutes from Nairobi using previously-defined B clade epitopes that tended to be conserved in A and D clades -- such cross-reactivity could protect against both A and D and confer protection in Nairobi where both subtypes are circulating.
The A subtype consensus is HPDIVIYQY.
The D subtype consensus is NPEIVIYQY.
Menendez-Arias1998, in a review, notes that the YXDD motif, highly conserved among polymerases, overlaps this epitope -- CTL activity to this epitope was originally detected in a long-term survivor, however it has since been found in normal progressors -- it is cross-reactive with HIV-2 (HPDILIYQY), but D3E and V5I substitutions reduce binding.
Database note: First author "RowlandJones" is also found as "Rowland-Jones" on annotated papers in this database.

References

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 466

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HXB2 Location	Pol(330-354) RT(175-199) DNA(3072..3146)	Pol Epitope Map
Author Location	RT(342-366 LAI)
Epitope	`NPDIVIYQYMDDLYVGSDLEIGQHR`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A11)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

One of five epitopes defined for RT-specific CTL clones in this study.

References

Walker1989 B. D. Walker, C. Flexner, K. Birch-Limberger, L. Fisher, T. J. Paradis, A. Aldovini, R. Young, B. Moss, and R. T. Schooley. Long-Term Culture and Fine Specificity of Human Cytotoxic T-Lymphocyte Clones Reactive with Human Immunodeficiency Virus Type 1. Proc. Natl. Acad. Sci. U.S.A., 86:9514-9518, 1989. Seven HIV-1 reverse transcriptase-specific cytotoxic T-lymphocyte (CTL) clones from the peripheral blood of two seropositive subjects were generated. Five different HLA restricted CTL epitopes were identified by peptide mapping. PubMed ID: 2480604. Show all entries for this paper.

Displaying record number 473

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HXB2 Location	Pol(334-342) RT(179-187) DNA(3084..3110)	Pol Epitope Map
Author Location	RT(346-354 LAI)
Epitope	`VIYQYMDDL`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human(A*02:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

The substitution VIYQYVDDL abrogates CTL response and confers drug resistance.
Menendez-Arias1998, in a review, notes that this epitope includes catalytic residues (Asp-185 and Asp-186) in the active site of RT.

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.

Displaying record number 477

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HXB2 Location	Pol(334-342) RT(179-187) DNA(3084..3110)	Pol Epitope Map
Author Location	RT(346-354)
Epitope	`VIYQYMDDL`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A*02:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review, escape

Notes

Of 17 infected HLA A*0201 subjects, 13 had CTL responses against the p17 SLYNTVATL epitope, six recognized ILKEPVHGV and five recognized VIYQYMDDL, and there was no correlation between viral load and recognition of a specific epitope or evidence of immune escape.
Only one subject had CTL against all three epitopes.
Subjects were part of the San Francisco City Clinic Cohort, the ARIEL project and from the Boston area.
In the review Menendez-Arias1998 the authors note that substitution of three residues in this epitope can confer resistance to RT inhibitors (1, 3, and 6) -- substitutions V1E and M6V abolish CTL activity, and M6V confers resistance to 3TC -- substitution Y3C reduces CTL activity and is associated with resistance to non-nucleoside RT inhibitors.

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.

Displaying record number 478

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HXB2 Location	Pol(335-344) RT(180-189) DNA(3087..3116)	Pol Epitope Map
Author Location	RT( LAI)
Epitope	`IYQYMDDLYV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*02:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Recognized by CTL from a progressor, spans important RT functional domain.
A previous study determined that this was an epitope recognized by a long-term survivor.

References

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 481

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HXB2 Location	Pol(347-371) RT(192-216) DNA(3123..3197)	Pol Epitope Map
Author Location	RT(359-383 HXB2)
Epitope	`DLEIGQHRTKIEELRQHLLRWGLTT`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B60)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

One of five epitopes defined for RT-specific CTL clones in this study.

References

Displaying record number 480

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HXB2 Location	Pol(347-371) RT(192-216) DNA(3123..3197)	Pol Epitope Map
Author Location	RT(191-215)
Epitope	`DLEIGQHRTKIEELRQHLLRWGFTT`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Experimental methods
Keywords	HAART, ART, escape

Notes

Polyclonal CTL recognition switched from RT 191-215 to RT 514-524 when AZT therapy selected for the resistance mutation, and presumably the escape variant, RT T215Y.

References

Haas1997 G. Haas, A. Hosmalin, F. Hadida, J. Duntze, P. Debre, and B. Autran. Dynamics of HIV Variants and Specific Cytotoxic T Cell Recognition in Nonprogressors and Progressors. Immunol. Lett., 57:63-68, 1997. PubMed ID: 9232427. Show all entries for this paper.

Displaying record number 483

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HXB2 Location	Pol(358-367) RT(203-212) DNA(3156..3185)	Pol Epitope Map
Author Location	RT( LAI)
Epitope	`EELRQHLLRW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B44)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

The only epitope recognized by CTL from a long-term survivor in two samples taken six years apart.
Recognized by CTL from a progressor, EILKEPVGHGV and TWETWWTEYW were also recognized.

References

Displaying record number 486

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HXB2 Location	Pol(398-407) RT(243-252) DNA(3276..3305)	Pol Epitope Map
Author Location	RT( LAI)
Epitope	`PIVLPEKDSW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	binding affinity, escape

Notes

Recognized by CTL from long-term survivor, whose CTL response persisted for more than 10 years -- the substitution V3M reduced affinity but was well recognized, on the other hand V3T and D8G did not reduce affinity, but abrogated CTL response.

References

Displaying record number 485

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HXB2 Location	Pol(399-407) RT(244-252) DNA(3279..3305)	Pol Epitope Map
Author Location	RT( LAI)
Epitope	`IVLPEKDSW`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Recognized by CTL from a progressor and a long-term survivor, KITTESIVIW was also recognized.

References

Displaying record number 490

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HXB2 Location	Pol(415-426) RT(260-271) DNA(3327..3362)	Pol Epitope Map
Author Location	RT(415-426 IIIB)
Epitope	`LVGKLNWASQIY`	Epitope Alignment
Species (MHC/HLA)	human(B62)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

P. Johnson, pers. comm.

References

Brander1996 Christian Brander and Bruce Walker. The HLA-Class I Restricted CTL Response in HIV-1 Infection: Systematic Identification of Optimal Epitopes. In The HLA-Class I Restricted CTL Response in HIV-1 Infection: Systematic Identification of Optimal Epitopes. pages IV--50--IV--60. Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, 1996. URL: http://hiv-web.lanl.gov/immunology. Show all entries for this paper.

Displaying record number 492

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HXB2 Location	Pol(426-434) RT(271-279) DNA(3360..3386)	Pol Epitope Map
Author Location	RT(438-446 IIIB)
Epitope	`YPGIKVRQL`	Epitope Alignment
Species (MHC/HLA)	human(B42)
Immunogen	HIV-1 infection
Experimental methods
Keywords	responses in children, mother-to-infant transmission

Notes

YAGIKVRQL and YPGIKVKQL are naturally occurring variants that are both reactive.
YHKIKVRQL is a naturally occurring variant that has not been tested.
Epitope defined in the context of the Pediatric AIDS Foundation ARIEL Project, a mother-infant HIV transmission study.

References

Displaying record number 494

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(448-456 SF2)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B35, B51)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Binds HLA-B*3501 and B*5101.
Reviewed in Menendez-Arias1998, this epitope lies in the thumb region of RT.

References

Displaying record number 496

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HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(448-456 SF2)
Epitope	`IPLTEEAEL`	Epitope Alignment
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

A CTL clone responsive to this epitope was obtained.
Only 1/7 B35-positive individuals had a CTL response to this epitope.
An E to K substitution at position 5 abrogates specific lysis, but not binding to B*3501.
An I to V substitution at position 1, P to Q at position 2, and E to K at 5, abrogates specific lysis and binding to B*3501.
An I to V substitution at position 1 did not alter reactivity.
Reviewed in Menendez-Arias1998, this epitope lies in the thumb region of RT.

References

Displaying record number 497

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HXB2 Location	Pol(449-473) RT(294-318) DNA(3429..3503)	Pol Epitope Map
Author Location	RT(461-485 HXB2)
Epitope	`PLTEEAELELAENREILKEPVHGVY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A2)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

One of five epitopes defined for RT-specific CTL clones in this study.

References

Displaying record number 498

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HXB2 Location	Pol(463-472) RT(308-317) DNA(3471..3500)	Pol Epitope Map
Author Location	RT( LAI)
Epitope	`EILKEPVGHV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*02:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Recognized by CTL from a long-term survivor, SPIETVPVKL was also recognized.
Recognized by CTL from a progressor, EELRQHLLRW and TWETWWTEYW were also recognized.

References

Displaying record number 516

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
Species (MHC/HLA)	human(A*02:01)
Immunogen	in vitro stimulation or selection
Experimental methods
Keywords	binding affinity

Notes

This epitope was included as a positive control.
Binding affinity to A*0201 was measured, C_{1/2 max} µM =12.

References

Konya1997 J. Konya, G. Stuber, A. Bjorndal, E. M. Fenyo, and J. Dillner. Primary induction of human cytotoxic lymphocytes against a synthetic peptide of the human immunodeficiency virus type 1 protease. J. Gen. Virol., 78:2217-2224, 1997. PubMed ID: 9292009. Show all entries for this paper.

Displaying record number 510

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
Species (MHC/HLA)	human(A*02:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

HLA-tetrameric complexes were used in a cross-sectional study of 14 untreated HLA A*0201 positive individuals, revealing an inverse relationship between HIV Gag and Pol specific CTL effector cells (CTLe) and viral load.
Inclusion of both the p17 SLYNTVATL and RT ILKEPVHGV epitopes gives a good representation of HLA A*0201-restricted activity.
No correlation was observed between the CTLe and CD4 count or clearance rate of productively infected cells.

References

Ogg1998 G. S. Ogg, X. Jin, S. Bonhoeffer, P. R. Dunbar, M. A. Nowak, S. Monard, J. P. Segal, Y. Cao, S. L. Rowland-Jones, V. Cerundolo, A. Hurley, M. Markowitz, D. D. Ho, D. F. Nixon, and A. J. McMichael. Quantitation of HIV-1-Specific Cytotoxic T Lymphocytes and Plasma Load of Viral RNA. Science, 279:2103-2106, 1998. PubMed ID: 9516110. Show all entries for this paper.

Displaying record number 528

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
Species (MHC/HLA)	human(A*02:01)
Immunogen	in vitro stimulation or selection
Experimental methods
Keywords	epitope processing

Notes

HLA-A*02 heavy chain and β2-microglobulin expressed in E. coli were refolded in the presence of this peptide.
The HLA-A*02-peptide complex elicited HLA-A2 peptide-specific CTL response in cells lacking HLA-A2.
Suggests that preformed HLA-peptide complexes could provide an alternate to intracellular processing for immunogens.

References

Walter1997 J. B. Walter, C. Brander, M. Mammen, D. N. Garboczi, S. A. Kalams, G. M. Whiteside, B. D. Walker, and H. N. Eisen. Stimulation of Human Cytotoxic T Cells with HIV-1-Derived Peptides Presented by Recombinant HLA-A2 Peptide Complexes. Int. Immunol., 9:451-459, 1997. HLA-A2 heavy chain and beta 2-microglobulin refolded in the presence of peptides became susceptible to lysis by HLA-A2-restricted cytotoxic T lymphocyte (CTL) clones specific for the peptides. Recombinant HLA-A2 peptide complexes covalently immobilized on microspheres stimulated the development of HLA-A2 peptide-specific CTL. PubMed ID: 9088983. Show all entries for this paper.

Displaying record number 521

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
Species (MHC/HLA)	human(A*02:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Mutational study: position 1 I to Y increases complex stability with HLA-A*0201.

References

Pogue1995 R. R. Pogue, J. Eron, J. A. Frelinger, and M. Matsui. Amino-Terminal Alteration of the HLA-A*0201-Restricted Human Immunodeficiency Virus Pol Peptide Increases Complex Stability and In Vitro Immunogenicity. Proc. Natl. Acad. Sci. U.S.A., 92:8166-8170, 1995. In this mutational study a substitution of 476 I to Y did not increase affinity but did increase complex stability with HLA-A*0201. The altered peptide (Y) provided a greater stimulation of wildtype pol-specific CTL response relative to the wildtype peptide (I), in three different seropositive individuals. PubMed ID: 7545295. Show all entries for this paper.

Displaying record number 522

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
Species (MHC/HLA)	human(A*02:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	023: A02, A03, B07, B51
Experimental methods
Keywords	review, escape

Notes

HLA-identical sibling hemophiliac brothers were both infected with the same batch of factor VIII.
One, Patient 003, had a response to gag A*02 epitope SLYNTVATL, the other, Patient 023, to pol A*02 epitope ILKEPVHGV. They were tested 6-8 years after infection.
Viral sequencing from the twin that had no response to SLYNTVATL indicated his virus had the substituted form SLHNAVAVL.
71% of an additional set of 22 HIV-1 infected HLA-A*0201 positive donors preferentially responded to gag SLYNTVATL.
Those individuals with a pol ILKEPVHGV response tended to have mutations in or around SLYNTVATL.
This entry, Goulder1997e, is a review of immune escape that summarizes this study.

References

Goulder1997 P. J. Goulder, A. K. Sewell, D. G. Lalloo, D. A. Price, J. A. Whelan, J. Evans, G. P. Taylor, G. Luzzi, P. Giangrande, R. E. Phillips, and A. J. McMichael. Patterns of Immunodominance in HIV-1-Specific Cytotoxic T Lymphocyte Responses in Two Human Histocompatibility Leukocyte Antigens (HLA)-Identical Siblings with HLA-A*0201 Are Influenced by Epitope Mutation. J. Exp. Med., 8:1423-1433, 1997. Primary human immunodeficiency virus (HIV) infection is controlled principally by HIV-specific cytotoxic T lymphocytes (CTL) to a steady- state level of virus load, which strongly influences the ultimate rate of progression to disease. Epitope selection by CTL may be an important determinant of the degree of immune control over the virus. This report describes the CTL responses of two HLA-identical hemophiliac brothers who were exposed to identical batches of Factor VIII and became seropositive within 10 wk of one another. Both have HLA-A*0201. The CTL responses of the two siblings were very dissimilar, one donor making strong responses to two epitopes within p17 Gag (HLA-A*0201-restricted SLYNTVATL and HLA-A3-restricted RLRPGGKKK). The sibling responded to neither epitope, but made strong responses to two epitopes presented by HLA-B7. This was not the result of differences in presentation of the epitopes. However, mutations in both immunodominant epitopes of the p17 Gag responder were seen in proviral sequences of the nonresponder. We then documented the CTL responses to two HLA-A*0201-restricted epitopes, in Gag (SLYNTVATL) and Pol (ILKEPVHGV) in 22 other HIV-infected donors with HLA-A*0201. The majority (71\%) generated responses to the Gag epitope. In the 29\% of donors failing to respond to the Gag epitope in standard assays, there was evidence of low frequency memory CTL responses using peptide stimulation of PBMC, and most of these donors also showed mutations in or around the Gag epitope. PubMed ID: 9126923. Show all entries for this paper.

Goulder1997e P. Goulder, D. Price, M. Nowak, S. Rowland-Jones, R. Phillips, and A. McMichael. Co-Evolution of Human Immunodeficiency Virus and Cytotoxic T-Lymphocyte Responses. Immunol. Rev., 159:17-29, 1997. PubMed ID: 9416500. Show all entries for this paper.

Displaying record number 530

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484 LAI)
Epitope	`ILKEPVHGV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A2)
Immunogen	peptide-HLA interaction
Experimental methods
Keywords

Notes

Promotes assembly of HLA*0-A2 molecules in T2 cell lysates.

References

Connan1994 F. Connan, F. Hlavac, J. Hoebeke, J. G. Guillet, and J. Choppin. A Simple Assay for Detection of Peptides Promoting the Assembly of HLA Class I Molecules. Eur. J. Immunol., 24:777-780, 1994. Peptides from influenza and HIV-1 were tested for their ability to promote the assembly of HLA-A2 and HLA-B51 molecules in T2 cell lysates. HIV Pol 476-484 allowed significant assembly of HLA-A2, and is a target for CTL. Nef peptide 186-194 produced significant assembly of HLA-B51. A hydrophobic anchor residue (V, L, I) at position 9 could occupy pocket F, and a hydrophobic residue (V, L) at position 3 or 4 may anchor to hydrophobic pocket D of HLA-B51. Proline at position 2 increases HLA-B51 anchoring. PubMed ID: 8125145. Show all entries for this paper.

Displaying record number 523

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
Species (MHC/HLA)	human(A2)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

CD4+ cell lines acutely infected with HIV were studied to determine their susceptibility to lysis by CTL.
Clones specific for RT lysed HIV-1 infected cells at lower levels than Env or Gag specific clones.
The distinction was thought to be due to lower expression of RT relative to Env and Gag.
CTL can lyse infected cells early after infection, possibly prior to viral production.

References

Yang1996 O. O. Yang, S. A. Kalams, M. Rosenzweig, A. Trocha, N. Jones, M. Koziel, B. D. Walker, and R. P. Johnson. Efficient Lysis of Human Immunodeficiency Virus Type 1-Infected Cells by Cytotoxic T Lymphocytes. J. Virol., 70:5799-5806, 1996. PubMed ID: 8709196. Show all entries for this paper.

Displaying record number 515

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A2)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

CTL clones recognize naturally processed peptide -- peptide abundance corresponded to level of CTL killing.

References

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

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A2)
Immunogen	HIV-1 infection
Experimental methods
Keywords	subtype comparisons

Notes

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.

Displaying record number 525

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(309-317)
Epitope	`ILKEPVHGV`	Epitope Alignment
Species (MHC/HLA)	human(A2)
Immunogen	HIV-1 infection
Experimental methods
Keywords	TCR usage

Notes

Two clones were obtained with different TCR usage, V_beta1 and V_beta21.

References

Moss1995 P. A. H. Moss, S. L. Rowland-Jones, P. M. Frodsham, S. McAdam, P. Giangrande, A. McMichael, and J. I. Bell. Persistent High Frequency of Human Immunodeficiency Virus-Specific Cytotoxic T Cells in Peripheral Blood of Infected Donors. Proc. Natl. Acad. Sci. U.S.A., 92:5773-5777, 1995. PubMed ID: 7597028. Show all entries for this paper.

Displaying record number 527

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484)
Epitope	`ILKEPVHGV`	Epitope Alignment
Species (MHC/HLA)	human(A2)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Cervical CTL clones from an HIV-infected woman recognized this epitope.

References

Musey1997 L. Musey, Y. Hu, L. Eckert, M. Christensen, T. Karchmer, and M. J. McElrath. HIV-1 Induces Cytotoxic T Lymphocytes in the Cervix of Infected Women. J. Exp. Med., 185:293-303, 1997. Mononuclear cells in cytobrush specimens from the cervical samples were stimulated with antigen. Eight women with CD4 positive counts $>=$ 500 cells/$\mu$l had HIV-1-specific CTL, but only 4/11 with counts $<$ 500 cells/$\mu$l had HIV-1-specific CTL responses. PubMed ID: 9016878. Show all entries for this paper.

Displaying record number 529

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HXB2 Location	Pol(464-472) RT(309-317) DNA(3474..3500)	Pol Epitope Map
Author Location	RT(476-484 LAI)
Epitope	`ILKEPVHGV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A2)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Precise identification of the nonamer that binds to A*02.

References

Tsomides1991 T. J. Tsomides, B. D. Walker, and H. N. Eisen. An Optimal Viral Peptide Recognized by CD8+ T Cells Binds Very Tightly to the Restricting Class I Major Histocompatibility Complex Protein on Intact Cells but Not to the Purified Class I Protein. Proc. Natl. Acad. Sci. U.S.A., 88:11276-11280, 1991. PubMed ID: 1722325. Show all entries for this paper.

Displaying record number 540

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HXB2 Location	Pol(464-473) RT(309-318) DNA(3474..3503)	Pol Epitope Map
Author Location	RT(476-485 LAI)
Epitope	`ILKEPVHGVY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B62)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

Review of HIV CTL epitopes.

References

McMichael1994 A. J. McMichael and B. D. Walker. Cytotoxic T Lymphocytes Epitopes: Implications for HIV Vaccine. AIDS, 8S:S155-S173, 1994. Comprehensive review summarizing CTL epitopes that have known HLA type and are fine mapped to indicate epitope boundaries. Anchor residues are indicated when known for different HLA restricted epitopes. Includes a summary of the published literature, as well as much work that was in press or submitted for publication. Show all entries for this paper.

Displaying record number 542

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HXB2 Location	Pol(483-507) RT(328-352) DNA(3531..3605)	Pol Epitope Map
Author Location	RT(495-515 LAI)
Epitope	`EIQKQGQGQWTYQIYQEPFKNLKTG`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A11)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

One of five epitopes defined for RT-specific CTL clones in this study.

References

Displaying record number 543

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HXB2 Location	Pol(495-505) RT(340-350) DNA(3567..3599)	Pol Epitope Map
Author Location	RT(507-516)
Epitope	`QIYQEPFKNLK`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Study of cytokines released by HIV-1 specific activated CTL.

References

Price1995 P. Price, R. P. Johnson, D. T. Scadden, C. Jassoy, T. Rosenthal, S. Kalams, and B. D. Walker. Cytotoxic CD8+ T Lymphocytes Reactive with Human Immunodeficiency Virus-1 Produce Granulocyte/Macrophage Colony-Stimulating Factor and Variable Amounts of Interleukins 2, 3, and 4 following Stimulation with the Cognate Epitope. Clin. Immunol. Immunopathol., 74:100-106, 1995. Cytokine release from stimulated CTL clones derived from either the peripheral blood or CSF of 3 patients was studied. HLA restriction was determined for two of seven clones. GM-CSF and TNF-$\alpha$ and IFN-$\gamma$ were produced by all clones; most clones produced low amounts of IL-2, IL-3, and IL-4. PubMed ID: 7527747. Show all entries for this paper.

Displaying record number 544

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HXB2 Location	Pol(495-507) RT(340-352) DNA(3567..3605)	Pol Epitope Map
Author Location	RT(507-519 LAI)
Epitope	`QIYQEPFKNLKTG`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A11)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

This epitope was listed in a review.

References

Johnson1994b R. P. Johnson and B. D. Walker. CTL in HIV-1 Infection: Responses to Structural Proteins. Curr. Topics Microbiol. Immunol., 189:35-63, 1994. Review. PubMed ID: 7523033. Show all entries for this paper.

Displaying record number 546

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HXB2 Location	Pol(519-527) RT(364-372) DNA(3639..3665)	Pol Epitope Map
Author Location	RT(518-526 U455)
Epitope	`DVKQLTEVV`	Epitope Alignment
Species (MHC/HLA)	human(A*68:02, A28)
Immunogen
Experimental methods
Keywords	subtype comparisons

Notes

Predicted on binding motif, no truncations analyzed.
Reacts with clade A consensus (U455), and with the peptide DVKQLAEAV, from the D clade.

References

Dong1998 T. Dong. Personal Communication, 1998. Show all entries for this paper.

Displaying record number 548

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HXB2 Location	Pol(529-538) RT(374-383) DNA(3669..3698)	Pol Epitope Map
Author Location	RT( LAI)
Epitope	`KITTESIVIW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	rate of progression

Notes

Patients studied were from the Amsterdam cohort.
CTL epitopes of 3 rapid progressors were compared to 4 long-term survivors (LTS); no differences could be found in the degree of conservation between them.
Epitope recognized by LTS and by a progressor.

References

Displaying record number 551

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HXB2 Location	Pol(547-556) RT(392-401) DNA(3723..3752)	Pol Epitope Map
Author Location	RT(559-568 LAI)
Epitope	`PIQKETWETW`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human(A*32:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	15160: A03, A32, B14, B44
Country	United States
Experimental methods	Chromium-release assay
Keywords	autologous responses, optimal epitope, novel epitope

Notes

Reviewed in Menendez-Arias1998, suggest the epitope is HLA B53/Cw2.
C. Brander notes that this is an A*3201 epitope in the 1999 database.
A long term non-progressor (LTNP) was studied for detailed analyses of CTL response to epitopes correlated to the subject's viral quasispecies. Epitope mapping revealed CTL response to 6 epitopes in p17, p24, RT, Env and Nef. Results show that (a) multiple epitopes were targeted simultaneously (b) viral heterogeneity/antigenic diversity is not necessary for such a multispecific CTL response (c) LTNP infection does not need to be associated with unique epitope targeting as 5/6 epitopes targeted have been seen in other subjects with disease progression (d) HIV-1-specific CTL can be highly active, disallowing viral escapes, but broadly cross-reactive (recognizing known variants) even with low viral load (VL).
An RT-specific clone, TR6, from the LTNP subject 15160 recognized an RT, HLA-A*32-restricted novel epitope, PIQKETWETW 10 aa. PIQKETWETW is the optimal epitope.

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.

Displaying record number 552

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HXB2 Location	Pol(552-561) RT(397-406) DNA(3738..3767)	Pol Epitope Map
Author Location	RT( LAI)
Epitope	`TWETWWTEYW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B44)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Recognized by CTL from two progressors, EILKEPVGHGV and EELRQHLLRW were also recognized by one, and RETKLGKAGY was also recognized by the other.

References

Displaying record number 554

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HXB2 Location	Pol(587-595) RT(432-440) DNA(3843..3869)	Pol Epitope Map
Author Location	RT(587-597 SF2)
Epitope	`EPIVGAETF`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B*35:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

A CTL clone responsive to this epitope was obtained.
5/7 B35-positive individuals had a CTL response to this epitope.
An E to D substitution at position 1, and V to I at position 4, reduces activity but not binding to B*3501.
Menendez-Arias1998 note in their review that this epitope is near the protease cleavage site and conservation of this region is important for proper viral maturation.

References

Displaying record number 558

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HXB2 Location	Pol(587-596) RT(432-441) DNA(3843..3872)	Pol Epitope Map
Author Location	RT(587-597 SF2)
Epitope	`EPIVGAETFY`	Epitope Alignment
Species (MHC/HLA)	mouse(B35)
Immunogen	HIV-1 infection
Experimental methods
Keywords	review

Notes

Binds HLA-B*3501, but not presented by B51, in contrast to the peptide EPIVGAETF.
Menendez-Arias1998 note in their review that this epitope is located near the protease cleavage site and conservation of this region is important for viral maturation.
This epitope spans the Pol p66 RT -- p15 (RNAse) domain.

References

Displaying record number 560

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HXB2 Location	Pol(589-602) RT(434-447) DNA(3849..3890)	Pol Epitope Map
Author Location	RT( LAI)
Epitope	`IVGAETFYVDGAAS`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*68:02)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Recognized by CTL from a long-term survivor that recognized a set of 5 overlapping peptides spanning IVGAETFYVDGAAS as well as PIVLPEKDSW and KITTESIVIW.
A*6802 is a subset of HLA-A*28.
This epitope spans the Pol p66 RT -- p15 (RNAse) domain.

References

Displaying record number 561

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HXB2 Location	Pol(591-600) RT(436-445) DNA(3855..3884)	Pol Epitope Map
Author Location	RT(591-600 IIIB)
Epitope	`GAETFYVDGA`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B45)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

This epitope spans the Pol p66 RT -- p15 (RNAse) domain.

References

Displaying record number 563

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HXB2 Location	Pol(592-602) RT(437-447) DNA(3858..3890)	Pol Epitope Map
Author Location	RT(592-602 LAI)
Epitope	`AETFYVDGAAN`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A28)
Immunogen
Experimental methods
Keywords

Notes

P. Johnson, pers. comm.
This epitope spans the Pol p66 RT -- p15 (RNAse) domain.

References

Displaying record number 564

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HXB2 Location	Pol(593-603) RT(438-448) DNA(3861..3893)	Pol Epitope Map
Author Location	RT(593-603 IIIB)
Epitope	`ETFYVDGAANR`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A26)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

This epitope spans the Pol p66 RT -- p15 (RNAse) domain.

References

Displaying record number 567

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HXB2 Location	Pol(636-660) RT(481-505) DNA(3990..4064)	Pol Epitope Map
Author Location	RT(648-672 PV22)
Epitope	`AIYLALQDSGLEVNIVTDSQYALGI`	Epitope Alignment
Species (MHC/HLA)	human(B14)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

A CTL response used to study gene usage in HLA-B14 response.
This epitope occurs in the p15 (RNAse) domain of Pol p66 RT.

References

Kalams1994 S.A. Kalams, R. P. Johnson, A. K. Trocha, M. J. Dynan, H. S. Ngo, R. T. D'Aquila, J. T. Kurnick, and B. D. Walker. Longitudinal Analysis of T Cell Receptor (TCR) Gene Usage by HIV-1 Envelope-Specific Cytotoxic T-Lymphocyte Clones Reveals a Limited TCR Repertoire. J. Exp. Med., 179:1261-1271, 1994. This paper presents an in-depth longitudinal study of T-cell receptor gene usage to a well defined HLA B14 restricted gp41 epitope. Ten CTL clones were derived from a single individual over 31 months. T-cell receptor V-D-J sequencing was performed on PCR amplification products. All ten clones utilized V$\alpha$14 and V$\beta$4 genes; observed limited T-cell receptor diversity to an immunodominant epitope was suggested to facilitate immune escape. gp41 epitope: ERYLKDQQL. An HLA B14 restricted RT epitope from this individual used V$\alpha$21 and V$\beta$14, showing use of these genes was not a feature of all HLA B14 restricted clones from this individual. RT epitope: AIYLALQDSGLEVNIVTDSQYALGI. PubMed ID: 8145043. Show all entries for this paper.

Displaying record number 568

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HXB2 Location	Pol(636-660) RT(481-505) DNA(3990..4064)	Pol Epitope Map
Author Location	RT(648-672)
Epitope	`AIYLALQDSGLEVNIVTDSQYALGI`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Study of cytokines released by HIV-1 specific activated CTL.
This epitope occurs in the p15 (RNAse) domain of Pol p66 RT.