Search CTL/CD8+ T-Cell Epitope Database

Found 22 matching records:

Displaying record number 59617

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	Gag(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Species (MHC/HLA)	human(A*24)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope, chronic infection

Notes

Correlation between HLA class I and spontaneous control of HIV-1 was significant for 7-8 epitopes when 341 chronic, HIV-infected subjects, divided into controllers and non-controllers, were tested for EliSpot responses to 257 optimally defined epitopes. 21 epitopes were associated with viral progression. Protective epitopes tend to cluster in regions of critical stability for the protein, therefore constraining escape.
ELRSLYNTV had a significantly positive association with HLA A*24; it was recognized by 4/31 A*24-positive subjects and 8/282 A*24-negative subjects.

References

Pereyra2014 Florencia Pereyra, David Heckerman, Jonathan M. Carlson, Carl Kadie, Damien Z. Soghoian, Daniel Karel, Ariel Goldenthal, Oliver B. Davis, Charles E. DeZiel, Tienho Lin, Jian Peng, Alicja Piechocka, Mary Carrington, and Bruce D. Walker. HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes. J. Virol., 88(22):12937-12948, Nov 2014. PubMed ID: 25165115. Show all entries for this paper.

Displaying record number 57302

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Subtype	B
Species (MHC/HLA)	(B*08)
Immunogen	peptide-HLA interaction
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Other
Keywords	epitope processing

Notes

Proteasomal cleavage effects on immunodominance were studied using 8 p17 and 11 p24 peptide variants. Epitope abundance due to Antigen processing was the prime influence on CTL dominance while HLA affinity was a moderate influence. Viral mutations modified processing [proteasomal digestion, transporter protein (TAP) affinity, Endoplasmic Reticulum Aminopeptidase (ERAAP) trimming].
Epitope EV9, ELRSLYNTV, overlaps epitopes SL9 (SLYNTVATL) and RY11 (RSLYNTVATLY) and may be affected by mutations in these epitopes especially since positions R76 and Y79 are anchor residues.
Subdominant EV9 was produced in ample quantities by both constitutive- and immuno-proteasomal digestion, but TAP transport disfavored its accumulation in the ER.

References

Tenzer2009 Stefan Tenzer, Edmund Wee, Anne Burgevin, Guillaume Stewart-Jones, Lone Friis, Kasper Lamberth, Chih-hao Chang, Mikkel Harndahl, Mirjana Weimershaus, Jan Gerstoft, Nadja Akkad, Paul Klenerman, Lars Fugger, E. Yvonne Jones, Andrew J. McMichael, Søren Buus, Hansjörg Schild, Peter van Endert, and Astrid K. N. Iversen. Antigen Processing Influences HIV-Specific Cytotoxic T Lymphocyte Immunodominance. Nat. Immunol., 10(6):636-646, Jun 2009. PubMed ID: 19412183. Show all entries for this paper.

Displaying record number 54580

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	Gag(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
		Show epitope variants
Epitope Name	EV9
Subtype	B
Species (MHC/HLA)	human(B*08)
Immunogen	HIV-1 infection
Patient MHC/HLA	A01, A02
Country	United States
Experimental methods	Intracellular cytokine staining, Other
Keywords	rate of progression, escape, mutation acquisition

Notes

To correlate evolving HIV-1 populations with HLA-A2 restricted immune responses for epitopes in Gag, Pol, Env and Nef, 11 treatment-naive subjects were longitudinally studied. Results show that increased viral load is often associated with broad CTL responses early in infection that persist as an "immunological footprint". Conversely, early, restricted responses may help limit viral load. Phylogenetic and functional evidence of viral escape is seen in Gag, Nef and Pol. Gag and Nef show flanking epitope changes restricted by non-HLA-A2 alleles. As far as modes of viral adaptation, CTL responses were seen to develop both against static viral populations resulting in viral evolution to HLA-A2 as well as against existing mutants resulting in reselection of consensus B-like variants. This study reinforces that CTL immune responses detected are not necessarily beneficial to patients, but may be "footprints" from early effective responses that the virus has since escaped.
No CTL responses were detected against the EV9 epitope, ELRSLYNTV. A V82I variant, ELRSLYNTi was found.

References

Karlsson2007 Annika C. Karlsson, Astrid K. N. Iversen, Joan M. Chapman, Tulio de Oliviera, Gerald Spotts, Andrew J. McMichael, Miles P. Davenport, Frederick M. Hecht, and Douglas F. Nixon. Sequential Broadening of CTL Responses in Early HIV-1 Infection Is Associated with Viral Escape. PLoS ONE, 2:e225, 2007. PubMed ID: 17311088. Show all entries for this paper.

Displaying record number 59615

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	Gag(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Species (MHC/HLA)	human(B*08)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope, chronic infection

Notes

Correlation between HLA class I and spontaneous control of HIV-1 was significant for 7-8 epitopes when 341 chronic, HIV-infected subjects, divided into controllers and non-controllers, were tested for EliSpot responses to 257 optimally defined epitopes. 21 epitopes were associated with viral progression. Protective epitopes tend to cluster in regions of critical stability for the protein, therefore constraining escape.
ELRSLYNTV had a significantly positive association with HLA B*08; it was recognized by 3/20 B*08-positive subjects and 5/262 B*08-negative subjects.

References

Displaying record number 1793

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Species (MHC/HLA)	human(B*08)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

B*08-restricted CTL accounted for about 1/3 of the total CTL response in one individual.

References

Day2001 C. L. Day, A. K. Shea, M. A. Altfeld, D. P. Olson, S. P. Buchbinder, F. M. Hecht, E. S. Rosenberg, B. D. Walker, and S. A. Kalams. Relative dominance of epitope-specific cytotoxic T-lymphocyte responses in human immunodeficiency virus type 1-infected persons with shared HLA alleles. J. Virol., 75(14):6279-91, Jul 2001. URL: http://jvi.asm.org/cgi/content/full/75/14/6279. PubMed ID: 11413294. Show all entries for this paper.

Displaying record number 56361

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Subtype	B
Species (MHC/HLA)	human(B*08)
Immunogen	HIV-1 infection
Country	Australia, Canada, Germany, United States
Experimental methods
Keywords	HLA associated polymorphism

Notes

98 newly infected patients were studied to track early host HLA and Gag/Pol/Nef epitope immune responses' association with viral evolution. Response hierarchies were the same as those for later infection, and 50% of the most rapidly substituting epitopes were restricted by protective HLA, e.g. Gag B*57-associated mutations which were the most rapidly reverting upon transmission to a non-B*57-host. While there are great differences in mutation rates and reversions across the HIV proteome, most early viral change is driven by immune pressure.
HLA-driven epitope evolution was seen in 80% of published CTL epitopes.
HLA-B*08-associated substitution within optimally defined epitope ELRSLYNTV is at positions T8, ELRSLYNtV. EV9 has very low recognition frequencies and no escape.

References

Brumme2008 Zabrina L. Brumme, Chanson J. Brumme, Jonathan Carlson, Hendrik Streeck, Mina John, Quentin Eichbaum, Brian L Block, Brett Baker, Carl Kadie, Martin Markowitz, Heiko Jessen, Anthony D. Kelleher, Eric Rosenberg, John Kaldor, Yuko Yuki, Mary Carrington, Todd M. Allen, Simon Mallal, Marcus Altfeld, David Heckerman, and Bruce D. Walker. Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection. J. Virol., 82(18):9216-9227, Sep 2008. PubMed ID: 18614631. Show all entries for this paper.

Displaying record number 62

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17
Epitope	`ELRSLYNTV`	Epitope Alignment
Species (MHC/HLA)	human(B*08:01)
Immunogen
Experimental methods
Keywords	optimal epitope, A-list

Notes

Noted by Brander to be a B*0801 epitope.

References

Llano2019 Anuska Llano, Samandhy Cedeño, Sandra Silva Arrieta, and Christian Brander. The 2019 Optimal HIV CTL Epitopes Update: Growing Diversity in Epitope Length and HLA restriction. 2019. Show all entries for this paper.

Displaying record number 58430

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	Gag(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Subtype	A1
Species (MHC/HLA)	human(B*08:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	ML1992: A02:01, A30:01, B08:01, B44:15, C02:02, C04:01.; ML1594: A01:01, A30:01, B08:01, B42:01, C07:04, C17:01
Country	Kenya
Experimental methods	Other
Keywords	assay or method development

Notes

Ultra-deep parallel pyrosequencing using nested PCR was compared to and found to be vastly superior to Sanger clone-based sequencing. 96 ART-naive HIV-1 (clade A1, B, C or D) -infected subjects' HIV-Gag protein when sequenced by both methods, revealed 14,034 variations by pyrosequencing technology versus 3,632 variations by Sanger's method. These variations were located in previously experimentally determined CTL epitopes of Gag. The sequencing method chosen for a study affects genetic variations found, host-virus interactions detected and evolutionary conclusions drawn.
Parallel 454 pyrosequencing method detected sequence that generated a cosensus epitope read of ELRSLYNTV from patients ML1992 and ML1594. When Sanger clone-based sequencing was used however, the same functional, immunogenic site output different consensus epitopes of EL(L/I)RSLYNTV and ELRSLYNT(T/A)V respectively.
Note: Restricting HLA is given as A*0801, a typo. It is corrected to B*08:01 per author communication (Dr. Ma Luo).

References

Liang2011 Binhua Liang, Ma Luo, Joel Scott-Herridge, Christina Semeniuk, Mark Mendoza, Rupert Capina, Brent Sheardown, Hezhao Ji, Joshua Kimani, Blake T. Ball, Gary Van Domselaar, Morag Graham, Shane Tyler, Steven J. M. Jones, and Francis A. Plummer. A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1. PLoS One, 6(10):e26745, 2011. PubMed ID: 22039546. Show all entries for this paper.

Displaying record number 60935

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*08:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	32645: A01:01, A02:01, B08:01, B35:03, C04:01, C07:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	acute/early infection

Notes

The extent to which set-point viremia is affected by early HIV-infection T cell responses to either conserved or variable epitopes was studied. 23 ART-naive subjects were characterized for CTL responses for 6 months, postinfection. While most CTL responses (73/123) were targeted against variable HIV-1 epitopes, recognition of conserved epitopes (16/123) was associated with lower set point viremia. This was independent of HLA type and also functional avidity of the CTL response. Most of the conserved responses were targeted to Gag and Pol epitopes.
ELRSLYNTV, restricted by B*0801, was recognized by 1 patient with the restricting allele.

References

Kunwar2013 Pratima Kunwar, Natalie Hawkins, Warren L. Dinges, Yi Liu, Erin E. Gabriel, David A. Swan, Claire E. Stevens, Janine Maenza, Ann C. Collier, James I. Mullins, Tomer Hertz, Xuesong Yu, and Helen Horton. Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design. PLoS One, 8(5):e64405, 2013. PubMed ID: 23741326. Show all entries for this paper.

Displaying record number 59614

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	Gag(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Species (MHC/HLA)	human(B*40)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope, chronic infection

Notes

Correlation between HLA class I and spontaneous control of HIV-1 was significant for 7-8 epitopes when 341 chronic, HIV-infected subjects, divided into controllers and non-controllers, were tested for EliSpot responses to 257 optimally defined epitopes. 21 epitopes were associated with viral progression. Protective epitopes tend to cluster in regions of critical stability for the protein, therefore constraining escape.
ELRSLYNTV had a significantly positive association with HLA B*40; it was recognized by 7/28 B*40-positive subjects and 12/313 B*40-negative subjects.

References

Displaying record number 59616

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	Gag(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Species (MHC/HLA)	human(B*52)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope, chronic infection

Notes

Correlation between HLA class I and spontaneous control of HIV-1 was significant for 7-8 epitopes when 341 chronic, HIV-infected subjects, divided into controllers and non-controllers, were tested for EliSpot responses to 257 optimally defined epitopes. 21 epitopes were associated with viral progression. Protective epitopes tend to cluster in regions of critical stability for the protein, therefore constraining escape.
ELRSLYNTV had a significantly positive association with HLA B*52; it was recognized by 2/12 B*52-positive subjects and 3/250 B*52-negative subjects.

References

Displaying record number 61

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17
Epitope	`ELRSLYNTV`	Epitope Alignment
Species (MHC/HLA)	human(B8)
Immunogen
Experimental methods
Keywords

Notes

Defined in a study of the B8 binding motif.

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.

Displaying record number 63

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

A study of p17 variation considering known p17 epitopes and individuals with known HLA types revealed that p17 evolution is influenced by immune pressure from CTLs.

References

Birk1998 M. Birk, A. Vahlne, A. Sonnerborg, and M. Sallberg. Nonsynonymous Mutations within the Human Immunodeficiency Virus Type 1 p17 Gene Are Clustered to Sequences Binding to the Host Human Leukocyte Antigen Class I Molecules. AIDS Res. Hum. Retroviruses, 14:241-248, 1998. PubMed ID: 9491914. Show all entries for this paper.

Displaying record number 1446

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

One of the 51 HIV-1 epitopes selected by Ferrari et al. as good candidate CTL epitopes for vaccines by virtue of being conserved and presented by common HLA alleles.

References

Ferrari2000 G. Ferrari, D. D. Kostyu, J. Cox, D. V. Dawson, J. Flores, K. J. Weinhold, and S. Osmanov. Identification of highly conserved and broadly cross-reactive HIV type 1 cytotoxic T lymphocyte epitopes as candidate immunogens for inclusion in Mycobacterium bovis BCG-vectored HIV vaccines. AIDS Res. Hum. Retroviruses, 16(14):1433-43, 20 Sep 2000. PubMed ID: 11018863. Show all entries for this paper.

Displaying record number 53360

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	( B consensus)
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Subtype	B
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Patient MHC/HLA	A11, A29, B44, B8, Cw4, Cw7
Country	United States
Experimental methods	Chromium-release assay, Cytokine production, Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Keywords	assay or method development, memory cells, characterizing CD8+ T cells

Notes

Using a flow-cytometric cytotoxicity assay based on caspase-3 activation in dying target cells, it was shown that the subset of HIV-1-specific CD8+ T cells secreting both IFN-gamma and TNF-alpha exhibit stronger cytotoxic activity than those secreting only IFN-gamma. These cells also exhibited stronger intracellular perforin expression. No association between HIV-1-specific CD8+ T-cell maturation phenotypes and intracellular perforin expression was found.
1/9 individuals recognized this epitope.

References

Lichterfeld2004b Mathias Lichterfeld, Xu G. Yu, Michael T. Waring, Stanley K. Mui, Mary N. Johnston, Daniel Cohen, Marylyn M. Addo, John Zaunders, Galit Alter, Eunice Pae, Daryld Strick, Todd M. Allen, Eric S. Rosenberg, Bruce D. Walker, and Marcus Altfeld. HIV-1-Specific Cytotoxicity Is Preferentially Mediated by a Subset of CD8+ T Cells Producing both Interferon-gamma and Tumor Necrosis Factor-alpha. Blood, 104(2):487-394, 15 Jul 2004. PubMed ID: 15059848. Show all entries for this paper.

Displaying record number 53685

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17
Epitope	`ELRSLYNTV`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Patient MHC/HLA	A1, A1, B55, B8, Cw3, Cw7
Country	Democratic Republic of the Congo
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	subtype comparisons

Notes

Cross-clade CTL responses in 10 non-B HIV-1 infected individuals were evaluated. T-cell reactivity was tested against peptide pools of clade B Gag, Pol, Nef, Rev and Tat. Nine individuals demonstrated cross-reactive T-cell responses to clade A, B, and C Gag pools; 6/7 patients that responded to Nef-B also reacted to clade A and C Nef pools. An inverse correlation was observed between the sequence divergence of the HLA class I restricted epitopes and the height of the T-cell responses, which in Gag could be explained through variations in the HLA-anchor residues. 42% of the responses were directed to regions containing new epitopes.
This previously described epitope was embedded in a B clade peptide that was recognized by T-cells from an infected person carrying subtype D Gag. The autologous epitope sequence ELRSLYNTV had dramatic changes, the epitope peptide was gikSLhNTV, and so likely not the actual reactive epitope in the larger peptide.

References

Geels2005 Mark J. Geels, Sheri A. Dubey, Kiersten Anderson, Elly Baan, Margreet Bakker, Georgios Pollakis, William A. Paxton, John W. Shiver, and Jaap Goudsmit. Broad Cross-Clade T-Cell Responses to Gag in Individuals Infected with Human Immunodeficiency Virus Type 1 Non-B Clades (A to G): Importance of HLA Anchor Residue Conservation. J. Virol., 79(17):11247-11258, Sep 2005. PubMed ID: 16103177. Show all entries for this paper.

Displaying record number 54810

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location
Epitope	`ELRSLYNTV`	Epitope Alignment
Species (MHC/HLA)	(B8)
Immunogen
Experimental methods
Keywords	review, immunodominance, escape, vaccine antigen design

Notes

This review discusses current literature on particular CTL escape mutations that significantly impair viral fitness and argues for a concerted effort to identify these targets.
This epitope is discussed in the context of the hierarchy of recognized HLA-B8 epitopes during acute infection.

References

Altfeld2006a Marcus Altfeld and Todd M. Allen. Hitting HIV Where It Hurts: An Alternative Approach to HIV Vaccine Design. Trends Immunol., 27(11):504-510, Nov 2006. PubMed ID: 16997629. Show all entries for this paper.

Displaying record number 55238

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17(74-82 B1 and B2)
Epitope	`ELRSLYNTV`	Epitope Alignment
		Show epitope variants
Subtype	B, CRF01_AE
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Patient MHC/HLA	A3, A32, B62, B8, Cw3
Country	Netherlands
Experimental methods	Other
Keywords	subtype comparisons, computational epitope prediction, superinfection

Notes

The influence of superinfection upon changes in HIV-1 strains was studied in a triple infected subject. While continuous expression of all three strains was observed, the LTR promoters of subtype AE had highest activity of all 3 strains, and subtype B2 had the lowest. Env-V3 sequences were present in higher numbers in strains B2 and CRF01_AE. Recombination was seen between viruses B1/B2 in gag and vpr genes.
This HLA-B08 restricted epitope, ELkSLYNTV, varied to ELRSLYNTV in 50% of viruses in B1 within 4 years, ELkSLfNTV in 67% of viruses in strain B2 within 3 years, and ELkSLYNTV in AE at the earliest time point taken, with no changes over time. A reversion was seen in B2 to ELkSLYNTV i.e. f to Y, suggesting a lack of CTL pressure on this sequence.

References

Kozaczynska2007 Karolina Kozaczynska, Marion Cornelissen, Peter Reiss, Fokla Zorgdrager, and Antoinette C. van der Kuyl. HIV-1 Sequence Evolution In Vivo after Superinfection with Three Viral Strains. Retrovirology, 4:59, 2007. PubMed ID: 17716368. Show all entries for this paper.

Displaying record number 55713

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	Gag
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9-B08
Subtype	B, F
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Country	Argentina
Experimental methods
Keywords	dynamics, HLA associated polymorphism

Notes

Dynamics of CTL escape mutations was studied theoretically by analyzing plasma samples from 302 subjects (collected over 20 years). HLA associated polymorphisms accumulated in a subtype-specific manner.
Epitope ELRSLYNTV with anchor residues at EL(R)SLYNTV contains a polymorphism ELrSLYNTV. The variant ELkSLYNTV increases in time.

References

Dilernia2008 Dario Alberto Dilernia, Leandro Jones, Sabrina Rodriguez, Gabriela Turk, Andrea E Rubio, Sandra Pampuro, Manuel Gomez-Carrillo, Christian Bautista, Gabriel Deluchi, Jorge Benetucci, María Beatriz Lasala, Leonardo Lourtau, Marcelo Horacio Losso, Héctor Perez, Pedro Cahn, and Horacio Salomón. HLA-Driven Convergence of HIV-1 Viral Subtypes B and F Toward the Adaptation to Immune Responses in Human Populations. PLoS ONE, 3(10):e3429, 2008. PubMed ID: 18941505. Show all entries for this paper.

Displaying record number 57835

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Subtype	B
Species (MHC/HLA)	human(B8)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, TCR binding
Keywords	rate of progression, TCR usage, optimal epitope

Notes

The study measured the functional avidities of HIV-specific CTL responses targeting 20 optimally defined CTL epitopes in a cohort of 44 HIV controllers and 68 non-controllers. Highest functional avidities were toward HLA-B-restricted epitopes in Gag. Avidities were higher in HIV controllers than non-controllers. Higher-avidity T-cell populations had narrower TCR repertoires.

References

Berger2011 Christoph T. Berger, Nicole Frahm, David A. Price, Beatriz Mothe, Musie Ghebremichael, Kari L. Hartman, Leah M. Henry, Jason M. Brenchley, Laura E. Ruff, Vanessa Venturi, Florencia Pereyra, John Sidney, Alessandro Sette, Daniel C. Douek, Bruce D. Walker, Daniel E. Kaufmann, and Christian Brander. High-Functional-Avidity Cytotoxic T Lymphocyte Responses to HLA-B-Restricted Gag-Derived Epitopes Associated with Relative HIV Control. J. Virol., 85(18):9334-9345, Sep 2011. PubMed ID: 21752903. Show all entries for this paper.

Displaying record number 59618

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	Gag(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Epitope Name	EV9
Species (MHC/HLA)	human(C*06)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope, chronic infection

Notes

Correlation between HLA class I and spontaneous control of HIV-1 was significant for 7-8 epitopes when 341 chronic, HIV-infected subjects, divided into controllers and non-controllers, were tested for EliSpot responses to 257 optimally defined epitopes. 21 epitopes were associated with viral progression. Protective epitopes tend to cluster in regions of critical stability for the protein, therefore constraining escape.
ELRSLYNTV had a significantly positive association with HLA C*06; it was recognized by 3/72 C*06-positive subjects and 0/178 C*06-negative subjects.

References

Displaying record number 62776

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HXB2 Location	Gag(74-82) p17(74-82) DNA(1009..1035)	Gag Epitope Map
Author Location	p17(74-82)
Epitope	`ELRSLYNTV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	assay or method development, protective allele

Notes

NL4-3 Gag polyprotein random mutagenesis, high-throughput fitness profiling and in silico prediction of MHC-peptide binding affinity revealed that mutations in CTL epitopes presented by protective MHC-I alleles, vs. non-protective alleles, showed greater loss of experimental replicative capacity and lower levels of predicted reduction in MHC-I binding affinity. Together, these two variables could predict protectiveness of MHC-I alleles in a linear regression model. Analyses of intraperson viral evolution in 4 LTNP vs. 4 paired progressor subjects further supported paper conclusions.
After mutagenesis and passaging through human T cells, 43 single nucleotide mutations were observed in epitope ELRSLYNTV (known to bind to B0801) with a log transformation of mean fitness score, relative to NL4-3, of -0.3252.

References

Du2017 Yushen Du, Tian-Hao Zhang, Lei Dai, Xiaojuan Zheng, Aleksandr M. Gorin, John Oishi, Ting-Ting Wu, Janice M. Yoshizawa, Xinmin Li, Otto O. Yang, Otoniel Martinez-Maza, Roger Detels, and Ren Sun. Effects of Mutations on Replicative Fitness and Major Histocompatibility Complex Class I Binding Affinity Are Among the Determinants Underlying Cytotoxic-T-Lymphocyte Escape of HIV-1 Gag Epitopes. mBio, 8(6), 28 Nov 2017. PubMed ID: 29184023. Show all entries for this paper.