Search CTL/CD8+ T-Cell Epitope Database

Found 22 matching records:

Displaying record number 62250

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(145-155)
Epitope	`QAISPRTLNAW`	Epitope Alignment
		Show epitope variants
Epitope Name	QW11
Subtype	B
Species (MHC/HLA)	human(A*25)
Immunogen	HIV-1 infection
Patient MHC/HLA	PIC1362: A02:01, A25:01, B18:01, B51:01, C01:02, C12:03; PIC1349: A02, A25, B58, B62, C04, C07; PIC1052: A25, A30, B07, B35, C04, C07; PIC1483: A01:01, A25:01, B38:01, B39:01, C12:03, C12:03
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	acute/early infection, mutation acquisition, viral fitness and reversion, viral replication

Notes

In a longitudinal study of patient 1362, escape mutations were tracked in 5 HIV Env gp120 and 2 Gag p24 CTL epitopes. Only 1/9 gp120 dominant mutations that appeared during acute infection within one year had fitness loss, 4/9 had no effect on fitness and 3/9 experienced a slight fitness increase. Meanwhile, all 4 Gag p24 mutations, which appeared in two years, decreased fitness! Thus, Gag p24 mutations are associated with significant fitness cost, but most Env escapes are fitness-neutral.
QW11 was 1 of 2 epitopes mutated over 3 years in Gag p24. Variants were not associated with VL or CD4 cell counts in four A*25+ subjects, but QW11 was recognized by the subjects.

References

Troyer2009 Ryan M. Troyer, John McNevin, Yi Liu, Shao Chong Zhang, Randall W. Krizan, Awet Abraha, Denis M. Tebit, Hong Zhao, Santiago Avila, Michael A. Lobritz, M. Juliana McElrath, Sylvie Le Gall, James I. Mullins, and Eric J. Arts. Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response. PLoS Pathog., 5(4):e1000365, Apr 2009. PubMed ID: 19343217. Show all entries for this paper.

Displaying record number 59187

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(13-23 NL4.3)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11, 2-ISW9
Subtype	B
Species (MHC/HLA)	human(A*25)
Immunogen	HIV-1 infection
Experimental methods	In vitro proteasome digestion, Other
Keywords	epitope processing

Notes

7 HIV protease inhibitors (PIs) were shown to alter not only proteasome but also aminopeptidase activities that generate epitopes for MHC presentation. These inhibitors altered degradation patterns, sensitivity of peptides to degradation, kinetics and amounts of epitope production and therefore recognition by CTLs.
Precursor 3ISW9, HQAISPRTLNAW, an A*25-restricted precursor to ISW9 was treated with different PIs. Ritonavir and Kaletra reduced production of 2-ISW9, QAISPRTLNAW, also an A*25 epitope.

References

Kourjian2014 Georgio Kourjian, Yang Xu, Ijah Mondesire-Crump, Mariko Shimada, Pauline Gourdain, and Sylvie Le Gall. Sequence-Specific Alterations of Epitope Production by HIV Protease Inhibitors. J. Immunol., 192(8):3496-3506, 15 Apr 2014. PubMed ID: 24616479. Show all entries for this paper.

Displaying record number 56365

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(145-155)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
Subtype	B
Species (MHC/HLA)	human(A*25)
Immunogen	HIV-1 infection
Country	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-A*25-associated substitution within optimally defined epitope QAISPRTLNAW is at positions 3I, QAiSPRTLNAW.

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 62108

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(145-155 NL4-3)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
Species (MHC/HLA)	human(A*25)
Immunogen	computer prediction
Experimental methods	Other, Relative replication capacity assay
Keywords	vaccine antigen design, viral fitness and reversion

Notes

Computational models were used to translate published HIV-1 sequence data into quantitative viral fitness landscapes with peaks and valleys, that are a function of the amino acid sequences of its constituent proteins. In this case, Clade B Gag was modeled. Predictions were tested against in vitro fitness measurements and were consistent.
Epitope -QAISPRTL is used as an example from Troyer2009, Draenert2004, Brockman2010 [Troyer et al. PLoS Pathog. 5:e1000365; Draenert et al. J. Exp. Med. 199:905-15; Brockman et al. J.Virol. 84:11937-49] where each amino acid position within the epitope is associated with a different energy cost, ΔE, and the greater the cost the higher the fitness penalty. Observed HLA-associated escape positions at I147 are one of the 2 positions (including A146) with the lowest h_i value, i.e. the least energetically costly to change.
Based on fitness costs, the authors created a rank-ordered bar chart called the "Epitope Index" and marked out immunodominant response associations on it. The epitope index reads Gag: (164-172)-B*57; (162-172)-B*57 i.e. KF11; (167-175)-A*26; (260-267)-B*08; (240-249)-B*57 i.e. TW10; (296-306)-B*14; (147-155)-B*57; (349-359)-A*11; (263-272)-B*27; (269-277)-B*15; (145-155)-A*25; (306-316)-B*44, from highest to lowest fitness costs.
Brumme2009 is not annotated in this database as epitopes were not immunologically defined, but the table of polymorphisms is available at https://www.hiv.lanl.gov/content/immunology/pdf/2010/escape_article_supplement.html. and a review of the work is available on the main page, hiv.lanl.gov under 'Tools and Data Sets', "Identifying HLA-Associated Polymorphisms in HIV-1" (PDF).

References

Ferguson2013a Andrew L. Ferguson, Jaclyn K. Mann, Saleha Omarjee, Thumbi Ndung'u, Bruce D Walker, and Arup K. Chakraborty. Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design. Immunity, 38(3):606-617, 21 Mar 2013. PubMed ID: 23521886. Show all entries for this paper.

Displaying record number 60051

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	Gag(145-155)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
Species (MHC/HLA)	human(A*25)
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.
QAISPRTLNAW had a significantly positive association with HLA A*25; it was recognized by 12/18 A*25-positive subjects and 13/219 A*25-negative subjects.
QAISPRTLNAW was significantly protective, associated with viral control when restricted by HLA-A*25 in a cohort of 245 controllers and 96 progressors.

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 52735

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	Gag(145-155 IIIB)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A25)
Immunogen	HIV-1 infection
Experimental methods	Chromium-release assay
Keywords

Notes

Three CD8+ CTL cell clones were derived from 2 HIV-1 positive asymptomatic patients, and their epitope specificities and HLA presenting proteins were defined.

References

Kurane2003 Ichiro Kurane, Kim West, Carmelita U. Tuazon, Weilan Zeng, and Francis A. Ennis. Definition of Two New Epitopes on Human Immunodeficiency Virus Type 1 Gag Protein Recognized by Human CD8+ Cytotoxic T Lymphocyte Clones. J. Clin. Virol., 27(1):38-43, May 2003. PubMed ID: 12727527. Show all entries for this paper.

Displaying record number 137

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(145-155 LAI)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A25)
Immunogen
Experimental methods
Keywords

References

KuranePerCom I. Kurane and K. West. Personal communication, 1998. Show all entries for this paper.

Displaying record number 55189

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location
Epitope	`QAISPRTLNAW`	Epitope Alignment
Species (MHC/HLA)	human(A25)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	supertype, HLA cross-presentation, optimal epitope

Notes

100 HIV-infected subjects were tested for response to optimally-defined CTL epitopes regardless of the subject's HLA type. Half of all detected responses were seen in the absence of the originally reported restricting HLA class I allele, and only 3% of epitopes were recognized exclusively in the presence of their original allele. Statistical and experimental methods were used to define additional HLA alleles associated with the epitopes.
Based on a prediction of the minimum number of HLA alleles needed to cover the HLA representation in all responders to this optimal epitope, a minimum set of 6 alleles was found: 1 allele previously known to be associated (A25) and 5 additional alleles (A23, A68, B44, Cw04, Cw07).

References

Frahm2007b Nicole Frahm, Karina Yusim, Todd J. Suscovich, Sharon Adams, John Sidney, Peter Hraber, Hannah S. Hewitt, Caitlyn H. Linde, Daniel G. Kavanagh, Tonia Woodberry, Leah M. Henry, Kellie Faircloth, Jennifer Listgarten, Carl Kadie, Nebojsa Jojic, Kaori Sango, Nancy V. Brown, Eunice Pae, M. Tauheed Zaman, Florian Bihl, Ashok Khatri, Mina John, Simon Mallal, Francesco M. Marincola, Bruce D . Walker, Alessandro Sette, David Heckerman, Bette T. Korber, and Christian Brander. Extensive HLA Class I Allele Promiscuity among Viral CTL Epitopes. Eur. J. Immunol., 37(9):2419-2433, Sep 2007. PubMed ID: 17705138. Show all entries for this paper.

Displaying record number 57843

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
Subtype	B
Species (MHC/HLA)	human(A25, B57)
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.
Promiscuously-presented epitope QW11 (A25, B57) exhibited higher functional avidity in the context of the HLA allele associated with better disease outcome (B57).

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 60978

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(13-23)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*25:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	94153: A25:01, A68:01, B14:02, B44:02, C05:01, C08:02
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.
QAISPRTLNAW, restricted by A*2501, 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 138

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(145-155 LAI)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*25:01)
Immunogen
Experimental methods
Keywords	optimal epitope, A-list

Notes

C. Brander notes that this is an A*2501 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 54145

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(13-23 HXB2)
Epitope	`QAISPRTLNAW`	Epitope Alignment
		Show epitope variants
Epitope Name	QW11
Subtype	B
Species (MHC/HLA)	human(A*25:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	PIC1362: A02:01, A25:01, B18:01, B51:01, C01:02, C12:03
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	escape, mutation acquisition, optimal epitope

Notes

T-cell immunity and the impact of selection were longitudinally studied in a patient from the time of transmission. New epitopes were detected at sites that were shown to be under positive selection. Env was found to be the major target of CTLs and most of the new epitopes were found here. One third of the sites examined were associated with epitope escape mutations from CTL. Acquisition of mutations found at high frequency in the database was suggested to be a result of reversion of CTL epitopes in the absence of immune targeting.
Amino acid site in the third position potentially experienced positive selection. QAlSPRTLNAW CTL escape mutant was found.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.

Displaying record number 58160

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(13-23)
Epitope	`QAISPRTLNAW`	Epitope Alignment
		Show epitope variants
Epitope Name	QW11
Subtype	B
Species (MHC/HLA)	human(A*25:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	PIC1362: A02:01, A25:01, B18:01, B51:01, C01:02, C12:03
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	escape, acute/early infection

Notes

CTL responses were studied in a drug-naive patient for 4 years, beginning at the time of infection. CTL recognition of 25 epitopes was observed, and 18 of them underwent mutational changes, usually indicative of escape.
Evolving epitope QAISPRTLNAW underwent weak selection during 4 years of infection.
Major variant QAlSPRTLNAW replaced the wild type sequence by 800 days post-infection. It did not abrogate EliSpot response to the epitope.

References

Liu2011a Yi Liu, John P. McNevin, Sarah Holte, M. Juliana McElrath, and James I. Mullins. Dynamics of Viral Evolution and CTL Responses in HIV-1 Infection. PLoS One, 6(1):e15639, 2011. PubMed ID: 21283794. Show all entries for this paper.

Displaying record number 59081

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(13-23)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*25:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	PIC1362: A02:01, A25:01, B18:01, B51:01, C01:02, C12:03
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	viral fitness and reversion

Notes

CTL responses were studied in a single drug-naive individual during the first 4 years of infection. 25 CTL epitopes were identified; 17 of them underwent evolution; 15 mutant forms that escaped or partially escaped were detected.
QAISPRTLNAW was an epitope whose frequency decreased during 4 years of infection; no escape mutants were detected.

References

Liu2007a Yi Liu, John McNevin, Hong Zhao, Denis M. Tebit, Ryan M. Troyer, Matthew McSweyn, Ananta K. Ghosh, Daniel Shriner, Eric J. Arts, M. Juliana McElrath, and James I. Mullins. Evolution of Human Immunodeficiency Virus Type 1 Cytotoxic T-Lymphocyte Epitopes: Fitness-Balanced Escape. J. Virol., 81(22):12179-12188, Nov 2007. PubMed ID: 17728222. Show all entries for this paper.

Displaying record number 60626

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(13-23)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
Subtype	B, C
Species (MHC/HLA)	human(A*25:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Subtype-specific substitutions in two HIV Gag regions (fragments F1, amino acids (aa) 5-46, and F2 aa 100-143) result in novel adaptations that affect epitope processing efficiency. Consequent low epitope abundance is associated with weak T cell response and greater immune escape and therefore with disease state. Conversely, epitopes from these regions when restricted by certain rare HLA I alleles, are associated with greater production and resulting CTL response, therefore delayed disease progression.
Most epitopes were found to be processed as precursors with N-terminal extensions beyond the optimal epitope. Only 4 epitopes in this region were associated with delayed progression - HLA-B*5701/03-restricted IW9 (ISPRTLNAW), KF11 (KAFSPEVIPMF), TW10 (TSTLQEQIGW) and HLA-B*2705-restricted KK10 (KRWIILGLNK).
Regardless of ethnic group, white or African, a significant three-way interaction was found between HLA allelic frequency, epitope yield and ethnicity for epitopes of N-terminal fragment F1 (NF1) and C-terminal as well as middle F2 (CF2 and MF2). C-terminal F1 (CF1) epitope yields however, showed a significant difference between ethnic groups. Also, for identical HLA-mediated selection pressure in both Africans and whites, HIV-C had a lower concentration than HIV-B, especially at lower HLA allelic frequencies.
Epitope QAISPRTLNAW, QW11, is from fragment F1, and restricted by HLA-A*25, A*2501. 94% NLQGQMVHQAISPRTLNAW, QW11's subtype B, natural processed epitope form, accumulated after 4 hours processing by constitutive proteasomes, and 97% with immuno proteasomal processing. For subtype C, the natural processed form was NLQGQMVHQAISPRTLNAW, 97% 4h post-constitutive- and 96% post-immuno-proteasomal processing.

References

Tenzer2014 Stefan Tenzer, Hayley Crawford, Phillip Pymm, Robert Gifford, Vattipally B. Sreenu, Mirjana Weimershaus, Tulio de Oliveira, Anne Burgevin, Jan Gerstoft, Nadja Akkad, Daniel Lunn, Lars Fugger, John Bell, Hansjörg Schild, Peter van Endert, and Astrid K. N. Iversen. HIV-1 Adaptation to Antigen Processing Results in Population-Level Immune Evasion and Affects Subtype Diversification. Cell Rep., 7(2):448-463, 24 Apr 2014. PubMed ID: 24726370. Show all entries for this paper.

Displaying record number 60052

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	Gag(145-155)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
Species (MHC/HLA)	human(B35:01, B35:08)
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.
QAISPRTLNAW had a significantly positive association with HLA B*3501,B*3508; it was recognized by 8/32 B*3501,B*3508-positive subjects and 5/187 B*3501,B*3508-negative subjects.
QAISPRTLNAW was significantly protective, associated with viral control when restricted by HLAs-B*3501, -B*3508 in a cohort of 245 controllers and 96 progressors.

References

Displaying record number 60050

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	Gag(145-155)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
Species (MHC/HLA)	human(B*57)
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.
QAISPRTLNAW had a significantly positive association with HLA B*57; it was recognized by 77/104 B*57-positive subjects and 25/237 B*57-negative subjects.
QAISPRTLNAW was significantly protective, associated with viral control when restricted by HLA-B*57 in a cohort of 245 controllers and 96 progressors.

References

Displaying record number 60053

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	Gag(145-155)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
Species (MHC/HLA)	human(B*58:01)
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.
QAISPRTLNAW had a significantly positive association with HLA B*5801; it was recognized by 2/8 B*5801-positive subjects and 3/179 B*5801-negative subjects.
QAISPRTLNAW was significantly protective, associated with viral control when restricted by HLA-B*5801 in a cohort of 245 controllers and 96 progressors.

References

Displaying record number 60054

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	Gag(145-155)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Epitope Name	QW11
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.
QAISPRTLNAW had a significantly positive association with HLA C*06; it was recognized by 2/22 C*06-positive subjects and 1/157 C*06-negative subjects.
QAISPRTLNAW was significantly protective, associated with viral control when restricted by HLA-C*06 in a cohort of 245 controllers and 96 progressors.

References

Displaying record number 62785

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(145-155)
Epitope	`QAISPRTLNAW`	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, 66 single nucleotide mutations were observed in epitope QAISPRTLNAW (known to bind to A2501) with a log transformation of mean fitness score, relative to NL4-3, of -0.4556.

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.

Displaying record number 54919

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location
Epitope	`QAISPRTLNAW`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, vaccine
Patient MHC/HLA	014A-001: A02:02, A80:01, B18:01, B53:01; 014A-005: A25:01, A30:02, B07:02, B18:01, C07:02, C12:03
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	vaccine-induced immune responses, acute/early infection

Vaccine Details

Vaccine type	canarypox prime with gp120 boost
Vaccine strain	B clade LAI, B clade MN
Vaccine component	Gag-Pol, gp120, gp41

Notes

T cell responses during early infection in individuals previously enrolled in HIV vaccine trials were compared with those of nonvaccinated subjects.
None of the breakthrough infections possessed vaccine-induced T-cell responses preinfection and 85-86% of vaccinees and nonvaccinees with primary infection developed T-cell responses postinfection, indicating that vaccinees' ability to mount T-cell response postinfection is not compromized by previous immunization.
Breakthrough subjects recognized 43 T-cell epitopes, 8 of them novel, and 25% were present in the vaccine.
Epitope QAISPRTLNAW was contained in the vaccine, and vCP205/gp120-vaccinated patient 014A-001 recognized it after breakthrough infection.

References

Horton2006a Helen Horton, Colin Havenar-Daughton, Deborah Lee, Erin Moore, Jianhong Cao, John McNevin, Thomas Andrus, Haiying Zhu, Abbe Rubin, Tuofu Zhu, Connie Celum, and M. Juliana McElrath. Induction of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific T-Cell Responses in HIV Vaccine Trial Participants Who Subsequently Acquire HIV-1 Infection. J. Virol., 80(19):9779-9788, Oct 2006. PubMed ID: 16973582. Show all entries for this paper.

Displaying record number 136

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HXB2 Location	Gag(145-155) p24(13-23) DNA(1222..1254)	Gag Epitope Map
Author Location	p24(145-155)
Epitope	`QAISPRTLNAW`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Experimental methods
Keywords	immunodominance

Notes

Only 4/11 HLA-A2+ HIV+ individuals had CTL that reacted to SLYNTVATL, calling into question whether it is immunodominant.
95 optimally-defined peptides from this database were used to screen for INFγ responses to other epitopes.
1/11 of the A2+ individuals was HLA A*0201, A1, B57 and responded to QAISPRTLNAW noted previously to be A25.

References

Betts2000 M. R. Betts, J. P. Casazza, B. A. Patterson, S. Waldrop, W. Trigona, T.-M Fu, F. Kern, L. J. Picker, and R. A. Koup. Putative Immunodominant Human Imunodeficiency Virus-Specific CD8+ T Cell Responses Cannot Be Predicted by Major Histocompatibility Complex Class I Haplotype. J. Virol., 74:9144-9151, 2000. PubMed ID: 10982361. Show all entries for this paper.