Search CTL/CD8+ T-Cell Epitope Database

Found 20 matching records:

Displaying record number 57388

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Subtype	B
Species (MHC/HLA)	human(A*03)
Immunogen	in vitro stimulation or selection, HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	TCR usage, assay or method development, chronic infection

Notes

By using a modified spectratyping (immunoscoping) method, epitope-specific TCR breadth and sequences were quantitated rapidly. Overall magnitude of HIV-1 specific CTL responses to chronic infection were limited by the clonal breadth of TCR generated against HIV-1 epitopes tested in 12 patients with chronic, untreated infection.
CTL response specific to epitope RK10 was studied, TCR usage was BV18 and BV28 in patient 0009.

References

Balamurugan2010 Arumugam Balamurugan, Hwee L. Ng, and Otto O. Yang. Rapid T Cell Receptor Delineation Reveals Clonal Expansion Limitation of the Magnitude of the HIV-1-Specific CD8+ T Cell Response. J. Immunol., 185(10):5935-5942, 15 Nov 2010. PubMed ID: 20944001. Show all entries for this paper.

Displaying record number 60117

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Species (MHC/HLA)	human(A*03)
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.
RIRTWKSLVK had a significantly positive association with HLA A*03; it was recognized by 15/58 A*03-positive subjects and 13/266 A*03-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 1987

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	Vif-RK10
Subtype	B
Species (MHC/HLA)	human(A*03)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Among HIV+ individuals who carried HLA A*03, 3/21 (14%) recognized this epitope.

References

Sabbaj2003 Steffanie Sabbaj, Anju Bansal, G. Douglas Ritter, Christopher Perkins, Bradley H. Edwards, Ethan Gough, Jianming Tang, James J. Szinger, Bette Korber, Craig M. Wilson, Richard A. Kaslow, Mark J. Mulligan, and Paul A. Goepfert. Cross-Reactive CD8+ T Cell Epitopes Identified in US Adolescent Minorities. J. Acquir. Immune Defic. Syndr., 33(4):426-438, 1 Aug 2003. PubMed ID: 12869831. Show all entries for this paper.

Displaying record number 57292

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Subtype	B
Species (MHC/HLA)	human(A*03)
Immunogen	HIV-1 infection
Country	Barbados, Haiti, Jamaica
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	mother-to-infant transmission, elite controllers

Notes

To dissect whether the protective effect of HLA-B*57 in HIV-1 infection is due to CTL that recognize HLA-B*57-restricted epitopes or by the presence of viral-fitness attenuating mutations in such B*57 epitopes, 13 mother-infant pairs were studied. The B57 advantage is primarily through the maintenance of a fitness-attenuating mutation in p24-Gag, T242N in epitope TW10 (TSTLQEQIGW).
Regardless of parental inheritance, HLA-B57 controls VL even in infancy and even when escape mutations from B*57 positive mothers are transmitted. Mutations in p24-Gag are predominant in mismatched-HLA subject pairs and arise after vertical transmission, impacting viral fitness.
Non-B57-epitope RK10-Vif, RIRTWKSLVK restricted by A*03, was recognized by an infant with maternally-inherited B57.

References

Schneidewind2009 Arne Schneidewind, Yanhua Tang, Mark A. Brockman, Elizabeth G. Ryland, Jacqueline Dunkley-Thompson, Julianne C. Steel-Duncan, M. Anne St. John, Joseph A. Conrad, Spyros A. Kalams, Francine Noel, Todd M. Allen, Celia D. Christie, and Margaret E. Feeney. Maternal Transmission of Human Immunodeficiency Virus Escape Mutations Subverts HLA-B57 Immunodominance but Facilitates Viral Control in the Haploidentical Infant. J. Virol., 83(17):8616-8627, Sep 2009. PubMed ID: 19515764. Show all entries for this paper.

Displaying record number 1267

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26 SF2)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Species (MHC/HLA)	human(A*03:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

CTL responses against HIV-1 Vpr, Vpu, and Vif were analyzed in multiple HIV-1-infected individuals.
10/29 (35%) individuals tested responded to Vif.
This epitope was recognized by 3/15 individuals expressing A*0301 allele.
HIV+ individual AC-06 was tested for reactive overlapping peptides spanning all HIV-1 proteins in an ELISPOT and was found to react with 12 peptides from 7 proteins, suggesting that the breadth of CTL responses are underestimated if accessory proteins are not included in the study.
Overlapping Vif peptides QVDRMRIRTWKSLVK and RIRTWKSLVKHHMYI both reacted with T-cells from AC-06 and contained epitope RIRTWKSLVK.

References

Altfeld2001c M. Altfeld, M. M. Addo, R. L. Eldridge, X. G. Yu, S. Thomas, A. Khatri, D. Strick, M. N. Phillips, G. B. Cohen, S. A. Islam, S. A. Kalams, C. Brander, P. J. Goulder, E. S. Rosenberg, B. D. Walker, and The HIV Study Collaboration.. Vpr is preferentially targeted by CTL during HIV-1 infection. J. Immunol., 167(5):2743-52, 1 Sep 2001. URL: http://www.jimmunol.org/cgi/content/full/167/5/2743. PubMed ID: 11509618. Show all entries for this paper.

Displaying record number 1210

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	( LAI)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*03:01)
Immunogen
Experimental methods
Keywords	optimal epitope, A-list

References

Altfeld2000c M. Altfeld. Personal communication, 2000. Show all entries for this paper.

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 52400

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*03:01)
Immunogen	HIV-1 infection
Experimental methods
Keywords	early-expressed proteins

Notes

CTL responses against regulatory and accessory proteins in 70 HIV-1 infected patients were studied using overlapping peptides and Elispot.
28% targeted one or more overlapping Tat peptides; 36%, Rev peptides; 33%, Vif peptides; 40%, Vpr peptides; and 2%, Vpu peptides.
All known optimally defined epitopes were summarized for the five proteins.

References

Addo2002a M. M. Addo, X. G. Yu, E. S. Rosenberg, B. D. Walker, and M. Altfeld. Cytotoxic T-Lymphocyte (CTL) Responses Directed against Regulatory and Accessory Proteins in HIV-1 Infection. DNA Cell Biol., 21(9):671-678, Sep 2002. PubMed ID: 12396610. Show all entries for this paper.

Displaying record number 61687

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Species (MHC/HLA)	human(A*03:01)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	review

Notes

This review makes the argument that T-cell subsets recognizing the HIV/SIV viral infectivity factor Vif, may be essential for control of HIV replication as vif-deficient strains can only complete one round of replication and Vif targets the cellular viral-restriction-factor, APOBEC3G (A3G) with the help of Elongin B/C and Cullin-5 to proteasomal degradation.
HIV-1 HLA-A*0301 restricted epitope RK10, RIRTWKSLVK (Vif 17-26) overlaps with the A3F binding site, WQVDRMR and the A3G binding site, WKSLVK.

References

Silver2017 Zachary A. Silver and David I. Watkins. The Role of MHC Class I Gene Products in SIV Infection of Macaques. Immunogenetics, 69(8-9):511-519, Aug 2017. PubMed ID: 28695289. Show all entries for this paper.

Displaying record number 60119

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Species (MHC/HLA)	human(A*29)
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.
RIRTWKSLVK had a significantly positive association with HLA A*29; it was recognized by 4/27 A*29-positive subjects and 7/234 A*29-negative subjects.

References

Displaying record number 54249

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	A3-RK10(Vif)
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	rate of progression, immunodominance, early-expressed proteins

Notes

Immunodominant HIV epitopes in early, primary infection of CTLs were identified and the relative contributions of immune responses restricted to individual HLA class I molecules were studied.
This epitope-HLA combination was recognized. The most frequently recognized epitopes also elicited the greatest CTL response.
HIV-1 Epitope sequence variability was not correlated with immunodominant versus immune sub-dominant responses.
HLA-B*57 and HLA-B*27 restricted responses were the strongest in these early and acute infections - due to dominant responses to a single epitope in each case (TW10 for B*57 and KK10 for B*27).
In the presence of HLA-B*57 and HLA-B*27 restricted responses, the relative contributions of other restricting HLA dropped greatly.

References

Altfeld2006 Marcus Altfeld, Elizabeth T. Kalife, Ying Qi, Hendrik Streeck, Mathias Lichterfeld, Mary N. Johnston, Nicole Burgett, Martha E. Swartz, Amy Yang, Galit Alter, Xu G. Yu, Angela Meier, Juergen K. Rockstroh, Todd M. Allen, Heiko Jessen, Eric S. Rosenberg, Mary Carrington, and Bruce D. Walker. HLA Alleles Associated with Delayed Progression to AIDS Contribute Strongly to the Initial CD8+ T Cell Response against HIV-1. PLoS Med., 3(10):e403, Oct 2006. PubMed ID: 17076553. Show all entries for this paper.

Displaying record number 52152

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	A3-RK10
Subtype	B
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Patient MHC/HLA	A3, B7, Cw7
Experimental methods
Keywords	dynamics, supervised treatment interruptions (STI), acute/early infection

Notes

CTL responses in 18 acutely HIV-infected HLA-A3 (n=7) or -B7 (n=4) or both -A3 and B7 (n=7) positive individuals were studied.
One individual, AC-06, was homozygous at all three class I alleles (A3, B7, Cw7), was treated during acute infection and had supervised treatment interruptions (STI). He had only two detectable CTL responses during acute infection, but after STI this broadened to 27 distinct epitopes including 15 restricted by HLA-A3, 11 by HLA-B7, and 1 by HLA-Cw7.
0/14 HLA-A3 positive individuals had detectable A3-restricted responses to this epitope during acute infection, but only 5/15 of HLA-A3 epitopes tested were targeted during acute infection. 1/7 individuals had detectable responses to this epitope after STI.

References

Yu2002b Xu G. Yu, Marylyn M. Addo, Eric S. Rosenberg, William R. Rodriguez, Paul K. Lee, Cecily A. Fitzpatrick, Mary N. Johnston, Daryld. Strick, Philip J. R. Goulder, Bruce D. Walker, and Marcus Altfeld. Consistent Patterns in the Development and Immunodominance of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific CD8+ T-Cell Responses Following Acute HIV-1 Infection. J. Virol., 76(17):8690-8701, Sep 2002. PubMed ID: 12163589. Show all entries for this paper.

Displaying record number 52813

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
		Show epitope variants
Epitope Name	A3-RK10 Vif
Subtype	B
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	supervised treatment interruptions (STI), escape, early treatment, superinfection

Notes

An HIV+ individual given acute ARV and undergoing STI developed a strong CTL immune response, but despite this was shown to be superinfected with second B clade virus. Some epitope variants of the second infecting virus were resistant to the initial CTL response.
The second infecting strain had the variant riStwkslvk. The initial CTL response to persisted to against both variants after the superinfection was established.

References

Altfeld2002a Marcus Altfeld, Todd M. Allen, Xu G. Yu, Mary N. Johnston, Deepak Agrawal, Bette T. Korber, David C. Montefiori, David H. O'Connor, Ben T. Davis, Paul K. Lee, Erica L. Maier, Jason Harlow, Philip J. R. Goulder, Christian Brander, Eric S. Rosenberg, and Bruce D. Walker. HIV-1 Superinfection Despite Broad CD8+ T-Cell Responses Containing Replication of the Primary Virus. Nature, 420(6914):434-439, 28 Nov 2002. PubMed ID: 12459786. Show all entries for this paper.

Displaying record number 52984

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Patient MHC/HLA	A3, A32, B15, B51, C*03, Cw6, DQ7, DR4, DR8
Country	Netherlands
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, escape

Notes

Both stable potential epitopes and epitopes with escape mutations were found in a patient with increasing viral load over a time period of 4 years. Fixation of escape mutations occurred sequentially and correlated with the rise in viral load and with the increased number of productively infected cells.
This is one of 17 potential epitopes from this individual, defined based on previously identified epitopes presented by appropriate HLA molecules. Full length genome sequence did not reveal changes in time in any of these epitopes over a four year period. Peptide pools initially revealed very little response to these epitopes, but this increased over time.

References

Geels2003 Mark J. Geels, Marion Cornelissen, Hanneke Schuitemaker, Kiersten Anderson, David Kwa, Jolanda Maas, John T. Dekker, Elly Baan, Fokla Zorgdrager, Remco van den Burg, Martijn van Beelen, Vladimir V. Lukashov, Tong-Ming Fu, William A. Paxton, Lia van der Hoek, Sheri A. Dubey, John W. Shiver, and Jaap Goudsmit. Identification of Sequential Viral Escape Mutants Associated with Altered T-Cell Responses in a Human Immunodeficiency Virus Type 1-Infected Individual. J. Virol., 77(23):12430-12440, Dec 2003. PubMed ID: 14610167. Show all entries for this paper.

Displaying record number 53357

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	( B consensus)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Subtype	B
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Patient MHC/HLA	A2, A3, B62, B8, Cw10, Cw7; A3, B7, Cw7
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.
2/9 individuals recognized this epitope, presented by HLA-A3.

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 53515

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Subtype	B
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Patient MHC/HLA	A1, A3, B57, B7, Cw6, Cw7
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	subtype comparisons, escape, characterizing CD8+ T cells, viral fitness and reversion

Notes

Two-thirds of all mutations arising in non-envelope proteins during the transition from acute to chronic infection were found to be due to either CD8 T-cell-associated selective pressures or reversion of HLA-I-associated mutations selected in a previous host.The predominance of escape mutations at highly polymorphic sites was observed across different HIV-1 clades.
One escape mutation, at position 6, rirtwNslvk, was found not to correspond to the most polymorphic residue in the epitope.

References

Allen2005a Todd M. Allen, Marcus Altfeld, Shaun C. Geer, Elizabeth T. Kalife, Corey Moore, Kristin M. O'Sullivan, Ivna DeSouza, Margaret E. Feeney, Robert L. Eldridge, Erica L. Maier, Daniel E. Kaufmann, Matthew P. Lahaie, Laura Reyor, Giancarlo Tanzi, Mary N. Johnston, Christian Brander, Rika Draenert, Jurgen K. Rockstroh, Heiko Jessen, Eric S. Rosenberg, Simon A. Mallal, and Bruce D. Walker. Selective Escape from CD8+ T-Cell Responses Represents a Major Driving Force of Human Immunodeficiency Virus Type 1 (HIV-1) Sequence Diversity and Reveals Constraints on HIV-1 Evolution. J. Virol., 79(21):13239-13249, Nov 2005. PubMed ID: 16227247. Show all entries for this paper.

Displaying record number 56429

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10(Vif)
Subtype	B
Species (MHC/HLA)	human(A3)
Immunogen	HIV-1 infection
Country	China
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	chronic infection

Notes

49 ART-naive chronically HIV-1 infected Chinese subjects' CTLs were tested with 413 OLPs in IFN-γ assays, determining optimal epitopes specific for Chinese Clade B HIV-1 sequences.
An inverse correlation was found between CTL response and viral load.
Targeted peptides have lower entropy than peptides that are not CTL targeted. This correlation is independent of HLA-restriction.
Although the tested peptides (IVWQVDRMRIRTWKSLVK and RIRTWKSLVKHHMYISKK) contained the exact sequence of a previously described HLA-A3 optimal epitope, RIRTWKSLVK, none of the 3 HLA-A3 carriers responded to it.

References

Zhai2008 Song Zhai, Yan Zhuang, Yang Song, Shu Li, Dedong Huang, Wenzhen Kang, Xinhong Li, Qi Liao, Yanhou Liu, Zhongfang Zhao, Yichen Lu, and Yongtao Sun. HIV-1-Specific Cytotoxic T Lymphocyte (CTL) Responses Against Immunodominant Optimal Epitopes Slow the Progression of AIDS in China. Curr. HIV Res., 6(4):335-350, Jun 2008. PubMed ID: 18691032. Show all entries for this paper.

Displaying record number 61831

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Species (MHC/HLA)	human(A*30:01)
Immunogen	HIV-1 infection, vaccine
Patient MHC/HLA	VID403: A01:01, A30:01, B13:02, B39:01, C06:02, C07:01, DQB102, DQB105, DRB107:01, DRB116:01, DRB4, DRB5
Country	United Kingdom
Experimental methods	Intracellular cytokine staining, Other
Keywords	vaccine-induced immune responses, novel epitope

Notes

Since CTL response in natural HIV-1 infections is mostly against variable but immunodominant epitopes, lymphocytes from 12 vaccine(HIVconsv)-exposed subjects of the HIV-CORE 002 study were used to determine and define 14 less variable but typically subdominant, optimal novel epitopes.
Epitope RIRTWKSLVK (RK10) is within peptide KQVDRMRIRTWKSLVK (HC102) that was recognized by VID403, 1/12 vaccinated subjects. RK10 is an HLA-A*3001-restricted novel epitope which is a candidate for the Los Alamos Immunology database A-list, it already exists as an A-list epitope when restricted by A*0301.

References

Borthwick2017 Nicola Borthwick, Zhansong Lin, Tomohiro Akahoshi, Anuska Llano, Sandra Silva-Arrieta, Tina Ahmed, Lucy Dorrell, Christian Brander, Hayato Murakoshi, Masafumi Takiguchi, and Tomáš Hanke. Novel, In-Natural-Infection Subdominant HIV-1 CD8+ T-Cell Epitopes Revealed in Human Recipients of Conserved-Region T-Cell Vaccines. PLoS One, 12(4):1-19, 2017. PubMed ID: 28448594. Show all entries for this paper.

Displaying record number 60120

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Species (MHC/HLA)	human(A*66)
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.
RIRTWKSLVK had a significantly positive association with HLA A*66; it was recognized by 2/5 A*66-positive subjects and 11/261 A*66-negative subjects.

References

Displaying record number 60118

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIRTWKSLVK`	Epitope Alignment
Epitope Name	RK10
Species (MHC/HLA)	human(C*14)
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.
RIRTWKSLVK had a significantly positive association with HLA C*14; it was recognized by 9/17 C*14-positive subjects and 28/324 C*14-negative subjects.

References

Displaying record number 52057

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location
Epitope	`RIRTWKSLVK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Experimental methods
Keywords	epitope processing, escape

Notes

Epitopes that have been described in the literature and included in this database tend to cluster in conserved regions and be absent or rarely found in highly variable regions in Nef, Env, and p17.
While the uneven distribution of epitopes may be in part due to a limited cross-recognition of specific responses because of differences between peptides used to probe the immune response and autologous strains, regions with a paucity of defined epitopes also had higher frequencies of amino acids that tend to not be found in C-terminal positions of epitopes, and had lower cleavage prediction scores for epitope processing. This suggests that in the regions of the virus where variation is best tolerated traces of immune escape have left an imprint on the viral population. Epitopes also were concentrated in alpha-helix and turn regions in the proteins.
In the more conserved p24, and Pol proteins RT and Protease, epitopes are more evenly distributed.
What was learned from proteins where many epitopes have been defined (Gag, Pol, Env and Nef) was used to develop an algorithm to predict where epitopes would be localized in Rev, Tat, Vif, and Vpr. Predictions were made blinded, and then compared to the first 15 epitopes defined in these proteins; the epitopes were concentrated in the predicted regions.

References

Yusim2002 Karina Yusim, Can Kesmir, Brian Gaschen, Marylyn M. Addo, Marcus Altfeld, S\oren Brunak, Alexandre Chigaev, Vincent Detours, and Bette T. Korber. Clustering Patterns of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1 (HIV-1) Proteins Reveal Imprints of Immune Evasion on HIV-1 Global Variation. J. Virol., 76(17):8757-8768, Sep 2002. PubMed ID: 12163596. Show all entries for this paper.