Search CTL/CD8+ T-Cell Epitope Database

Found 7 matching records:

Displaying record number 62160

Download this epitope record as JSON.

HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	RT(269-277)
Epitope	`QIYPGIKVK`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A*03)
Immunogen	HIV-1 infection
Country	Australia, Canada, United States
Experimental methods	Other
Keywords	escape, HLA associated polymorphism

Notes

Though no immunological assays were used in this study, several associations were detected that exist within already known and immunologically verified epitopes. In RT, Mexican and B consensus were K277 and HOMER consensus was R277, an escape form. This falls within epitope A*03-QIYPGIKVK.

References

Avila-Rios2009 Santiago Avila-Rios, Christopher E. Ormsby, Jonathan M. Carlson, Humberto Valenzuela-Ponce, Juan Blanco-Heredia, Daniela Garrido-Rodriguez, Claudia Garcia-Morales, David Heckerman, Zabrina L. Brumme, Simon Mallal, Mina John, Enrique Espinosa, and Gustavo Reyes-Teran. Unique Features of HLA-Mediated HIV Evolution in a Mexican Cohort: A Comparative Study. Retrovirology, 6:72, 2009. PubMed ID: 19664284. Show all entries for this paper.

Displaying record number 61135

Download this epitope record as JSON.

HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	Pol
Epitope	`QIYPGIKVK`	Epitope Alignment
Epitope Name	QPK9
Subtype	C
Species (MHC/HLA)	human(A*03:01)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Other
Keywords	escape, mutation acquisition

Notes

A metric to determine degree of HIV adaptation to HLA and HLA profile was developed. It was found that transmission of pre-adapted HIV to recipients with the associated HLA in a population resulted in elevated VL, impaired immunity and CD4+ T cell decline. Also, pre-adaptation of circulating HIV accounts for much of the variation in immune outcome that was previously attributed to HLA alleles.
Transmission was studied in HIV-C chronically-infected subjects from Southern African cohorts. Adapted QPK9 (QIYPGIKVK) when transmitted to PBMCs elicited a depressed CTL response in an in vitro killing assay as compared to non-adapted QK9 (QIYAGIKVK) when infecting similar PBMC targets.

References

Carlson2016 Jonathan M. Carlson, Victor Y. Du, Nico Pfeifer, Anju Bansal, Vincent Y. F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung'u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J. R. Goulder, Zabrina L. Brumme, Eric Hunter, and Paul A. Goepfert. Impact of Pre-Adapted HIV Transmission. Nat. Med., 22(6):606-613, Jun 2016. PubMed ID: 27183217. Show all entries for this paper.

Displaying record number 61174

Download this epitope record as JSON.

HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	Pol(424-432)
Epitope	`QIYPGIKVK`	Epitope Alignment
		Show epitope variants
Epitope Name	QPK9
Subtype	B
Species (MHC/HLA)	human(A*03:01)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection, variant cross-reactivity

Notes

An 11-member cohort of acutely infected patients was studied to find that CTL cross-recognition of variant epitopes during acute infection is absent or poor as opposed to during chronic HIV-infection.
Pol epitope QIYPGIKVK, QPK9_424-432,-specific T cells were less cytotoxic to variants than autologous QPK9 in acute infection. No variants tested cross-reacted with T cells specific to autologous QPK9.

References

Du2016 Victor Y. Du, Anju Bansal, Jonathan Carlson, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Kristin Ladell, Stephanie Gras, Tracy M. Josephs, Sonya L. Heath, David A. Price, Jamie Rossjohn, Eric Hunter, and Paul A. Goepfert. HIV-1-Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection. J. Immunol., 196(8):3276-3286, 15 Apr 2016. PubMed ID: 26983786. Show all entries for this paper.

Displaying record number 53504

Download this epitope record as JSON.

HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	Pol
Epitope	`QIYPGIKVK`	Epitope Alignment
Epitope Name	QK9
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 9, qiypgikvR, was found not to correspond to the most polymorphic residues 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 62162

Download this epitope record as JSON.

HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	RT(269-277)
Epitope	`QIYPGIKVK`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B08, B42)
Immunogen	HIV-1 infection
Country	Australia, Canada, United States
Experimental methods	Other
Keywords	escape, HLA associated polymorphism

Notes

Though no immunological assays were used in this study, several associations were detected that exist within already known and immunologically verified epitopes. P272 is seen in the Mexican consensus while A272 is seen in HOMER and B consensus, restricted by B*08 mostly in the Mexican cohort and mostly B*42 in the HOMER. This falls within epitope A*03-QIYPGIKVK. The escape is QIYsGIKVK.

References

Displaying record number 57000

Download this epitope record as JSON.

HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	Pol
Epitope	`QIYPGIKVK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Country	Sweden
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	subtype comparisons, computational epitope prediction, vaccine antigen design

Notes

From HIV-1 sequences of multiple subtypes, bioinformatic prediction generated 174 CTL epitopes from Gag, Pol, Nef, Env and Tat restricted by HLA supertypes A1, A2, A3, A24, B7, B44 and B58; 10 previously-published A2- and B58-restricted epitopes were also included. Of these 184 epitopes, 113 were recognized experimentally in serum from 31 HIV+ patients.
While Gag, Pol, Env and Nef were highly immunogenic, only 38% of Tat epitopes elicited a response.
QIYPGIKVK was a predicted epitope restricted by A3 supertype. 1/31 patient(s) responded to it; the patient was known to carry an allele of A3 supertype. Responding patients were infected with HIV clade(s) B.

References

Perez2008 Carina L. Pérez, Mette V. Larsen, Rasmus Gustafsson, Melissa M. Norström, Ann Atlas, Douglas F. Nixon, Morten Nielsen, Ole Lund, and Annika C. Karlsson. Broadly Immunogenic HLA Class I Supertype-Restricted Elite CTL Epitopes Recognized in a Diverse Population Infected with Different HIV-1 Subtypes. J. Immunol., 180(7):5092-5100, 1 Apr 2008. PubMed ID: 18354235. Show all entries for this paper.

Displaying record number 61102

Download this epitope record as JSON.

HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	RT(269-277)
Epitope	`QIYPGIKVK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH470: A01:01, A03:01, B08:01, B49:01, C*07:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope QIYPGIKVK had a fitness cost ΔE of 0.507 and T cell response was first detected to it at 13d, escape time was 50.54 days.

References

Barton2016 John P. Barton, Nilu Goonetilleke, Thomas C. Butler, Bruce D. Walker, Andrew J. McMichael, and Arup K. Chakraborty. Relative Rate and Location of Intra-Host HIV Evolution to Evade Cellular Immunity Are Predictable. Nat. Commun., 7:11660, 23 May 2016. PubMed ID: 27212475. Show all entries for this paper.