Search CTL/CD8+ T-Cell Epitope Database

Found 19 matching records:

Displaying record number 58994

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Pol
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	Pol934
Subtype	A
Species (MHC/HLA)	human(A*01)
Immunogen	HIV-1 infection, vaccine
Patient MHC/HLA	P4: A30:02, A68:01, B56:01, B58:01
Country	Guinea-Bissau
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	vaccine-induced immune responses, vaccine antigen design, therapeutic vaccine, chronic infection

Vaccine Details

Vaccine type	peptide
Vaccine strain	A clade
Adjuvant	CAF01

Notes

Therapeutic vaccination of chronically infected HIV-1 subjects was evaluated as a means of halting disease progression. A subdominant peptide vaccine containing 15 CTL epitopes and 3 helper T-cell peptides along with an adjuvant was delivered to 18 infected subjects, and this Guinea-Bissau study compared to a similar Danish one. Using IFN-γ EliSpot, 9 new T-cell responses were detected in 6/14 subjects whose viral loads (VL) remained stable. Other pre-existing responses, including CTL responses, however, were not significantly detected.
Pol934, KIQNFRVYY, is a CTL epitope sequence used as a vaccine component.

References

Roman2013 Victor Raúl Gómez Román, Kristoffer Jarlov Jensen, Sanne Skov Jensen, Christian Leo-Hansen, Sanne Jespersen, David da Silva Té, Candida Medina Rodrigues, Christoph Mikkel Janitzek, Lasse Vinner, Terese Lea Katzenstein, Peter Andersen, Ingrid Kromann, Lars Vibe Andreasen, Ingrid Karlsson, and Anders Fomsgaard. Therapeutic Vaccination Using Cationic Liposome-Adjuvanted HIV Type 1 Peptides Representing HLA-Supertype-Restricted Subdominant T Cell Epitopes: Safety, Immunogenicity, and Feasibility in Guinea-Bissau. AIDS Res Hum Retroviruses, 29(11):1504-1512, Nov 2013. PubMed ID: 23634822. Show all entries for this paper.

Displaying record number 61946

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Pol(934-)
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	KY9
Subtype	A3, B, C, CRF02_AG
Species (MHC/HLA)	human(A03:01, A11:01, A29:02, A30:01, A30:02, A32:01, A*80:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	1213: A30:01, A30:02, B07:02, B58:01
Country	Denmark, Guinea-Bissau
Experimental methods	HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	binding affinity, vaccine antigen design

Notes

95% and 100% of untreated, asymptomatic HIV-1-infected patients, from Guinea-Bissau and Denmark respectively, were able to subdominantly recognize 15 predicted CTL epitopes restricted by at least one of the 5 most common HLA supertypes, HLA-A*01, -A*02, -A*03, -B*07 and -B*44.
Epitope KY9, KIQNFRVYY, predicted and validated to be restricted by supertype A01, was found across geographic regions in 100% of HIV-1 sequences in Denmark clade-B and 86% Guinea-Bissau/Western Africa subtypes A3, C and CRF02_AG. Its equivalent peptide, Pol934 was able to elicit cytokine production and bound the following HLA alleles moderately or well: A*3002, A*2902, A*3201 (A01 supertype); A*0301, A*1101, A*8001 (A03 supertype); A*3001 (A0103 supertype).

References

Karlsson2012 Ingrid Karlsson, Henrik Kløverpris, Kristoffer Jarlov Jensen, Anette Stryhn, Søren Buus, Annika Karlsson, Lasse Vinner, Philip Goulder, and Anders Fomsgaard. Identification of Conserved Subdominant HIV Type 1 CD8+ T Cell Epitopes Restricted within Common HLA Supertypes for Therapeutic HIV Type 1 Vaccines. AIDS Res. Hum. Retroviruses, 28(11):1434-1443, Nov 2012. PubMed ID: 22747336. Show all entries for this paper.

Displaying record number 58406

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Pol
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	Pol934
Subtype	B, CRF02_AG
Species (MHC/HLA)	human(A1)
Immunogen	HIV-1 infection
Country	Cote D'Ivoire, Denmark, Ghana, Guinea-Bissau, Mali, Senegal
Experimental methods	Intracellular cytokine staining, Pentamer labeling
Keywords	vaccine antigen design

Notes

15 subdominant CTL epitopes were used to study 2 new Guinea-Bissau HIV-1 isolates, a newly completed Danish subtype B genome sequence and other previously published West African sequences. Subtype analysis showed the 2 new Guinea-Bissau sequences were CRF02_AG inter-subtype recombinant forms with typical cross-over points. The 15 epitopes were restricted by common HLA alleles (A1, A2, A3, B7, B44) and were present and conserved in all sequences studied. Mean conservation of the epitopes in local strains was 76% and 70% for Denmark and West Africa respectively. All epitopes had been previously confirmed as antigenic Perez2008].
Pol934 epitope, KIQNFRVYY, showed a conservation of amino acid identity of 100% for the Danish sequence and 86% for the West African sequences.

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.

Vinner2011 Lasse Vinner, Birgitta Holmgren, Kristoffer J. Jensen, Joakim Esbjornsson, Marie Borggren, Julie L. Hentze, Ingrid Karlsson, Betina S. Andresen, Gregers J. Gram, Henrik Kloverpris, Peter Aaby, Zacarias José Da Silva, Eva-Maria Fenyö, and Anders Fomsgaard. Sequence Analysis of HIV-1 Isolates from Guinea-Bissau: Selection of Vaccine Epitopes Relevant in Both West African and European Countries. APMIS, 119(8):487-497, Aug 2011. PubMed ID: 21749448. Show all entries for this paper.

Displaying record number 59915

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Pol(934-942)
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	KYY9
Species (MHC/HLA)	human(A*11)
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.
KIQNFRVYY had a significantly positive association with HLA A*11; it was recognized by 3/25 A*11-positive subjects and 2/235 A*11-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 58555

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Integrase
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	A30-KYY9
Subtype	B
Species (MHC/HLA)	human(A*30)
Immunogen	HIV-1 infection
Country	United States
Experimental methods
Keywords	review, rate of progression, acute/early infection

Notes

Acute infection with HIV-1 is accompanied by high viral load (VL) and loss of CD4 helper T cells. Early inhibition of VL by CTL results in a 'set point' that is correlated with disease progression. The early CTL response during acute infection if successful is to a known immunodominant epitope. Following, chronic infection sets in with a greater breadth and magnitude of CTL response, but no change in VL or HIV-1 replication. Immunodominant epitopes from several studies that help set a lower VL during acute phase are listed in this review.
KIQNFRVYY, A30-KYY9, when restricted by HLA-A*30 is recognized by 25% acutely-infected and 80% chronically-infected North American subjects expressing the same HLA allele. HLA-A*30 is present at a frequency of 7.4% in North American white populations.

References

Streeck2010 Hendrik Streeck and Douglas F. Nixon. T Cell Immunity in Acute HIV-1 Infection. J. Infect. Dis., 202(Suppl 2):S302-8, 15 Oct 2010. PubMed ID: 20846037. Show all entries for this paper.

Displaying record number 59914

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Pol(934-942)
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	KYY9
Species (MHC/HLA)	human(A*30)
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.
KIQNFRVYY had a significantly positive association with HLA A*30; it was recognized by 25/53 A*30-positive subjects and 20/288 A*30-negative subjects.

References

Displaying record number 55949

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Integrase
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	KY9(Integrase)
Subtype	B
Species (MHC/HLA)	human(A30)
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 peptides tested, FKIQNFRVYYRDSRDPLW and TKELQKQITKIQNFRVYY, contained the exact sequence of a previously described HLA-A30 epitope, KIQNFRVYY, none of the 15 HLA-A30 carriers responded to it (author communication and Fig.1).

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 53138

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Integrase
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	KY9
Species (MHC/HLA)	human(A30)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay, Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Keywords	epitope processing, supervised treatment interruptions (STI), immunodominance

Notes

Protease and integrase are shown to be frequently targeted by CD8 T-cell responses (23% and 68% of 56 HIV+ patients, respectively). Responses tend to cluster in conserved regions of Int, although 1 high conserved region had no responses. CTL frequencies per unit protein length for Pro and Int were similar to other HIV non-structural proteins. Three novel HLA class I-restricted optimal epitopes were found and characterized with fine mapping.

References

Rodriguez2004 William R. Rodriguez, Marylyn M. Addo, Almas Rathod, Cecily A. Fitzpatrick, Xu G. Yu, Beth Perkins, Eric S. Rosenberg, Marcus Altfeld, and Bruce D. Walker. CD8+ T Lymphocyte Responses Target Functionally Important Regions of Protease and Integrase in HIV-1 Infected Subjects. J. Transl. Med., 2(1):15, 21 May 2004. PubMed ID: 15154967. Show all entries for this paper.

Displaying record number 1966

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Integrase(219-227)
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	Pol-KY9; IN-KY9
Subtype	B
Species (MHC/HLA)	human(A*30:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	A02:05, A30:02, B14:02, B53:01, C04:01, C08:02; 00RCH28: A02:05, A30:02, B14:02, B53:01, C04:01, C08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay
Keywords	novel epitope

Notes

This study monitored epitope responses in HIV-1 infected minority women living in the United States.
24 epitopes were described -- 8 were novel, 8 used new restricting elements but were previously defined epitopes, and 8 were previously described. This epitope though previously described as being restricted by A*0301, A*1101, A*3301, A*6801, is now identified with novel restriction A*3002 as well.
Serial peptide truncations were used to define optimal epitopes for CTL cell lines isolated from 12 individuals, assayed by a Cr-release.
Patient 00RCH28 was African American, not on HAART, had a viral load of 5,900 and CD4 count of 889, and she also recognized RIRQGLERA, gp160(846-854), A*0205.
Among HIV+ individuals who carried HLA A30, 6/16 (38%) 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 52539

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Integrase(219-227)
Epitope	`KIQNFRVYY`	Epitope Alignment
Species (MHC/HLA)	human(A*30:02)
Immunogen	HIV-1 infection
Experimental methods
Keywords	optimal epitope, A-list

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 53284

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	( C consensus)
Epitope	`KIQNFRVYY`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(A*30:02)
Immunogen	HIV-1 infection
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	characterizing CD8+ T cells

Notes

HLA class I restricted CD8+ T-cell responses against HIV-1 were analyzed in African patients. Significantly more responses were shown to be HLA-B restricted. Viral load, CD4 count, and thus rate of disease progression were also associated with HLA-B alleles. In addition, the selection pressure imposed on HIV-1 by HLA-B alleles was shown to be substantially greater than by other alleles.
This epitope was suggested to be the epitope within a longer reactive peptide based on correspondence with a known epitope in the HIV database. Also, a significantly higher frequency of people in the Durban cohort who reacted with the peptide had this HLA type.

References

Kiepiela2004 Photini Kiepiela, Alasdair J. Leslie, Isobella Honeyborne, Danni Ramduth, Christina Thobakgale, Senica Chetty, Prinisha Rathnavalu, Corey Moore, Katja J. Pfafferott, Louise Hilton, Peter Zimbwa, Sarah Moore, Todd Allen, Christian Brander, Marylyn M. Addo, Marcus Altfeld, Ian James, Simon Mallal, Michael Bunce, Linda D. Barber, James Szinger, Cheryl Day, Paul Klenerman, James Mullins, Bette Korber, Hoosen M. Coovadia, Bruce D. Walker, and Philip J. R. Goulder. Dominant Influence of HLA-B in Mediating the Potential Co-Evolution of HIV and HLA. Nature, 432(7018):769-775, 9 Dec 2004. LA-UR 04-5920. PubMed ID: 15592417. Show all entries for this paper.

Displaying record number 54331

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Integrase(219-227)
Epitope	`KIQNFRVYY`	Epitope Alignment
Species (MHC/HLA)	human(A*30:02)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay, Cytokine production, HLA binding, Other
Keywords	vaccine-induced immune responses, HLA cross-presentation, HLA associated polymorphism

Notes

25 CTL epitopes with sequence conservation were studied. Population protection coverage (PPC) for 5 different ethnic groups in the US was estimated by combining HLA binding predictions and known HLA frequencies. HIV-1-naive individuals mounted a better response to the epitope pools than HIV-1 infected individuals.
A more detailed evaluation of HIV-naive T-cell responses was undertaken, limiting the study to only those peptides that are restricted to A*0201. Though the peptides could cross-recognize and bind different HLA, they were able to specifically lyse only cells of the same (A*0201) HLA-restriction. Thus, the CTL response was less degenerate than peptide binding to MHC.
In addition to the published restriction above, epitope KIQNFRVYY was predicted to be restricted by HLA A1 and A*3002.

References

Reche2006 Pedro A. Reche, Derin B. Keskin, Rebecca E. Hussey, Petronela Ancuta, Dana Gabuzda, and Ellis L. Reinherz. Elicitation from Virus-Naive Individuals of Cytotoxic T Lymphocytes Directed against Conserved HIV-1 Epitopes. Med. Immunol., 5:1, 2006. PubMed ID: 16674822. Show all entries for this paper.

Displaying record number 54605

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Integrase
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	KLY9
Subtype	C
Species (MHC/HLA)	human(A*30:02)
Immunogen	HIV-1 infection
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Degranulation, CD107a and b cell surface mobilization, Intracellular cytokine staining, Proliferation, Tetramer binding
Keywords	rate of progression

Notes

Eight epitopes and 113 subjects were used to test whether correlations existed between HIV-1 Clade C viral load and CTL proliferation, cytokine production or degranulation in therapy-naive patients. Only CTL proliferation showed a strong inverse correlation with viral load.
The tetramer A*3002 KLY9 was used to test 20 patients and gave a median ex vivo tetramer frequency of 0.45.

References

Day2007 Cheryl L. Day, Photini Kiepiela, Alasdair J. Leslie, Mary van der Stok, Kriebashne Nair, Nasreen Ismail, Isobella Honeyborne, Hayley Crawford, Hoosen M. Coovadia, Philip J. R. Goulder, Bruce D. Walker, and Paul Klenerman. Proliferative Capacity of Epitope-Specific CD8 T-cell Responses Is Inversely Related to Viral Load in Chronic Human Immunodeficiency Virus Type 1 Infection. J. Virol., 81(1):434-438, Jan 2007. PubMed ID: 17050606. Show all entries for this paper.

Displaying record number 55169

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Integrase(219-227)
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	KIY9
Species (MHC/HLA)	human(A*30:02)
Immunogen	HIV-1 infection
Country	South Africa
Experimental methods	Intracellular cytokine staining, Proliferation, Tetramer binding
Keywords

Notes

PD-1 (inhibitory receptor programmed death) expression on CD8 and CD4 cells was studied. There was a positive correlation with viral load and inverse correlation with CD4 T cell count, and blockage of PD-1 pathway augmented CD4 and CD8 T cell function.

References

Day2006 Cheryl L. Day, Daniel E. Kaufmann, Photini Kiepiela, Julia A. Brown, Eshia S. Moodley, Sharon Reddy, Elizabeth W. Mackey, Joseph D. Miller, Alasdair J. Leslie, Chantal DePierres, Zenele Mncube, Jaikumar Duraiswamy, Baogong Zhu, Quentin Eichbaum, Marcus Altfeld, E. John Wherry, Hoosen M. Coovadia, Philip J. R. Goulder, Paul Klenerman, Rafi Ahmed, Gordon J. Freeman, and Bruce D. Walker. PD-1 Expression on HIV-Specific T Cells Is Associated with T-Cell Exhaustion and Disease Progression. Nature, 443(7109):350-354, 21 Sep 2006. PubMed ID: 16921384. Show all entries for this paper.

Displaying record number 59913

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Pol(934-942)
Epitope	`KIQNFRVYY`	Epitope Alignment
Epitope Name	KYY9
Species (MHC/HLA)	human(A*32)
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.
KIQNFRVYY had a significantly positive association with HLA A*32; it was recognized by 15/28 A*32-positive subjects and 5/260 A*32-negative subjects.

References

Displaying record number 58068

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Pol
Epitope	`KIQNFRVYY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	vaccine
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	vaccine-induced immune responses

Vaccine Details

Vaccine type	adenovirus type 5 (Ad5), DNA prime with Ad5 boost
Vaccine strain	B clade IIIB, B clade JRFL, B clade CAM-1
Vaccine component	Gag, Nef, Pol

Notes

T-cell epitope response specificities were examined in uninfected subjects who received the Gag/Pol/Nef vaccine used in the Step trial. Variable epitopes were detected more frequently than would be expected from an unbiased sampling. The most conserved epitopes were detected at a lower frequency, similar to the frequency reported for responses to natural infection, suggesting potential epitope masking. This may be a mechanism used by the virus in both contexts to escape effective T-cell surveillance. Development of vaccine strategies that can elicit a greater breadth, and towards conserved regions of the genome in particular, are critical requirements for effective T-cell based vaccines.
All vacinees had responses to the Gag peptide pool, and most also had responses to the Nef and/or Pol pools. Subsequent mapping using 9mer minipools demonstrated that T-cell epitopes were recognized across the length of all 3 proteins. A total of 105 distinct 9mers were detected, although some of these may have been overlapping 9mers representing a single epitope.
5 vaccinees recognized 9mer KIQNFRVYY.
Database note: The HLA restriction of this epitope in the LANL database is A30, and all 5 responders carry either A*3002 or A*3201.

References

Li2011a Fusheng Li, Adam C. Finnefrock, Sheri A. Dubey, Bette T. M. Korber, James Szinger, Suzanne Cole, M. Juliana McElrath, John W. Shiver, Danilo R. Casimiro, Lawrence Corey, and Steven G Self. Mapping HIV-1 Vaccine Induced T-Cell Responses: Bias Towards Less-Conserved Regions and Potential Impact on Vaccine Efficacy in the Step Study. PLoS One, 6(6):e20479, 2011. PubMed ID: 21695251. Show all entries for this paper.

Displaying record number 55465

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location	Pol
Epitope	`KIQNFRVYY`	Epitope Alignment
Subtype	B, CRF01_AE, D
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.
KIQNFRVYY was a predicted epitope restricted by A1 supertype. 4/31 patient(s) responded to it; 1 responding patient was known to carry an allele of A1 supertype. Responding patients were infected with HIV clade(s) B, D, CRF01_AE.
One of 21 epitopes denoted as elite, having a response in 4 or more of the 31 patients.
Epitope KIQNFRVYY was recognized by at least 4 patients with restricting HLA supertype and infected with several HIV subtypes. Predicted HLA restriction for this epitope was to suptertype A1.

References

Displaying record number 54954

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location
Epitope	`KIQNFRVYY`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, vaccine
Patient MHC/HLA	203-157: A30:01, A30:02, B42, B44
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, polyepitope
Vaccine strain	B clade LAI, B clade MN
Vaccine component	Gag, gp120, gp41, Nef, Pol, Protease

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.
This epitope was not contained in the vaccine, but the linked vaccinated patient in whom the study was conducted recognized it after developing 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 54927

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HXB2 Location	Pol(934-942) Integrase(219-227) DNA(4884..4910)	Pol Epitope Map
Author Location
Epitope	`KIQNFRVYY`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, vaccine
Patient MHC/HLA	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.
This epitope was not contained in the vaccine, but the linked vaccinated patient in whom the study was conducted recognized it after developing infection.