Search CTL/CD8+ T-Cell Epitope Database

Found 35 matching records:

Displaying record number 60280

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	SV9
Species (MHC/HLA)	human(A*02)
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.
SPRTLNAWV had a significantly positive association with HLA A*02; it was recognized by 8/134 A*02-positive subjects and 2/172 A*02-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 60278

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	SV9
Species (MHC/HLA)	human(A*68:02)
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.
SPRTLNAWV had a significantly positive association with HLA A*6802; it was recognized by 18/26 A*6802-positive subjects and 18/315 A*6802-negative subjects.

References

Displaying record number 1781

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	human(B*07)
Immunogen	HIV-1 infection
Experimental methods
Keywords	rate of progression, acute/early infection

Notes

The CTL response to optimally defined CTL epitopes restricted by HLA class I A and B alleles in individuals who coexpressed HLA A*02, A*03, and B*07 was studied in eight HIV-1-infected subjects, two with acute infection, five with chronic, and one long-term non-progressor (LTNP).
2 to 17 epitopes were recognized in a given individual, A*02-restricted CTL response tended to be narrow and never dominated the response, and 25/27 epitopes were targeted by at least one person.
Subjects with chronic HIV-1 infection recognized between 2-8 out of 11 B*07-restricted epitopes.
An acute seroconvertor homozygous for the B*07 allele recognized five B*07-restricted epitopes.
The other acute seroconvertor failed to recognize any of the 11 B*07-restricted epitopes tested.
The B*07-restricted CTL response was highly variable and there was no clearly dominant epitope.

References

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

Displaying record number 58527

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*07)
Immunogen	HIV-1 infection
Country	Canada
Experimental methods	Other
Keywords	characterizing CD8+ T cells, elite controllers

Notes

Dual color EliSpot testing for IL-2 and IFN-γ was used to determine whether CTL restricted by MHC Class I alleles associated with slow progression to disease, viz. B*57 and B*27, had a more poly-functional profile than other CD8+ cells in a treatment-naive cohort from Montreal. B*57/B*27-restricted CTL producing IL-2 or IFN-γ or IL-2/IFN-γ, were similar in both slow progressors (SP) and progressors. Other non-protective MHC-I-restricted CTL producing both IL-2/IFN-γ, were greater in number in SP than progressors.
Within SP, peptides restricted by both protective and non-protective MHC-I alleles elicited CTL with the same functional profile. For progressors, peptides and epitopes restricted by protective B*57/B*27 alleles stimulated a higher proportion of dual-(IL-2/IFN-γ)secreting CTL.
HLA-B*07-restricted p24 optimal epitope SPRTLNAWV was tested in a dual color EliSpot and was found to elicit CTL that could produce IL-2 and/or IFN-γ.

References

Peretz2011 Yoav Peretz, Olivia Marra, Réjean Thomas, Danielle Legault, Pierre Côté, Mohamed-Rachid Boulassel, Danielle Rouleau, Jean-Pierre Routy, Rafick-Pierre Sékaly, Christos M Tsoukas, Cécile Tremblay, and Nicole F. Bernard. Relative Contribution of HIV-Specific Functional Lymphocyte Subsets Restricted by Protective and Non-Protective HLA Alleles. Viral Immunol, 24(3):189-198, Jun 2011. PubMed ID: 21668360. Show all entries for this paper.

Displaying record number 59005

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag(73-)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	Gag148
Subtype	A
Species (MHC/HLA)	human(B*07)
Immunogen	HIV-1 infection, vaccine
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.
Gag148, SPRTLNAWV, 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 53104

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	human(B*07)
Immunogen	HIV-1 infection
Country	Spain
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay, Proliferation
Keywords	HAART, ART, supervised treatment interruptions (STI)

Notes

Structured treatment interruption (STI) alone is not able to control viral replication in chronically infected patients, probably due to lack of strong, maintained T-helper cell responses. HIV-1 specific CD8+ T-cell responses were shown to increase significantly until the end of the follow up, but were not correlated with viral load.
Less than 2 of 7 patients recognized this epitope.

References

Plana2004 Montserrat Plana, Felipe Garcia, Annette Oxenius, Gabriel M. Ortiz, Anna Lopez, Anna Cruceta, Gabriel Mestre, Emilio Fumero, Catherine Fagard, Maria Antonia Sambeat, Ferran Segura, José M. Miró, Mireia Arnedo, L. Lopalcos, Tomas Pumarola, Bernard Hirschel, Rodney E. Phillips, Douglas F. Nixon, Teresa Gallart, and Jose M. Gatell. Relevance of HIV-1-Specific CD4+ Helper T-Cell Responses During Structured Treatment Interruptions in Patients With CD4+ T-Cell Nadir Above 400/mm3. J. Acquir. Immune Defic. Syndr., 36(3):791-799, 1 Jul 2004. PubMed ID: 15213562. Show all entries for this paper.

Displaying record number 57525

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	S9WV
Species (MHC/HLA)	human, transgenic mouse(B*07)
Immunogen	HIV-1 infection, vaccine
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay, HLA binding
Keywords	vaccine-induced immune responses, vaccine antigen design

Vaccine Details

Vaccine type	polyepitope
Vaccine strain	multiple epitope immunogen
Vaccine component	HIV-1

Notes

The study objective was to design a vaccine construct containing HIV-1 epitopes that would generate broad CD8+ responses. Among 14 known B7-restricted epitopes, 11 induced a response in B*07 transgenic mice. Among 11 novel candidate epitopes, all induced a response in B*07 mice, and all induced a response in at least 1 human B7+ donor. Immunological recognition of these epitopes was confirmed in HLA-B*0702 HIV-1-infected individuals.
SPRTLNAWV is a known B07 epitope that was recognized by 9/12 B*07 transgenic mice.
This epitope was recognized by 3/8 HLA-B*0702 HIV-1-infected individuals.

References

Cardinaud2009 Sylvain Cardinaud, Romain Bouziat, Pierre-Simon Rohrlich, Sophie Tourdot, Laurence Weiss, Pierre Langlade-Demoyen, Anne Burgevin, Susana Fiorentino, Peter van Endert, and François A. Lemonnier. Design of a HIV-1-Derived HLA-B07.02-Restricted Polyepitope Construct. AIDS, 23(15):1945-1954, 24 Sep 2009. PubMed ID: 19644347. Show all entries for this paper.

Displaying record number 1992

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	Gag-SV9; p24-SV9
Subtype	B
Species (MHC/HLA)	human(B07, B81)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	HAART, ART

Notes

Among HIV+ individuals who carried HLA B*07, 1/9 (11%) recognized this epitope.
Among HIV+ individuals who carried HLA B*81, 1/6 (17%) 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 61972

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Subtype	A, D
Species (MHC/HLA)	human(B*07:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	2230: A01:01, A03:01, B07:02, B58:02, C06:06, C07:02; 2044: A03:08, A29:01, B07:02, B08:01, C*07:02
Country	Kenya
Experimental methods	CD8 T-cell Elispot - IFNγ, Other, Tetramer binding
Keywords	subtype comparisons, HIV exposed persistently seronegative (HEPS), assay or method development

Notes

A systematic analysis of clade A or D epitopes that bind either protective HLA-A*0101 or susceptible HLA-B*0702 using the iTopia epitope discovery system was conducted. Broad epitope and variant recognition, and immune response was seen with the susceptible HLA allele, while a focused recognition of multiple epitope subtypes was seen associated with the protective HLA allele.
Novel epitopes were discovered using the iTopia system (3 assays: peptide binding, binding affinity, and off-rate).
Four new amino acids at anchor positions P2 (Lys, Arg, Thr, Iso) and P9 (Lys, Thr, Arg, Gly) were identified for B*0702 binding, including polar basic residues K and R, showing that B*0702-restricted epitopes are more tolerant to amino acid changes than known previously.
Previously known B*0702-restricted Gag epitope SPRTLNAWV was recognized by seronegative subjects as well as HIV-1 patients and bound HLA-B*0702. 2/8 B*0702+ female subjects responded to the epitope, with a mean of 245 SFU/million cells.

References

Luo2012 Ma Luo, Christina A. Daniuk, Tamsir O. Diallo, Rupert E. Capina, Joshua Kimani, Charles Wachihi, Makubo Kimani, Thomas Bielawny, Trevor Peterson, Mark G. R. Mendoza, Sandra Kiazyk, T. Blake Ball, and Francis A. Plummer. For Protection from HIV-1 Infection, More Might Not Be Better: A Systematic Analysis of HIV Gag Epitopes of Two Alleles Associated with Different Outcomes of HIV-1 Infection. J. Virol., 86(2):1166-1180, Jan 2012. PubMed ID: 22072744. Show all entries for this paper.

Displaying record number 59042

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	SV9-p24
Subtype	B, C
Species (MHC/HLA)	human(B*07:02)
Immunogen	HIV-1 infection
Country	Japan, South Africa, United Kingdom, United States
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding
Keywords	binding affinity, subtype comparisons

Notes

HLA-B*0702 is associated with rapid progression to disease in B-clade HIV-1 infected subjects. B*0702+ C-clade infected subjects however are not associated with a high viral setpoint of infection, and target a broader range of Gag epitopes at higher magnitudes. Increased magnitudes of Nef-specific responses were also detected in C-clade infected B*0702+ cohorts. A C-clade specific, B*0702-restricted novel p17 epitope, RPGGKKHYM, RM9, was defined.
Epitope SV9, SPRTLNAWV, a B- and C-clade Gag epitope was targeted more by C-clade infected subjects than B-clade ones. The B-clade and C-clade consensus epitope is the same. Binding affinity of SV9 to B*0702 was K_d = 3 nM. SV9 is contained within OLP20, QMVHQAISPRTLNAWVKV.

References

Kloverpris2014 Henrik N. Kløverpris, Emily Adland, Madoka Koyanagi, Anette Stryhn, Mikkel Harndahl, Philippa C. Matthews, Roger Shapiro, Bruce D. Walker, Thumbi Ndung'u, Christian Brander, Masafumi Takiguchi, Søren Buus, and Philip Goulder. HIV Subtype Influences HLA-B*07:02-Associated HIV Disease Outcome. AIDS Res. Hum. Retroviruses, 30(5):468-475, May 2014. PubMed ID: 24010680. Show all entries for this paper.

Displaying record number 59230

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human(B*07:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	Subject 8: A02:01, A24:02, B07:02, B40:01, C03:04, C07:02
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding
Keywords	dynamics, acute/early infection, dendritic cells

Notes

Variants of Gag, Env, and Nef epitopes were studied in one subject over >10 years of infection. A set of known HLA A*0201- and B*0702-restricted epitopes, plus additional predicted epitopes, was assembled. Epitope and variant responses were studied from 4 timepoints post-seroconversion (SC): early infection post-SC (0-2.8 yrs), late infection post-SC (3.25-7.8 yrs), early ART treatment (8.3-10.1 yrs), and late ART treatment. Despite evolutionary changes, CD8+ T cells could still be primed to HIV-1 variants. The percent of epitope variants inducing HIV-1-specific memory T cell responses peaked early post-SC, then declined and remained minimal shortly after establishment of viral set point. Peptide variants with medium binding affinity were more frequent than variants with low or high binding affinity but variants with different MHC class I binding capabilities induced equally broad memory T cell responses. A trimodal pattern in the breadth of T cell memory was seen, at early SC before viral set point, and then two peaks during later infection prior to commencing cART.
SPRTLNAWV was 1 of 7 epitopes with a positive correlation between predicted and observed MHC affinity. SPRTLNAWV had a pattern of transient changes in the dominance of variants, with the founder variant eventually being more dominant.

References

Melhem2014 Nada M Melhem, Kellie N. Smith, Xiao-Li Huang, Bonnie A Colleton, Weimin Jiang, Robbie B. Mailliard, James I. Mullins, and Charles R. Rinaldo. The Impact of Viral Evolution and Frequency of Variant Epitopes on Primary and Memory Human Immunodeficiency Virus Type 1-Specific CD8+ T Cell Responses. Virology, 450-451:34-48, Feb 2014. PubMed ID: 24503065. Show all entries for this paper.

Displaying record number 54308

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	human(B*07:02)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay, Cytokine production, HLA binding, Other
Keywords	computational epitope prediction, vaccine-induced immune responses, HLA cross-presentation

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 published restriction above, epitope SPRTLNAWV was predicted to be restricted by HLA B*0702, B*3501, B*5102, B*5103, B*5301, B*5401 and B*5502 as well.

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 61957

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag(148-)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	AV9
Subtype	A3, B, C, CRF02_AG
Species (MHC/HLA)	human(B*07:02)
Immunogen	HIV-1 infection
Patient MHC/HLA	1127: A02:02, A30:02, B07:05, B18:01; 1214: A02:01, A34:02, B44:03, B82:01; 1224: A30:01, B15:03, B*42:01
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 AV9, SPRTLNAWV, predicted and validated to be restricted by supertype B07, was found across geographic regions in 94% of HIV-1 sequences in Denmark clade-B and 98% Guinea-Bissau/Western Africa subtypes A3, C and CRF02_AG. Its equivalent peptide, Gag148 was able to elicit cytokine production and bound the following HLA alleles moderately or well: B*0702 (B07 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 147

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	human(B*07:02)
Immunogen
Experimental methods
Keywords	optimal epitope, A-list

Notes

C. Brander notes this is a B*0702 epitope.
Optimal peptide mapped by titration.

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 60630

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	SV-9
Subtype	B, C
Species (MHC/HLA)	human(B07:02, B81)
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 SPRTLNAWV, SV-9, from fragment F1, restricting HLA-B*07,B*0702, B*81, had no determined natural processed epitope forms for subtypes B or C.

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 59446

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	Gag-SV9
Subtype	C
Species (MHC/HLA)	human(B*42:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, United Kingdom
Experimental methods	CD8 T-cell Elispot - IFNγ, Other, Tetramer binding
Keywords	immunodominance, optimal epitope

Notes

2,093 HLA-B*4201⁺ ART-naive female adults from 5 cohorts with chronic C-clade infection were studied to determine factors controlling immunodominance. Immunodominant hierarchy of response observed across 20 HLA-B*4201-restricted epitopes was not linked to peptide-B*4201 binding affinity or stability. Immunodominance correlated instead with the particular amino acid residues within (TCRβ) TRB sequences. Extreme TCR biases towards generating identical or 'public' epitope-specific TCRs in multiple individuals therefore were statistically the greatest influence upon Immunodomination.
13 B*4201⁺-restricted novel epitopes were identified by EliSpot screening of 181 females with 410 HIV-1 OLPs.
11 different public clonotypes were identified and were used by the top 3 ranked immunodominant epitope-specificities.
6/10 most immunodominant epitopes were Gag/Pol/Vpr-specific and 100% showed selection pressure on HIV. Of 4 epitopes that were Nef/Vif-specific and among most immunodominant, only 25% i.e one epitope experienced selection pressure in the virus.
Optimal epitope SPRTLNAWV from OLP Gag-20 (QMVHQAISPRTLNAWVKV) had a targeting frequency of ˜3% of 154 HLA-B*4201⁺ subjects. Immunodominance rank was 18/20 tested epitopes.
Gag-SV9-HLA-B*4202's binding affinity, K_d = 2 nM; stability, K_1/2 = 2h.

References

Kloverpris2015 Henrik N Kløverpris, Reuben McGregor, James E. McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan M. Carlson, Catherine Koofhethile, Bram Gerritsen, Can Keşmir, Fabian Chen, Lynn Riddell, Graz Luzzi, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, David A. Price, and Philip J. Goulder. CD8+ TCR Bias and Immunodominance in HIV-1 Infection. J. Immunol., 194(11):5329-5345, 1 Jun 2015. PubMed ID: 25911754. Show all entries for this paper.

Displaying record number 60281

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	SV9
Species (MHC/HLA)	human(B*58:02)
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.
SPRTLNAWV had a significantly positive association with HLA B*5802; it was recognized by 1/3 B*5802-positive subjects and 1/169 B*5802-negative subjects.

References

Displaying record number 143

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	human(B7)
Immunogen
Experimental methods
Keywords

Notes

Optimal peptide mapped by titration, pers. comm. from D. Lewinsohn to C. Brander and B. Walker.

References

Brander1997 Christian Brander and Bruce Walker. Systematic Identification of Optimal HIV-1 CTL Epitopes. In Systematic Identification of Optimal HIV-1 CTL Epitopes. pages IV--1--IV--11. Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, 1997. URL: http://hiv-web.lanl.gov/immunology. Show all entries for this paper.

Displaying record number 56437

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	SV9(p24)
Subtype	B
Species (MHC/HLA)	human(B7)
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.
Previously described HLA-B7-restricted epitope SPRTLNAWV elicited no immune response in Chinese HIV-1 positive subjects as part of peptide QMVHQPISPRTLNAWVKV.
Although the tested peptide sequence contains the exact sequence of a previously described HLA-B7 optimal epitope, SPRTLNAWV, none of the 9 HLA-B7 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 55212

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	human(B7)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	supertype, HLA cross-presentation

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.
In addition to its known HLA association (B07), an additional HLA (B42) was statistically predicted to be associated with this epitope.

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 58418

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	Gag148
Subtype	B, CRF02_AG
Species (MHC/HLA)	human(B7)
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].
Gag148 epitope, SPRTLNAWV, showed a conservation of amino acid identity of 94% for the Danish sequence and 98% 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 54297

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	B7-SV9(p24)
Species (MHC/HLA)	human(B7)
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 53030

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B7)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, CD8 T-cell Elispot granzyme B
Keywords	characterizing CD8+ T cells

Notes

Only 20% of CD8+ T-cells produce IFN-gamma and granzyme B simultaneously (Tc1a). Two additional subpopulations of HIV specific CD8 cells are found, each one constituting 30-40% of the CD8 cell pool. One of these (Tc1b) secretes IFN-gamma only, and the other one (Tc1c) secretes GzB only.
None of seven patients responded to this peptide with GzB producing cells or IFN-gamma producing cells.
The authors describe the epitope as SPRTLNNQWV -- the double N's may be a typo or an unusual form of the epitope; it is atypical and may be why there was no response.

References

Kleen2004 Thomas O. Kleen, Robert Asaad, Samuel J. Landry, Bernhard O. Boehm, and Magdalena Tary-Lehmann. Tc1 Effector Diversity Shows Dissociated Expression of Granzyme B and Interferon-gamma in HIV Infection. AIDS, 18(3):383-392, 20 Feb 2004. PubMed ID: 15090789. Show all entries for this paper.

Displaying record number 52817

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	B7-SV9 Gag
Subtype	B
Species (MHC/HLA)	human(B7)
Immunogen	HIV-1 infection
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, but in this case the epitope did not vary.

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 52156

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	B7-SV9
Subtype	B
Species (MHC/HLA)	human(B7)
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.
1/11 HLA-B7 positive individuals had detectable B7-restricted responses to this epitope during acute infection -- 10/15 of HLA-B7 epitopes tested were targeted by at least one person during acute infection. 1/4 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 1671

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	human(B7)
Immunogen	HIV-1 exposed seronegative, HIV-1 infection
Experimental methods
Keywords	HIV exposed persistently seronegative (HEPS)

Notes

ELISPOT was used to study CTL responses to a panel of 54 predefined HIV-1 epitopes in 91 HIV-1-exposed, persistently seronegative (HEPS) and 87 HIV-1-infected female Nairobi sex workers.
Responses in HEPS women tended to be lower, and focused on different epitopes with HLA presenting molecules that have previously been associated with reduced risk of infection, and there was a shift in the response in the HEPS women upon late seroconversion to epitopes recognized by the HIV-1 infected women.
43/91 HEPS women had CD8+ responses and detection of HIV-1-specific CTL in HEPS women increased with the duration of viral exposure.
Subject ML 1203 started with CTL responses to A*6802 DTVLEDINL and to B7 FPVTPQVPLR prior to seroconversion, and upon seroconversion acquired additional responses to A*6802 ETAYFILKL which became dominant, B7 TPGPGVIRYPL, B7 IPRRIRQGL, and B7 SPRTLNAWV.

References

Kaul2001a R. Kaul, T. Dong, F. A. Plummer, J. Kimani, T. Rostron, P. Kiama, E. Njagi, E. Irungu, B. Farah, J. Oyugi, R. Chakraborty, K. S. MacDonald, J. J. Bwayo, A. McMichael, and S. L. Rowland-Jones. CD8(+) lymphocytes respond to different HIV epitopes in seronegative and infected subjects. J. Clin. Invest., 107(10):1303-10, May 2001. URL: http://www.jci.org/cgi/content/full/107/10/1303. PubMed ID: 11375420. Show all entries for this paper.

Displaying record number 149

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	human(B7)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Study tracks and quantifies in vivo migration of neo-marked CD8 HIV-specific CTL.
Adoptively transferred gene-marked HIV-specific CTL homed to specific lymph node sites, colocalizing within the parafollicular regions of the lymph node adjacent to cells expressing HIV tat-fusion transcripts, indicative of viral replication.
The CTL clones expressed CCR5 and localized among HIV-1 infected cells expressing MIP-1alpha and MIP-1beta, CC-chemokines produced at sites of viral replication, suggesting a possible homing mechanism.
This study provides a methodology for tracking and studying antigen specific CTL in vivo.

References

Brodie2000 S. J. Brodie, B. K. Patterson, D. A. Lewinsohn, K. Diem, D. Spach, P. D. Greenberg, S. R. Riddell, and L. Corey. HIV-Specific Cytotoxic T Lymphocytes Traffic to Lymph Nodes and Localize at Sites of HIV Replication and Cell Death. J. Clin. Invest., 105:1407-1417, 2000. PubMed ID: 10811848. Show all entries for this paper.

Displaying record number 148

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag( subtype B)
Epitope	`SPRTLNAWV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*81:01, B7)
Immunogen	HIV-1 exposed seronegative
Experimental methods
Keywords	subtype comparisons

Notes

HIV-specific CTL were found in exposed seronegative prostitutes from Nairobi -- these CTL may confer protection.
Seroprevalence in this cohort is 90-95% and their HIV-1 exposure is among the highest in the world.
Most isolated HIV strains are clade A in Nairobi, although clades C and D are also found -- B clade epitopes are often cross-reactive, however stronger responses are frequently observed using A or D clade versions of epitopes.
This epitope is conserved among A, B, and D clade viruses.
Database note: First author "Rowland-Jones" is also found as "RowlandJones" on annotated papers in this database.

References

Rowland-Jones1998 S. L. Rowland-Jones, T. Dong, K. R. Fowke, J. Kimani, P. Krausa, H. Newell, T. Blanchard, K. Ariyoshi, J. Oyugi, E. Ngugi, J. Bwayo, K. S. MacDonald, A. J. McMichael, and F. A. Plummer. Cytotoxic T cell responses to multiple conserved HIV epitopes in HIV-resistant prostitutes in Nairobi. J. Clin. Invest., 102(9):1758-65, 1 Nov 1998. PubMed ID: 9802890. Show all entries for this paper.

Displaying record number 146

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24( subtype B)
Epitope	`SPRTLNAWV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*81:01, B7)
Immunogen	HIV-1 exposed seronegative
Experimental methods
Keywords

Notes

11/16 heavily HIV exposed but persistently seronegative sex-workers in Nairobi had HIV-specific CD8 gamma-IFN responses in the cervix -- systemic CD8+ T cell responses tended to be to the same epitopes but at generally lower levels than cervical CD8+ T cell responses.
Low risk individuals did not have such CD8+ cells.
CD8+ T cell epitopes: DTVLEDINL (3 individuals), SLYNTVATL (4 individuals), LSPRTLNAW (3 individuals) and YPLTFGWCF (4 individuals) were most commonly recognized by the HIV-resistant women.

References

Kaul2000 R. Kaul, F. A. Plummer, J. Kimani, T. Dong, P. Kiama, T. Rostron, E. Njagi, K. S. MacDonald, J. J. Bwayo, A. J. McMichael, and S. L. Rowland-Jones. HIV-1-Specific Mucosal CD8+ Lymphocyte Responses in the Cervix of HIV-1-Resistant Prostitutes in Nairobi. J. Immunol., 164:1602-1611, 2000. PubMed ID: 10640781. Show all entries for this paper.

Displaying record number 60279

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	SV9
Species (MHC/HLA)	human(B*81)
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.
SPRTLNAWV had a significantly positive association with HLA B*81; it was recognized by 8/9 B*81-positive subjects and 10/306 B*81-negative subjects.

References

Displaying record number 56589

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(148-156)
Epitope	`SPRTLNAWV`	Epitope Alignment
Epitope Name	SV9
Subtype	C
Species (MHC/HLA)	human(B*81:01)
Immunogen	HIV-1 infection
Country	South Africa, Zambia
Experimental methods
Keywords	viral fitness and reversion, HLA associated polymorphism

Notes

A cohort of clade C-infected Zambian HIV-1 transmission pairs was studied. Accumulation in the donor of HLA-B restricted mutations in Gag, but not in Nef resulted in a reduced viral load in a recipient upon transmission.
20 mutations in Gag and 11 mutations in Nef, within or flanking CTL epitopes, were considered based on data from a Clade C South African cohort. HLA-B*8101-restricted SPRTLNAWV (SV9) was associated with polymorphisms flanking SV9 at QAISPRTLNAWVKV(I).

References

Goepfert2008 Paul A. Goepfert, Wendy Lumm, Paul Farmer, Philippa Matthews, Andrew Prendergast, Jonathan M. Carlson, Cynthia A. Derdeyn, Jianming Tang, Richard A. Kaslow, Anju Bansal, Karina Yusim, David Heckerman, Joseph Mulenga, Susan Allen, Philip J. R. Goulder, and Eric Hunter. Transmission of HIV-1 Gag Immune Escape Mutations Is Associated with Reduced Viral Load in Linked Recipients. J. Exp. Med., 205(5):1009-1017, 12 May 2008. PubMed ID: 18426987. Show all entries for this paper.

Displaying record number 58443

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(16-24)
Epitope	`SPRTLNAWV`	Epitope Alignment
Subtype	A1
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Country	Kenya
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Proliferation
Keywords	assay or method development, characterizing CD8+ T cells

Notes

24 longitudinally studied HIV-1 (clades A1 or D)-chronically-infected Kenyan subjects were tested for CTL response to 9-mer overlapping p24 peptides. Epitope mapping was assessed not just by IFN-γ EliSpot assays, but by multiparametric flow cytometry of intracellular cytokine staining for IL-2, tumor necrosis factor (TNF-α), chemokine macrophage inflammatory protein 1β (MIP-1β) and degranulation marker CD107a, as well as by proliferation assays. 50/69 epitope-specific responses detected were IFN-γ negative. Several epitope responses had polyfunctional (33%) and proliferative (19%) components. Long term non progressors (LTNP) had more polyfunctional responses of greater magnitude and proliferation than normal progressors (NP).
16 subjects were tested specifically with 126 putative epitopes, 50 of which were confirmed. Clade A1 epitope iSPRTLNAW, corresponds to B consensus of the same sequence, and elicited a single IL-2 response in one ART-treated subject. This epitope is or is contained within a best-defined epitope.

References

Richmond2011 Meika Richmond, Lyle R. McKinnon, Sandra A. Koesters Kiazyk, Charles Wachihi, Makobu Kimani, Joshua Kimani, Francis A. Plummer, and T. Blake Ball. Epitope Mapping of HIV-Specific CD8+ T Cell Responses by Multiple Immunological Readouts Reveals Distinct Specificities Defined by Function. J. Virol., 85(3):1275-1286, Feb 2011. PubMed ID: 21084478. Show all entries for this paper.

Displaying record number 57016

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	Gag
Epitope	`SPRTLNAWV`	Epitope Alignment
Subtype	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.
SPRTLNAWV was a predicted epitope restricted by B7 supertype. 1/31 patient(s) responded to it; the patient was known to carry an allele of B7 supertype. Responding patients were infected with HIV clade(s) D.

References

Displaying record number 144

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24
Epitope	`SPRTLNAWV`	Epitope Alignment
Species (MHC/HLA)	chimpanzee
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

3/4 animals displayed HIV-1 Gag-specific CTL activity.
Effector cells from two chimpanzees were able to recognize epitopes also recognized by human HIV-1 Gag-specific CTL (SPRTLNAWV, HLA-B7, and DLNTMLNTV, HLA-B14)
No chimpanzee CTL were detected to the following human HIV-1 specific Gag epitopes, although they were embedded within 20mer peptides that contained a reactive epitope: ISPRTLNAW, HLA-B57; KRWIILGLNK, HLA-B27; and DRFYKTLRA, HLA-B14.

References

Santra1999 S. Santra, P. N. Fultz, and N. L. Letvin. Virus-Specific Cytotoxic T Lymphocytes in Human Immunodeficiency Virus Type 1-Infected Chimpanzees. J. Virol., 73:7065-7069, 1999. PubMed ID: 10400811. Show all entries for this paper.

Displaying record number 62787

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HXB2 Location	Gag(148-156) p24(16-24) DNA(1231..1257)	Gag Epitope Map
Author Location	p24(148-156)
Epitope	`SPRTLNAWV`	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, 49 single nucleotide mutations were observed in epitope SPRTLNAWV (known to bind to B0702) with a log transformation of mean fitness score, relative to NL4-3, of -0.4252.

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.