Search CTL/CD8+ T-Cell Epitope Database

Found 27 matching records:

Displaying record number 60256

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env(375-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
Epitope Name	SF9
Species (MHC/HLA)	human(A*23)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope

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.
SFNCGGEFF had a significantly positive association with HLA A*23; it was recognized by 2/15 A*23-positive subjects and 1/205 A*23-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 52996

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(375-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B15)
Immunogen	HIV-1 infection
Patient MHC/HLA	A3, A32, B15, B51, Cw03, Cw6, DQ7, DR4, DR8
Country	Netherlands
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	rate of progression, escape

Notes

Both stable potential epitopes and epitopes with escape mutations were found in a patient with increasing viral load over a time period of 4 years. Fixation of escape mutations occurred sequentially and correlated with the rise in viral load and with the increased number of productively infected cells.
This is one of 5 epitopes from this individual that varied over time where the internal mutations became fixed; a dramatic decrease in CTL activity against the wild type epitope was observed as the mutation arose. The sfncRgeff variant residue found at 20 and 47 months postseroconversion.

References

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

Displaying record number 56006

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120
Epitope	`SFNCGGEFF`	Epitope Alignment
Epitope Name	SF9(gp120)
Subtype	B
Species (MHC/HLA)	human(B15)
Immunogen	HIV-1 infection
Country	China
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords

Notes

49 ART-naive chronically HIV-1 infected Chinese subjects' CTLs were tested with 413 OLPs in IFN-gamma 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-B15-restricted epitope SFNCGGEFF elicited an immune response in Chinese HIV-1 positive subjects as peptide GDPEIVMHSFNCGGEFFY but not as peptide SFNCGGEFFYCNTTQLF.
2 of the 21 HLA-B15 carriers responded to FLGKIWPShK-containing peptide with average magnitude of CTL response of 495 SFC/million PBMC.

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 1569

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(375-383 SF2)
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human(B15)
Immunogen	HIV-1 infection
Experimental methods
Keywords	HAART, ART, acute/early infection

Notes

Therapy provided during acute infection resulted in a narrower CTL response, stronger T help response, and a less diverse viral population than was seen in individuals treated during chronic infection.
The breadth and specificity of the response was determined using ELISPOT by studying 19 individuals with pre-seroconversion therapy (Group 1), 11 individuals with primary infection but post-seroconversion therapy (Group 2), and 10 individuals who responded to HAART given during chronic infection (Group 3), using 259 overlapping peptides spanning p17, p24, RT, gp41, gp120 and Nef.
Previously described and newly defined optimal epitopes were tested for CTL response.
Number of HLA-B15+ individuals that had a CTL response to this epitope broken down by group: 0/0 group 1, 1/1 group 2, and 0/1 group 3.

References

Altfeld2001b M. Altfeld, E. S. Rosenberg, R. Shankarappa, J. S. Mukherjee, F. M. Hecht, R. L. Eldridge, M. M. Addo, S. H. Poon, M. N. Phillips, G. K. Robbins, P. E. Sax, S. Boswell, J. O. Kahn, C. Brander, P. J. Goulder, J. A. Levy, J. I. Mullins, and B. D. Walker. Cellular immune responses and viral diversity in individuals treated during acute and early HIV-1 infection. J. Exp. Med., 193(2):169-80, 15 Jan 2001. URL: http://www.jem.org/cgi/content/full/193/2/169. PubMed ID: 11148221. Show all entries for this paper.

Displaying record number 55136

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(375-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B*1516, B15, B63)
Immunogen
Experimental methods
Keywords	subtype comparisons, viral fitness and reversion

Notes

Determined the frequencies of known CD8+ and CD4+ Env epitope sequences among Brazilian HIV sequences of various subtypes.
Present in 121/200 Brazilian HIV sequences; common variants are tFNCGGEFF and SFNCrGEFF.

References

Queiroz2007 Artur Trancoso Lopo de Queiroz, Luciane Amorim Santos, Domingos Ramon Moreau, Tulio de Oliveira, David I. Watkins, Bernardo Galvão-Castro, and Luiz Carlos Junior Alcantara. Identification and Characterization of Previously Described Epitopes in HIV-1 Subtypes B, C, F and BF in Brazil. Braz. J. Infect. Dis., 11(1):27-30, Feb 2007. PubMed ID: 17625722. Show all entries for this paper.

Displaying record number 779

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(375-383 IIIB)
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human(B15, B63)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

This is the optimal peptide for two CTL clones that recognize this epitope in the context of two different HLA molecules, Cw4 and B15.
Predominant form in proviral DNA of the individual with B15 restricted CTL was SFTCGGEFF and this was recognized.
Recognition of a minor autologous variant (SFNCRGEFF) from the B15 donor was greatly reduced.

References

Wilson1997 C. C. Wilson, S. A. Kalams, B. M. Wilkes, D. J. Ruhl, F. Gao, B. H. Hahn, I. C. Hanson, K. Luzuriaga, S. Wolinsky, R. Koup, S. P. Buchbinder, R. P. Johnson, and B. D. Walker. Overlapping Epitopes in Human Immunodeficiency Virus Type 1 gp120 Presented by HLA A, B, and C Molecules: Effects of Viral Variation on Cytotoxic T-Lymphocyte Recognition. J. Virol., 71:1256-1264, 1997. CTL clones were isolated from four individuals that interact with the same 25 amino-acid peptide using three different HLA presenting molecules. PubMed ID: 8995649. Show all entries for this paper.

Displaying record number 55838

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env(375-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human(B15, Cw0401, Cw0407, Cw4)
Immunogen	HIV-1 infection
Country	Philippines, Taiwan
Experimental methods
Keywords	escape

Notes

1100 unique full-length Env sequences were analyzed and the positive selection (PS) pressure determined. The QUASI method was used across Clades A, B, C and D, to find PS sites dispersed across Env.
Frequency of PS sites is stable over time.
25% to 61% PS sites are shared between subtypes A, B, C and D, so it is inferred that immune responses are targeted against the same general regions.
Significant correlations between PS sites and neutralizing antibody response, helper response, antibody plus CTL response are found. This suggests that the NAb response might be the driving force behind HIV-1 Env evolution.
PS-free sites that are targeted greatly by NAb and CTL were found. Functional reasons for the lack of positive selection in such regions must exist.
PS-site-rare regions (conserved regions of Env) were examined for PS, and epitopes located in such regions. Epitope SFNCGGEFF, restricted by HLA-B15, -Cw4, -Cw*0401, -C*0407, is on a region free from positive selection. It is found in Filipino and Taiwanese populations and has no known association with progression to AIDS.

References

Liang2008 Binhua Liang, Ma Luo, T Blake Ball, Xiaojian Yao, Gary Van Domselaar, Wilfred R. Cuff, Mary Cheang, Steven J. M. Jones, and Francis A. Plummer. Systematic Analysis of Host Immunological Pressure on the Envelope Gene of Human Immunodeficiency Virus Type 1 by an Immunobioinformatics Approach. Curr. HIV Res., 6(4):370-379, Jun 2008. PubMed ID: 18691035. Show all entries for this paper.

Displaying record number 53911

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env
Epitope	`SFNCGGEFF`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*1516)
Immunogen	HIV-1 infection
Patient MHC/HLA	A0202, A0301, B0702, B1516
Country	United States
Experimental methods
Keywords	escape, acute/early infection

Notes

Full HIV genomes from nine individuals were analyzed for mutations prior to seroconversion and 7 to 28 days later. It was found that the influence of the host's HLA type was reflected within weeks of infection; a statistically significant number of early nonsynonymous mutations were observed within previously reported CTL epitopes.
E to G mutation was observed in position 7.

References

Bernardin2005 Flavien Bernardin, Denice Kong, Lorraine Peddada, Lee Ann Baxter-Lowe, and Eric Delwart. Human Immunodeficiency Virus Mutations During the First Month of Infection are Preferentially Found in Known Cytotoxic T-Lymphocyte Epitopes. J. Virol., 79(17):11523-11528, Sep 2005. PubMed ID: 16103205. Show all entries for this paper.

Displaying record number 1143

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(379-387 LAI)
Epitope	`SFNCGGEFF`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(B*1516)
Immunogen	HIV-1 infection
Experimental methods
Keywords	optimal epitope

Notes

C. Brander notes this is a B*1516 epitope.

References

Llano2019 Anuska Llano, Samandhy Cedeño, Sandra Silva Arrieta, and Christian Brander. The 2019 Optimal HIV CTL Epitopes Update: Growing Diversity in Epitope Length and HLA restriction. 2019. Show all entries for this paper.

Displaying record number 55035

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human(B*1516, Cw4)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding
Keywords	binding affinity, immunodominance, optimal epitope

Notes

CTL responses were tested for both HIV-1 and EBV derived epitopes restricted by HLA-A, -B and -C alleles. HLA-B alleles more frequently induce detectable responses and that the responses are generally of greater magnitude than those for HLA-A and -C alleles.
The magnitude and frequency of CTL recognition were related to each other and that TCR avidity for HLA/peptide complexes is a more important determinant for magnitude of response than peptide binding affinity to HLA.
EBV response patterns were not significantly altered by HIV coinfection.
Epitope SFNCGGEFF when restricted by HLA-B1516, elicited a magnitude of response of 765 SFC with a functional avidity of 0.5nM. When restricted by HLA-Cw04, it elicited a magnitude of response of 640 SFC with a functional avidity of 0.5nM.

References

Bihl2006 Florian Bihl, Nicole Frahm, Loriana Di Giammarino, John Sidney, Mina John, Karina Yusim, Tonia Woodberry, Kaori Sango, Hannah S. Hewitt, Leah Henry, Caitlyn H. Linde, John V. Chisholm, III, Tauheed M. Zaman, Eunice Pae, Simon Mallal, Bruce D Walker, Alessandro Sette, Bette T. Korber, David Heckerman, and Christian Brander. Impact of HLA-B Alleles, Epitope Binding Affinity, Functional Avidity, and Viral Coinfection on the Immunodominance of Virus-Specific CTL Responses. J. Immunol., 176(7):4094-4101, 1 Apr 2006. PubMed ID: 16547245. Show all entries for this paper.

Displaying record number 60255

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env(375-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
Epitope Name	SF9
Species (MHC/HLA)	human(B*40)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope

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.
SFNCGGEFF had a significantly positive association with HLA B*40; it was recognized by 3/23 B*40-positive subjects and 3/220 B*40-negative subjects.

References

Displaying record number 53670

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120
Epitope	`SFNCGGEFF`	Epitope Alignment
Subtype	B, C
Species (MHC/HLA)	human(B63)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	HLA cross-presentation, optimal epitope

Notes

HLA-B63-positive subjects were shown to be able to generate CTL responses early in acute HIV infection and to control HIV replication in the absence of antiretroviral treatment. Since HLA-B63 shares the epitope binding motif of HLA-B57 and -B58, it was shown that HLA-B63-positive individuals mounted CTL responses to previously identified B57-restricted epitopes, as well as novel, B63-restricted epitopes. Moreover, these novel B63-restricted epitopes can also be presented by HLA-B57 and -B58.
This is a putative HLA-B63/57/58 epitope containing the B58 supertype binding motif. Borderline significantly more often recognized in subjects who carry B63, but not B57/B58.

References

Frahm2005a Nicole Frahm, Sharon Adams, Photini Kiepiela, Caitlyn H. Linde, Hannah S. Hewitt, Mathias Lichterfeld, Kaori Sango, Nancy V. Brown, Eunice Pae, Alysse G. Wurcel, Marcus Altfeld, Margaret E. Feeney, Todd M. Allen, Timothy Roach, M. Anne St. John, Eric S. Daar, Eric Rosenberg, Bette Korber, Francesco Marincola, Bruce D. Walker, Philip J. R. Goulder, and Christian Brander. HLA-B63 Presents HLA-B57/B58-Restricted Cytotoxic T-Lymphocyte Epitopes and Is Associated with Low Human Immunodeficiency Virus Load. J. Virol., 79(16):10218-10225, Aug 2005. PubMed ID: 16051815. Show all entries for this paper.

Displaying record number 60253

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env(375-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
Epitope Name	SF9
Species (MHC/HLA)	human(C*04)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope

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.
SFNCGGEFF had a significantly positive association with HLA C*04; it was recognized by 37/81 C*04-positive subjects and 16/260 C*04-negative subjects.

References

Displaying record number 60254

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env(375-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
Epitope Name	SF9
Species (MHC/HLA)	human(C*14)
Immunogen	HIV-1 infection
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	rate of progression, optimal epitope

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.
SFNCGGEFF had a significantly positive association with HLA C*14; it was recognized by 10/17 C*14-positive subjects and 6/243 C*14-negative subjects.

References

Displaying record number 61616

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env
Epitope	`SFNCGGEFF`	Epitope Alignment
		Show epitope variants
Epitope Name	Env Cw4-SF9
Subtype	B
Species (MHC/HLA)	human(Cw*04)
Immunogen	HIV-1 infection
Patient MHC/HLA	9213: A01, A24, B38, B44, Cw*04
Country	Germany, Switzerland, United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	escape, acute/early infection

Notes

A high throughput whole HIV-1 genome deep sequencing platform combining 454 pyrosequencing with novel assembly and detection of low-frequency variants was used to quantify early stage, poorly represented variants. Application of this method to longitudinal samples from subject 9213 suggests that during acute infection early, low-frequency mutations result from viral adaptation to strong host cellular immune responses during the early decline of peak viral load (VL). Rapid viral escapes from the most dominant immune responses, however, correlate with the loss of this initial viral control.
Non-dominant WT Env epitope SFNCGGEFF was targeted during chronic infection in patient 9213 and is present at 100% frequency at all times tested until d476. By d1543, variant tFNCGGEFF had taken over at 100% frequency.

References

Henn2012 Matthew R. Henn, Christian L. Boutwell, Patrick Charlebois, Niall J. Lennon, Karen A. Power, Alexander R. Macalalad, Aaron M. Berlin, Christine M. Malboeuf, Elizabeth M. Ryan, Sante Gnerre, Michael C. Zody, Rachel L. Erlich, Lisa M. Green, Andrew Berical, Yaoyu Wang, Monica Casali, Hendrik Streeck, Allyson K. Bloom, Tim Dudek, Damien Tully, Ruchi Newman, Karen L. Axten, Adrianne D. Gladden, Laura Battis, Michael Kemper, Qiandong Zeng, Terrance P. Shea, Sharvari Gujja, Carmen Zedlack, Olivier Gasser, Christian Brander, Christoph Hess, Huldrych F. Günthard, Zabrina L. Brumme, Chanson J. Brumme, Suzane Bazner, Jenna Rychert, Jake P. Tinsley, Ken H. Mayer, Eric Rosenberg, Florencia Pereyra, Joshua Z. Levin, Sarah K. Young, Heiko Jessen, Marcus Altfeld, Bruce W. Birren, Bruce D. Walker, and Todd M. Allen. Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection. PLoS Pathog., 8(3):e1002529, 2012. PubMed ID: 22412369. Show all entries for this paper.

Displaying record number 57184

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120
Epitope	`SFNCGGEFF`	Epitope Alignment
Epitope Name	SF9
Species (MHC/HLA)	human(Cw*04)
Immunogen	HIV-1 infection
Country	United Kingdom
Experimental methods	Chromium-release assay, Tetramer binding
Keywords	variant cross-reactivity

Notes

"Double escape", where mutations that escape both CTL and NK recognition is studied associated with gp120 epitope SF9, SFNCGGEFF and its escape variant SL9, SFNCGGEFl.
HLA-Cw*04-restricted CTL bind and respond best to index SF9 peptide, SFNCGGEFF; while their binding to SL9 is reduced. On the other hand, KIR2DL1 receptor on NK cells binds better to variant SL9, SFNCGGEFl, than to the index SF9.

References

Thananchai2009 Hathairat Thananchai, Tariro Makadzange, Katsumi Maenaka, Kimiko Kuroki, Yanchun Peng, Chris Conlon, Sarah Rowland-Jones, and Tao Dong. Reciprocal Recognition of an HLA-Cw4-Restricted HIV-1 gp120 Epitope by CD8+ T Cells and NK Cells. AIDS, 23(2):189-193, 14 Jan 2009. PubMed ID: 19098488. Show all entries for this paper.

Displaying record number 61608

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env
Epitope	`SFNCGGEFF`	Epitope Alignment
		Show epitope variants
Epitope Name	Cw4-SF9 Env
Species (MHC/HLA)	human(Cw*04)
Immunogen	HIV-1 infection
Experimental methods	Other
Keywords	escape

Notes

Proof of principle is given to show that HIV-1 genome sequence from short reads can be used to reconstruct actual whole genome haplotypes including immune escape mutations. 30 whole genome haplotypes from subject 9213 were reconstructed longitudinally and published. Mutations are found to change depending on linkage and resulting clonal interference shows that selection coefficients to study HIV evolution must be estimated for complete haplotypes and not individual escapes.
Subdominant Env epitope, SF9, SFNCGGEFF was present as WT in haplotypes studied, at days 0-476, and escape was detected only on day 1543 for Patient 9213. Mutation seen was tFNCGGEFF (S1T).

References

Pandit2014 Aridaman Pandit and Rob J. de Boer. Reliable Reconstruction of HIV-1 Whole Genome Haplotypes Reveals Clonal Interference and Genetic Hitchhiking among Immune Escape Variants. Retrovirology, 11:56, 4 Jul 2014. PubMed ID: 24996694. Show all entries for this paper.

Displaying record number 57640

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location
Epitope	`SFNCGGEFF`	Epitope Alignment
Epitope Name	SF9
Subtype	A, B
Species (MHC/HLA)	(Cw*0401)
Immunogen	HIV-1 infection
Country	Kenya, United Kingdom
Experimental methods	CD8 T-cell Elispot - IFNγ, Chromium-release assay, Tetramer binding
Keywords

Notes

Frequency, function and phenotype of HLA-C-restricted CTL was examined in 10 chronicly infected, therapy naive patients that carried HLA-Cw04.
HLA-C-restricted CTL accounted for up to 54% of the HIV peptide-specific CTL response. HLA-C-restricted CTL lacked expression of CD28 and expressed low levels of perforin.
SF9 epitope lies within a conserved region of gp120. The response to epitope SF9 represented 27-54% of total CTL response in 4 individuals.

References

Makadzange2010 Azure T. Makadzange, Geraldine Gillespie, Tao Dong, Peter Kiama, Job Bwayo, Joshua Kimani, Frank Plummer, Philippa Easterbrook, and Sarah L. Rowland-Jones. Characterization of an HLA-C-Restricted CTL Response in Chronic HIV Infection. Eur. J. Immunol., 40(4):1036-1041, Apr 2010. PubMed ID: 20104487. Show all entries for this paper.

Displaying record number 57927

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env(375-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
		Show epitope variants
Subtype	B
Species (MHC/HLA)	human(Cw*0401)
Immunogen	HIV-1 infection
Patient MHC/HLA	A0101, A0301, B0801, B3503, Cw0401, Cw0701
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ
Keywords	acute/early infection

Notes

The study tracked changes in amino acid residues across the whole genome over time during the first year of infection in 11 individuals representing 4 donor-recipient pairs and 3 independent seroconverters. 9 of the 11 individuals were enrolled during acute infection. In most cases, a single founder virus underwent selection, primarily in env and nef. Mutations were detected in the first week, and became consensus as early as 21 days post-onset of symptoms. Putative escape mutations were often rapidly replaced with mutually-exclusive mutations nearby. Escape mutations were more frequent than reversions.
Previously-documented Cw*0401-restricted epitope SFNCGGEFF was recognized by 1 Cw*0401-positive patient by EliSpot assay at day 127 post-seroconversion.
Founder sequence SFNCGGEFF was replaced by day 68 post-seroconversion by two mutually exclusive variants, SvNCGGEFF and SFNCrGEFF. EliSpot response to the original peptide was not measured a day 7, but was significant by day 127.

References

Herbeck2011 Joshua T. Herbeck, Morgane Rolland, Yi Liu, Sherry McLaughlin, John McNevin, Hong Zhao, Kim Wong, Julia N. Stoddard, Dana Raugi, Stephanie Sorensen, Indira Genowati, Brian Birditt, Angela McKay, Kurt Diem, Brandon S. Maust, Wenjie Deng, Ann C. Collier, Joanne D. Stekler, M. Juliana McElrath, and James I. Mullins. Demographic Processes Affect HIV-1 Evolution in Primary Infection before the Onset of Selective Processes. J. Virol., 85(15):7523-7534, Aug 2011. PubMed ID: 21593162. Show all entries for this paper.

Displaying record number 777

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(376-383 PV22)
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human(Cw*0401)
Immunogen	HIV-1 infection
Experimental methods
Keywords	optimal epitope

Notes

C. Brander notes this is a C*0401 epitope.

References

Displaying record number 52249

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120
Epitope	`SFNCGGEFF`	Epitope Alignment
Subtype	A
Species (MHC/HLA)	human(Cw0401, Cw0407)
Immunogen	HIV-1 infection
Experimental methods
Keywords	HIV exposed persistently seronegative (HEPS), HLA cross-presentation

Notes

4/123 (2 HIV-1 positive, 2 HEPS) Kenyan female sex workers carried the novel allele HLA Cw*0407.
HLA Cw*0407 did not differ from Cw*0401 in the region associated with the binding pocket, and Cw*0407 was shown to cross-present a previously defined Cw*0401 epitope, SFNCGGEFF (gp120).

References

Bird2002 Thomas G. Bird, Rupert Kaul, Timothy Rostron, Joshua Kimani, Joanne Embree, Paul P. Dunn, Job J. Bwayo, Francis A. Plummer, Sarah L. Rowland-Jones, Tao Dong, and The Oxford-Nairobi HLA Collaborative Group. HLA Typing in a Kenyan Cohort Identifies Novel Class I Alleles that Restrict Cytotoxic T-Cell Responses to Local HIV-1 Clades. AIDS, 16(14):1899-1904, 27 Sep 2002. PubMed ID: 12351949. Show all entries for this paper.

Displaying record number 776

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(376-383 PV22)
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human(Cw4)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Conserved epitope.

References

Johnson1993 R. P. Johnson, A. Trocha, T. M. Buchanan, and B. D. Walker. Recognition of a Highly Conserved Region of Human Immunodeficiency Virus Type 1 gp120 by an HLA-Cw4-Restricted Cytotoxic T-Lymphocyte Clone. J. Virol., 67:438-445, 1993. The epitope sequence FNCGGEFF stimulates CTL response; the natural variants FNCRGEFF (SF2), TNCRGEFL (ROD) and LNCGGEFF (NDK) do not serve as epitopes. This was the first report of an HIV antigen specific target cells restricted by an HLA-C molecule, Cw4. PubMed ID: 7677956. Show all entries for this paper.

Displaying record number 57840

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120
Epitope	`SFNCGGEFF`	Epitope Alignment
Epitope Name	SF9
Subtype	B
Species (MHC/HLA)	human(Cw4)
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, TCR binding
Keywords	rate of progression, TCR usage, optimal epitope

Notes

The study measured the functional avidities of HIV-specific CTL responses targeting 20 optimally defined CTL epitopes in a cohort of 44 HIV controllers and 68 non-controllers. Highest functional avidities were toward HLA-B-restricted epitopes in Gag. Avidities were higher in HIV controllers than non-controllers. Higher-avidity T-cell populations had narrower TCR repertoires.
SFNCGGEFF was one of 20 optimal epitopes tested.
CTL response magnitude and functional avidity for this epitope did not change before and after initiation of HAART.

References

Berger2011 Christoph T. Berger, Nicole Frahm, David A. Price, Beatriz Mothe, Musie Ghebremichael, Kari L. Hartman, Leah M. Henry, Jason M. Brenchley, Laura E. Ruff, Vanessa Venturi, Florencia Pereyra, John Sidney, Alessandro Sette, Daniel C. Douek, Bruce D. Walker, Daniel E. Kaufmann, and Christian Brander. High-Functional-Avidity Cytotoxic T Lymphocyte Responses to HLA-B-Restricted Gag-Derived Epitopes Associated with Relative HIV Control. J. Virol., 85(18):9334-9345, Sep 2011. PubMed ID: 21752903. Show all entries for this paper.

Displaying record number 1697

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(376-383)
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human(Cw4)
Immunogen	HIV-1 exposed seronegative, HIV-1 infection
Experimental methods
Keywords	HIV exposed persistently seronegative (HEPS), immunodominance

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.
Among HLA-Cw4 women, 1/2 HEPS and 10/11 HIV-1 infected women recognized this epitope.
The dominant response to this HLA allele was to this epitope in 6 of the 10/11 responsive HIV-1 infected women, and not in the HEPS case.

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 778

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	gp120(376-383 PV22)
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human(Cw4)
Immunogen	HIV-1 infection
Experimental methods
Keywords

Notes

Longitudinal study of epitope variation in vivo.

References

Wolinsky1996 S. M. Wolinsky, B. T. M. Korber, A. U. Neumann, M. Daniels, K. J. Kuntsman, A. J. Whetsell, M. R. Furtado, Y. Chao, D. D. Ho, J. T. Safrit, and R. A. Koup. Adaptive Evolution of Human Immunodeficiency Virus-Type 1 during the Natural Course of Infection. Science, 272:537-542, 1996. In a longitudinal study of six patients, epitope variation occurred only when there was a notable CTLp frequency and the individual had the appropriate HLA type. PubMed ID: 8614801. Show all entries for this paper.

Displaying record number 54951

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, vaccine
Patient MHC/HLA	A3, A33; B15 (63), B27
Experimental methods	CD8 T-cell Elispot - IFNγ, Flow cytometric T-cell cytokine assay
Keywords	vaccine-induced immune responses

Vaccine Details

Vaccine type	canarypox prime with gp120 boost
Vaccine strain	other
Vaccine component	gp160

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 contained in the vaccine, the vaccinated patient recognized it after 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 56130

HXB2 Location	gp160(375-383) gp120(375-383) DNA(7347..7373)	gp160 Epitope Map
Author Location	Env
Epitope	`SFNCGGEFF`	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A0101, B1567, B8101, Cw1402, Cw*1801
Country	Kenya
Experimental methods	CD8 T-cell Elispot - IFNγ, Proliferation
Keywords	assay or method development

Notes

To evaluate the use of IFN-gamma ELISpot and proliferation assays, the two were compared in a cohort of HIV-1-infected Kenyan sex-workers. ELISpot does not always correlate with viral load and replication or disease progression. The exclusive use of these assays makes definition of CTL response in disease incomplete, especially for memory T cells.
Despite assaying for 24 INF-gamma and 41 proliferative responses, only 5 of these responses overlapped in the same subject. 18 peptide-epitopes including 10 epitopes and their variants were used in this study.
SFNCGGEFF did not elicit proliferation, but elicited an ELISpot response in 1 subject.

References

McKinnon2008 Lyle R. McKinnon, T. Blake Ball, Charles Wachihi, Nyakio Chinga, Anne Maingi, Ma Luo, Keith R. Fowke, and Francis A. Plummer. Substantial Intrapatient Differences in the Breadth and Specificity of HIV-Specific CD8+ T-Cell Interferon-gamma and Proliferation Responses. J. Acquir. Immune Defic. Syndr., 49(2):123-127, 1 Oct 2008. PubMed ID: 18769359. Show all entries for this paper.