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Found 3 matching records:

Displaying record number 61609

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HXB2 Location	gp160(585-593) gp41(74-82) DNA(7977..8003)	gp160 Epitope Map
Author Location	Env
Epitope	`RYLRDQQLL`	Epitope Alignment
		Show epitope variants
Epitope Name	A24-RL9 Env
Species (MHC/HLA)	human(A*24)
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, RL9, RYLRDQQLL was present as WT in haplotypes studied, at days 0-1543, and one escape was detected only on day 476 for Patient 9213. Mutation seen was RYLkDQQLL (R4K).

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 61617

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HXB2 Location	gp160(585-593) gp41(74-82) DNA(7977..8003)	gp160 Epitope Map
Author Location	Env
Epitope	`RYLRDQQLL`	Epitope Alignment
		Show epitope variants
Epitope Name	Env A24-RL9
Subtype	B
Species (MHC/HLA)	human(A*24)
Immunogen	HIV-1 infection
Patient MHC/HLA	9213: A01, A24, B38, B44, C*04
Country	Germany, Switzerland, United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	escape, acute/early infection, assay or method development

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 RYLRDQQLL was targeted during chronic infection in patient 9213 and is present at 100% frequency until d165. By d476, reversion to WT consensus B sequence had appeared within the epitope, which persisted t od1543 when another variant RYLRDQQgi also appeared.
Epitope RYLrDQQLL, RL9, is different from the consensus B sequence, RYLKDQQLL.

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 837

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HXB2 Location	gp160(585-593) gp41(74-82) DNA(7977..8003)	gp160 Epitope Map
Author Location	gp41(584-591 SF2)
Epitope	`RYLRDQQLL`	Epitope Alignment
Epitope Name	Env584-9
Subtype	B
Species (MHC/HLA)	human(A*24:02)
Immunogen	HIV-1 infection
Country	Japan
Experimental methods
Keywords

Notes

Defined using reverse immunogenetics -- 59 HLA-A*2402 binding peptides were predicted by searching for A*2402 anchors in HIV proteins (Tyr at 2, and Phe, Leu or Ile at the C term) -- 53 of the 59 peptides bound A*2402.
This peptide induced CTL in 4/4 HIV-1+ people tested.
RYLRDQQLL bound to A*2402 strongly, the epitope can be processed in a vaccinia construct and presented -- two specific CTL clones were obtained.

References

IkedaMoore1997 Y. Ikeda-Moore, H. Tomiyama, K. Miwa, S. Oka, A. Iwamoto, Y. Kaneko, and M. Takiguchi. Identification and Characterization of Multiple HLA-A24-Restricted HIV-1 CTL Epitopes: Strong Epitopes Are Derived from V Regions of HIV-1. J. Immunol., 159:6242-6252, 1997. PubMed ID: 9550428. Show all entries for this paper.