Search CTL/CD8+ T-Cell Epitope Database

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Displaying record number 58959

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HXB2 Location	Nef(82-90) DNA(9040..9066)	Nef Epitope Map
Author Location	Nef(82-90)
Epitope	KAAVDLSFF	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP239: A*01:01, A*29:02, B*42:01, B*58:01, C*06:02, C*07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	escape, acute/early infection

Notes

• Amino acid mutations in HIV-1 subtype C were tracked within the first 6 months following transmission in 5 subjects. Early, rapid adaptations (55 mutations) to the viral genome were predominantly driven by CTL pressure (38%), but also by antibody pressure (35%) and reversions (16%). Most CTL escape occurred in Nef, followed by Pol and Env.
• Epitope KAAVDLSFF underwent mutations at amino acids A position 2, V position 4 . These changes were first seen 11-22 weeks after transmission. The escapes were tracked in subject CAP239.
• Using autologous peptides, 13/21 putative epitopes were confirmed to be responsive [see Liu et al. J. Clinical Investigation. 123:380-93 (2013) for details]

References

Abrahams2013 Melissa-Rose Abrahams, Florette K. Treurnicht, Nobubelo K. Ngandu, Sarah A. Goodier, Jinny C. Marais, Helba Bredell, Ruwayhida Thebus, Debra de Assis Rosa, Koleka Mlisana, Cathal Seoighe, Salim Abdool Karim, Clive M. Gray, and Carolyn Williamson. Rapid, Complex Adaptation of Transmitted HIV-1 Full-Length Genomes in Subtype C-Infected Individuals with Differing Disease Progression. AIDS, 27(4):507-518, 20 Feb 2013. PubMed ID: 23370465. Show all entries for this paper.

Displaying record number 61052

Download this epitope record as JSON.

HXB2 Location	Nef(82-90) DNA(9040..9066)	Nef Epitope Map
Author Location	Nef(82-90)
Epitope	KAAVDLSFF	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP239: A*01:01, A*29:02, B*42:01, B*58:01, C*06:02, C*07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

• 17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
• Epitope KAAVDLSFF had a fitness cost ΔE of 1.139 and T cell response was first detected to it at 22d, escape time was 65.8 days.

References

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