Search CTL/CD8+ T-Cell Epitope Database

Found 17 matching records:

Displaying record number 58693

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HXB2 Location	Gag(34-44) p17(34-44) DNA(889..921)	Gag Epitope Map
Author Location	p17(81-89)
Epitope	LVWASRELERF	Epitope Alignment
Epitope Name	LF11
Subtype	C
Species (MHC/HLA)	human(B*57:03)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel epitope LF11, LVWASRELERF, was confirmed to be optimal by peptide truncation and restricted by HLA-B*5703 using CTL from subject R014.
• The binding affinity and stability of LF11 is greatest to B*5703.
• ˜50% B*57-positive and non-B*57-subjects carried mutations in LF11.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58674

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HXB2 Location	Gag(147-155) p24(15-23) DNA(1228..1254)	Gag Epitope Map
Author Location	Gag(147-155)
Epitope	ISPRTLNAW	Epitope Alignment
		Show epitope variants
Epitope Name	ISW9
Subtype	C
Species (MHC/HLA)	human(B*57:01, B*57:02, B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding
Keywords	HLA associated polymorphism

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Epitope ISW9, ISPRTLNAW, was previously known to be restricted by HLA-B*5701, but is shown here to be restricted by HLA-B*5702 and B*5703, and less frequently by HLA-B*5801 as well.
• The binding affinity and HLA-peptide stability of ISW9 to each HLA follows the same pattern as its restriction i.e. highest affinity and stability are seen with B*5702, then B*5703 and much less with B*5801.
• There were no epitope escapes detected in HLA-B*5801 positive subjects as there is a very low number of these subjects recognizing ISW9. Escapes were detected in B*5703 and B*5702 subjects.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58684

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HXB2 Location	Gag(162-172) p24(30-40) DNA(1273..1305)	Gag Epitope Map
Author Location	Gag(162-172)
Epitope	KAFSPEVIPMF	Epitope Alignment
		Show epitope variants
Epitope Name	KF11
Subtype	C
Species (MHC/HLA)	human(B*57:03)
Immunogen	HIV-1 infection
Country	Botswana, South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding
Keywords	HLA associated polymorphism

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Immunodominant epitope KF11, KAFSPEVIPMF, was previously known to be restricted by HLA-B*5703. KF11 was targeted by 76% subjects expressing B*5703, 10% expressing B*5801 and none of those expressing B*5702.
• The binding affinity and HLA-peptide stability of KF11 to each HLA follows the same pattern as its restriction i.e. highest affinity and stability are seen with B*5703, much less with B*5801 and least with B*5702.
• There were no escapes detected in HLA-B*5801 or -B*5702 positive subjects as these HLA do not recognize KF11. Escapes were detected in B*5703 subjects though.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58828

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HXB2 Location	Gag(203-212) p24(71-80) DNA(1396..1425)	Gag Epitope Map
Author Location	p24
Epitope	DTINEEAAEW	Epitope Alignment
Epitope Name	DW10
Subtype	C
Species (MHC/HLA)	human(B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel epitope DW10 p24, DTINEEAAEW, was confirmed to be optimal by peptide truncation and restricted by HLA-B*5801 using CTL from subject N067. ˜50% B*5801-positive responders recognized DW10 p24, while <20% of B*5702- and B*5703-positive responders recognized it.
• The binding affinity of DW10 is greatest to B*5702, but stability is greatest with HLA-B*5801.
• No B*5702-positive subjects carried mutations in DW10 p24, while <10% of HLA-B*801 subjects and ∼10% HLA-B*5703 and non-B*57 subjects sustained DW10 variations.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58688

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HXB2 Location	Gag(240-249) p24(108-117) DNA(1507..1536)	Gag Epitope Map
Author Location	Gag(240-249)
Epitope	TSTLQEQIAW	Epitope Alignment
		Show epitope variants
Epitope Name	TW10
Subtype	C
Species (MHC/HLA)	human(B*57:02, B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding
Keywords	HLA associated polymorphism

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Epitope TW10, TSTLQEQIAW, was previously known to be restricted by HLA-B*5801 and to a lesser extent by B*5703. Here it is shown to be restricted, though rarely, by HLA-B*5702 as well.
• The binding affinity and HLA-peptide stability of TW10 to each HLA follows the reverse pattern of its restriction i.e. highest affinity and stability are seen with B*5702, less with B*5703 and least with B*5801.
• There were fewer to very few escapes detected in HLA-B*5801 or -B*5702 positive subjects. Most escapes were detected in B*5703 subjects.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58690

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HXB2 Location	Gag(308-316) p24(176-184) DNA(1711..1737)	Gag Epitope Map
Author Location	Gag(308-316)
Epitope	QATQDVKNW	Epitope Alignment
		Show epitope variants
Epitope Name	QW9
Subtype	C
Species (MHC/HLA)	human(B*57:02, B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding
Keywords	HLA associated polymorphism

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Epitope QW9, QATQDVKNW, was previously known to be restricted by HLA-B*5703. Here it is shown to be restricted, though rarely, by HLAs B*5702 and B*5801 as well. QW9 was recognized by ˜50% of B*5702 and B*5801 subjects and by >20% of B*5703 subjects. QW9 was confirmed to be optimal by peptide truncation using B*5801-restricted CTL from chronically infected subject N067.
• The binding affinity of QW9 is greatest to B*5702, followed by B*5703 and B*5801. HLA-peptide stability of QW9 to HLA-B*5702 is less than to HLAs B*5703 and B*5801.
• There were very few escapes detected in HLA-B*5801 positive subjects only.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58824

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HXB2 Location	Pol(271-279) RT(116-124) DNA(2895..2921)	Pol Epitope Map
Author Location	RT
Epitope	FSVPLDEGF	Epitope Alignment
Epitope Name	FF9
Subtype	C
Species (MHC/HLA)	human(B*57:02, B*57:03)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel RT epitope FF9, FSVPLDEGF, was confirmed to be optimal by peptide truncation using B*5703-restricted CTL from chronically infected subject N087.
• The binding affinity and stability of FF9 is greatest to B*5703.
• While ˜70% non-B*57 subjects carried mutations in FF9, >60% B*5801- and B*5703-positive subjects carried mutations in FF9. ˜40% B*5702-positive subjects sustained FF9 variations.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58823

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HXB2 Location	Pol(530-538) RT(375-383) DNA(3672..3698)	Pol Epitope Map
Author Location	RT
Epitope	IAMESIVIW	Epitope Alignment
Epitope Name	IW9, IAW9 RT
Subtype	C
Species (MHC/HLA)	human(B*57:02, B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel epitope IW9, IAMESIVIW, was previously known to be restricted by HLA-B*5703. Here it was found also be to restricted by HLAs - B*5702 and -B*5801. It was also confirmed to be optimal by peptide truncation using B*5703-restricted CTL from chronically infected subject N102 and B*5801-restricted CTL from subject R007.
• The binding affinity of IW9 is greatest to B*5702, then B*5703 and B*5801 in descending order; but stability is in reverse order with stability of IW9 RT-B*5801 being by far the greatest. >60% B*5801-responders recognized IW9, >50% B*5703- and ˜20% B*5702-responders recognized IW9 RT.
• >90% B*5801- -positive subjects carried mutations in IW9. ˜80% B*5703-positive subjects and ˜70% B*5702- and non-B*57 subjects sustained IW9 variations.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58825

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HXB2 Location	Pol(562-571) RT(407-416) DNA(3768..3797)	Pol Epitope Map
Author Location	RT
Epitope	QATWIPEWEF	Epitope Alignment
Epitope Name	QF10
Subtype	C
Species (MHC/HLA)	human(B*57:02, B*57:03)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel epitope QF10 RT, QATWIPEWEF, was confirmed to be optimal by peptide truncation using CTL from a B*5703- and B*5702-chronically infected subjects N099 and R014 respectively.
• The binding affinity and stability of QF10 is greatest to B*5703.
• >40% B*5702- and > 20% B*5703-positive subjects carried mutations in QF10. ˜10% of both B*5801 and and nonB*57-positive subjects sustained QF10 RT variations.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58827

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HXB2 Location	Pol(838-846) Integrase(123-131) DNA(4596..4622)	Pol Epitope Map
Author Location	Integrase
Epitope	SAAVKAACW	Epitope Alignment
Epitope Name	SW9
Subtype	C
Species (MHC/HLA)	human(B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel epitope SW9 Int, SAAVKAACW, is shown to be restricted by B*5801. >50% B*5801-positive responders recognized SW9 Int, while ˜35% of B*702- and ˜15% B*5703-positive responders recognized it.
• >60% B*5801-positive subjects carried mutations in SW9 Int. ˜20% each of HLA-B*5702-, B*5703-, non-B*57-subjects sustain variations in SW9, SAAVKAACW.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58826

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HXB2 Location	Pol(888-896) Integrase(173-181) DNA(4746..4772)	Pol Epitope Map
Author Location	Integrase
Epitope	KTAVQMAVF	Epitope Alignment
Epitope Name	KF9 Int
Subtype	C
Species (MHC/HLA)	human(B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel epitope KF9 Int, KTAVQMAVF, was previously known to bind HLA-B*5703, but here was found to also be restricted by B*5801. ˜10% B*5702-positive responders recognized KF9 Int, while <10% of B*5801- and B*5703-positive responders recognized it.
• The binding affinity of KF9 Int is greatest to B*5702, but stability is greatest with HLA-B*5703, followed by -B*5801.
• ˜10% B*5702-positive subjects carried mutations in KF9 Int, while <10% of non-B*57 subjects sustained KF9 variations. At 20%, the largest number of KF9 mutations were seen in HLA-B*5801-positive subjects, but there were no detectable changes in KF9 Int in B*5703-subjects.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58692

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HXB2 Location	Vif(81-89) DNA(5281..5307)	Vif Epitope Map
Author Location	Vif(81-89)
Epitope	LGHGVSIEW	Epitope Alignment
Epitope Name	LW9
Subtype	C
Species (MHC/HLA)	human(B*57:03)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Peptides containing epitope LW9, LGHGVSIEW, were previously known to be restricted by HLA-B*5703. Novel Vif epitope LW9 was confirmed to be optimal by peptide truncation and restricted by HLA-B*5703 using CTL from chronically infected subject R014 of Zimbabwe.
• The binding affinity and stability of LW9 is greatest to B*5703; ∼30% B*5703-responders recognized LW9, <5% B*5801-responders and no B*5702-responders recognized LW9 Vif.
• >30% B*5703-positive subjects carried mutations in LW9. Lower numbers of B*5702 and B*5801-positive subjects sustained LW9 variations.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58816

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HXB2 Location	Rev(14-23) DNA(6009..6038)	Rev Epitope Map
Author Location	Rev(81-89)
Epitope	QAVRIIKILY	Epitope Alignment
Epitope Name	QY10
Subtype	C
Species (MHC/HLA)	human(B*57:03)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Tetramer binding
Keywords	optimal epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Epitope QY10, QAVRIIKILY, was known to be restricted by HLA-B*5703 and -B*5801; ˜45% B*5801-responders, ˜30% B*5703-responders and even ˜10% B*5702-responders recognized QY10. QY10 was confirmed to be optimal by peptide truncation using B*5703-restricted CTL from chronically infected subject R059.
• The binding affinity and stability of QY10 is greatest to B*5703.
• >60% B*5801-positive and lesser numbers of B*57-subjects carried mutations in QY10.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58819

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HXB2 Location	gp160(37-45) gp120(37-45) DNA(6333..6359)	gp160 Epitope Map
Author Location	Env(81-89)
Epitope	TVYYGVPVW	Epitope Alignment
Epitope Name	TW9
Subtype	C
Species (MHC/HLA)	human(B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Tetramer binding
Keywords	optimal epitope, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Epitope TW9,TVYYGVPVW, was known to be restricted by HLA-B*5703 and -B*5801.
• ˜10% B*5703-positive, and <5% non-B*57 carried mutations in TW9.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58818

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HXB2 Location	gp160(59-69) gp120(59-69) DNA(6399..6431)	gp160 Epitope Map
Author Location	Env(81-89)
Epitope	KAYEKEVHNVW	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Tetramer binding
Keywords	optimal epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Epitope KAYEKEVHNVW was known to be restricted by HLA-B*5703 and -B*5801, with 40% of B*5801-responders recognizing it. 10% B*5702- and >15% B*5703-responders also recognized it. It was confirmed to be optimal by peptide truncation using B*5801-restricted CTL from chronically infected subject R076.
• The binding affinity of KAYEKEVHNVW is greatest to B*5702 and its binding to B*5801 has greatest stability .
• >70% B*5702- and B*5801-positive, ˜60% B*5703 and non-B*57 carried mutations in KAYEKEVHNVW.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58821

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HXB2 Location	Nef(82-90) DNA(9040..9066)	Nef Epitope Map
Author Location	Nef(81-89)
Epitope	KAAFDLSFF	Epitope Alignment
Epitope Name	KF9 Nef
Subtype	C
Species (MHC/HLA)	human(B*57:02, B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel epitope KF9 Nef, KAAFDLSFF, was confirmed to be optimal by peptide truncation using B*5703-restricted CTL from chronically infected subject N102.
• The binding affinity and stability of KF9 is greatest to B*5702; ˜45% B*5702-responders recognized KF9, >20% B*5703- and B*5801-responders recognized KF9 Nef.
• Almost 100% B*5702- and B*5703-positive subjects carried mutations in KF9. ˜90% B*5801-positive subjects and ˜60% non-B*57 subjects sustained KF9 variations.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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Displaying record number 58820

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HXB2 Location	Nef(116-124) DNA(9142..9168)	Nef Epitope Map
Author Location	Nef(81-89)
Epitope	HTQGFFPDW	Epitope Alignment
Epitope Name	HW9
Subtype	C
Species (MHC/HLA)	human(B*57:03, B*58:01)
Immunogen	HIV-1 infection
Country	Botswana, South Africa, Zimbabwe
Experimental methods	CD8 T-cell Elispot - IFNγ, HLA binding, Intracellular cytokine staining, Tetramer binding
Keywords	optimal epitope, HLA associated polymorphism, novel epitope

Notes

• 1,010-HIV C clade-chronically infected subjects were tested in order to distinguish levels of immune control by related but different HLA-B*57/58. B*57 micropolymorphisms (B*5703 and B*5702) as well as B*5801 have differing CTL specificity and also present different p24 Gag epitopes. This results in different immune selection pressures on the HIV-C virus.
• Though all three studied HLA alleles, B*5801, B*5702 and B*5703 are significantly associated with lower viral-load (VL) set points, HLA-B*5703, followed closely by B*5702 is the most potent controller with lowest VL and HLA-B*5702, followed by B*5703 and then B*5801 are associated with highest CD4 counts.
• By using 410 overlapping 18-mers that span the HIV-C proteome in EliSpot assays, 17 epitopes were identified that are presented by one of HLAs-B*5801/5702/5703, 13 of them novel.
• Novel epitope HW9 Nef, HTQGFFPDW, was confirmed to be optimal by peptide truncation and restricted by HLA-B*5703, B*5801 using CTL from chronically infected subjects R046, N087.
• The binding affinity and stability of HW9 is greatest to B*5703; >30% B*5801-responders recognized HW9, >20% B*5703-responders recognized it, and ∼10% B*5702-responders recognized HW9 Nef.
• Near 100% B*5703- and B*5801-positive subjects carried mutations in HW9. ˜70% of B*5702 and and even ˜60% nonB*57-positive subjects sustained HW9 variations.

References

Kloverpris2012 Henrik N. Kloverpris, Anette Stryhn, Mikkel Harndahl, Mary van der Stok, Rebecca P. Payne, Philippa C. Matthews, Fabian Chen, Lynn Riddell, Bruce D. Walker, Thumbi Ndung'u, Søren Buus, and Philip Goulder. HLA-B*57 Micropolymorphism Shapes HLA Allele-Specific Epitope Immunogenicity, Selection Pressure, and HIV Immune Control. J. Virol., 86(2):919-929, Jan 2012. PubMed ID: 22090105. Show all entries for this paper.

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