Search CTL/CD8+ T-Cell Epitope Database

Found 12 matching records:

Displaying record number 56345

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HXB2 Location	Gag(28-36) p17(28-36) DNA(871..897)	Gag Epitope Map
Author Location	Gag
Epitope	`KYMLKHIVW`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(A*24)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-A*24-restricted epitope KYMLKHIVW is a clade C optimal epitope. Its clade B equivalent epitope is KYKLKHIVW.

References

Carlson2008 Jonathan M. Carlson, Zabrina L. Brumme, Christine M. Rousseau, Chanson J. Brumme, Philippa Matthews, Carl Kadie, James I. Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J. R. Goulder, and David Heckerman. Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag. PLoS Comput Biol, 4(11):e1000225, Nov 2008. PubMed ID: 19023406. Show all entries for this paper.

Displaying record number 55769

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HXB2 Location	Gag(28-36) p17(28-36) DNA(871..897)	Gag Epitope Map
Author Location	Gag
Epitope	`KYKLKHIVW`	Epitope Alignment
Subtype	B, C
Species (MHC/HLA)	human(A*24)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-A*24-restricted optimal epitope KYKLKHIVW has a mutant, resistant form, KYrLKHIVW in clade B consensus sequences. The clade C susceptible consensus sequence is KYMLKHIVW.

References

Displaying record number 56349

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HXB2 Location	Gag(77-85) p17(77-85) DNA(1018..1044)	Gag Epitope Map
Author Location	Gag(77-85)
Epitope	`SLFNTVATL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(A*02)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-A*02-restricted, clade C consensus SL9, SLFNTVATL, has previously reported escapes that PDN did not find.

References

Displaying record number 56339

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HXB2 Location	Gag(77-85) p17(77-85) DNA(1018..1044)	Gag Epitope Map
Author Location	Gag(77-85)
Epitope	`SLYNTVATL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human(A*02)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-A*02-restricted, clade B consensus SL9, SLYNTVATL, has previously reported escapes that PDN did not find.

References

Displaying record number 56343

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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
Epitope Name	IW9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-B*57-restricted IW9, ISPRTLNAW, escapes from AISPRTLNAW to pISPRTLNAW (A146P), an antigen processing mutation, in the context of escape substitutions T242N in TW10 (TSTLQEQIGW).
A putative epitope, pSG9, showed escape that was correlated with escape at this epitope, IW9 (as well as epitopes TW10, TSTLQEQIGW, and QW9, Gag 308-316).

References

Displaying record number 56342

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HXB2 Location	Gag(162-172) p24(30-40) DNA(1273..1305)	Gag Epitope Map
Author Location	Gag(16-172)
Epitope	`KAFSPEVIPMF`	Epitope Alignment
Epitope Name	KF11
Subtype	B, C
Species (MHC/HLA)	human(B*57)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-B*57-restricted KAFSPEVIPMF escape, A163G i.e. KgFSPEVIPMF is predicted by escape substitutions in other epitopes, viz. T242N in TW10, I147M in IW9 and lack of escape at 310 in QW9.

References

Displaying record number 56341

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HXB2 Location	Gag(240-249) p24(108-117) DNA(1507..1536)	Gag Epitope Map
Author Location	Gag(240-249)
Epitope	`TSTLQEQIGW`	Epitope Alignment
Epitope Name	TW10
Subtype	B, C
Species (MHC/HLA)	human(B*57)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-B*57-restricted TW10, TSTLQEQIGW, has an escape mutation, T242N, TSnLQEQIGW which can partially abrogate B*57 binding, but comes with fitness cost. PDN confirms that partial compensatory mutations to offset fitness cost are found in H219Q, I223V and M228I.
T242N, TSnLQEQIGW, also predicts G248A, TSTLQEQIaW as well as E210D. G248A, TSTLQEQIaW, predicts compensatory substitutions V218A and M228V; while G248T, TSTLQEQItW, predicts H219Q and M228I. These are examples of distal compensations where compensatory mutations are distal in three-dimensional space but alter functional dependencies.
A putative epitope, pSG9, showed escape that was correlated with escape at this epitope, TW10 (as well as epitopes IW9, ISPRTLNAW, and QW9, Gag 308-316).

References

Displaying record number 56346

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HXB2 Location	Gag(254-262) p24(122-130) DNA(1549..1575)	Gag Epitope Map
Author Location	Gag
Epitope	`NPVPVGNIY`	Epitope Alignment
Subtype	B, C
Species (MHC/HLA)	human(B*35)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-B*35-restricted epitope NPVPVGNIY has a resistant, mutant form, NPVPVGeIY found mostly in clade B. This optimal epitope is found mostly in clade C.

References

Displaying record number 56336

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HXB2 Location	Gag(254-262) p24(122-130) DNA(1549..1575)	Gag Epitope Map
Author Location	Gag
Epitope	`PPIPVGDIY`	Epitope Alignment
Subtype	B, C
Species (MHC/HLA)	human(B*35)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-B*35-restricted epitope PPIPVGDIY has a resistant, mutant form, PPIPVGeIY found mostly in clade B. The optimal epitope is found mostly in clade C.

References

Displaying record number 56340

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HXB2 Location	Gag(263-272) p24(131-140) DNA(1576..1605)	Gag Epitope Map
Author Location	Gag(263-272)
Epitope	`KRWIILGLNK`	Epitope Alignment
Epitope Name	KK10
Subtype	B, C
Species (MHC/HLA)	human(B*27)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape, HLA associated polymorphism, compensatory mutation

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
In these cohorts HLA-B27 is found to correlate with escape at position 264 of its restricted epitope KK10, KRWIILGLNK, to KkWIILGLNK and KgWIILGLNK. Moreover, most KK10 compensations are proximal where codon pairs in a compensatory pathway are in close proximity and are likely required to maintain structural fidelity.
As reported before, the KkWIILGLNK mutation is preceded by L268M, KRWIImGLNK in this prediction. L268M, KRWIImGLNK, itself is predicted by the HLA, B*27. Substitution A146P is associated with wildtype L268 sequence.
A replicative compensation, S173A, was previously described for R264K, KkWIILGLNK. A strong association was confirmed using PDN, with new associations with I267V, KRWIvLGLNK and L215M. I267V, KRWIvLGLNK is predicted by the substitution A163X.
Another association confirmed by PDN is that E260D compensates for the R264G mutation KgWIILGLNK but not R264K. Also, regardless of position 260's being E in clade B and D in clade B, if a viral sequence possessed mutant R264G i.e. KgWIILGLNK, then it was always a 260D. KgWIILGLNK is strongly associated with the Q136R substitution.

References

Displaying record number 56347

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HXB2 Location	Gag(306-316) p24(174-184) DNA(1705..1737)	Gag Epitope Map
Author Location	Gag
Epitope	`AEQASQDVKNW`	Epitope Alignment
Subtype	B, C
Species (MHC/HLA)	human(B*44)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords	escape

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
HLA-B*44-restricted optimal epitope AEQASQDVKNW has a mutant, resistant form, AEQASQeVKNW, found primarily in clade B. The optimal epitope form is found mostly in clade C sequences.

References

Displaying record number 56337

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HXB2 Location	Gag(355-363) p24(223-231) DNA(1852..1878)	Gag Epitope Map
Author Location	Gag
Epitope	`GPGHKARVL`	Epitope Alignment
Subtype	B, C
Species (MHC/HLA)	human(B*07)
Immunogen	HIV-1 infection
Country	Canada, South Africa
Experimental methods
Keywords

Notes

A statistical model, the phylogenetic dependency network (PDN), was developed to differentiate the confounding effects of codon variation, linkage disequilibrium of HLA alleles and HIV phylogeny from HLA-associated evolution including HIV selection by HLA-pressure and codon evolution.
This approach was applied to 2 cohorts of 1144 Gag sequences from HIV-infected individuals, generating associations between HIV codons themselves and codons with HLA alleles. Results generated predicted escapes that confirmed that escape kinetics and compensating mutations are consistent across clades. General patterns of covariation and CTL adaptation were determined. Some clade-based differences were identified.
Clades B and C, HLA-B*07-restricted optimal epitope GPGHKARVL has a susceptible form, GPsHKARVL.