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Found 10 matching records:

Displaying record number 54577

HXB2 Location Gag(71-79) Gag Epitope Map
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GSEELRSLY

`GSEELRSLf`		escape documented in this paper
`GSEELRSLc`		inferred escape

Epitope Name GY9

Species (MHC/HLA) human(A*01)

Variant Details

Showing all: 2 variant(s).

Variant ID.	`627`
Epitope Seq.	`GSEELRSLY`
Variant Seq.	`GSEELRSLf`
Mutations	Y/F
Epitope Location	Y9F
HXB2 Location	Y79F
Mutation Type	E: escape documented in this paper
Note	The variant was present in most of the clones by week 139 and was not recognized by the CTLs.

Variant ID.	`628`
Epitope Seq.	`GSEELRSLY`
Variant Seq.	`GSEELRSLc`
Mutations	Y/C
Epitope Location	Y9C
HXB2 Location	Y79C
Mutation Type	IE: inferred escape
Note	Author tabulates this minor variant (1/12) found in patient OP428 at week 63 as viral escape. No CTL response.

References

Karlsson2007 Annika C. Karlsson, Astrid K. N. Iversen, Joan M. Chapman, Tulio de Oliviera, Gerald Spotts, Andrew J. McMichael, Miles P. Davenport, Frederick M. Hecht, and Douglas F. Nixon. Sequential Broadening of CTL Responses in Early HIV-1 Infection Is Associated with Viral Escape. PLoS ONE, 2:e225, 2007. PubMed ID: 17311088. Show all entries for this paper.

Displaying record number 54580

HXB2 Location Gag(74-82) Gag Epitope Map
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Epitope

ELRSLYNTV

Epitope Alignment

Variants

`ELRSLYNTi`		observed variant
`ELRSLfNTi`		observed variant
`ELRSLcNTi`		observed variant
`ELRSLYNai`		observed variant

Epitope Name EV9

Species (MHC/HLA) human(B*08)

Variant Details

Showing all: 4 variant(s).

Variant ID.	`629`
Epitope Seq.	`ELRSLYNTV`
Variant Seq.	`ELRSLYNTi`
Mutations	V/I
Epitope Location	V9I
HXB2 Location	V82I
Mutation Type	OV: observed variant
Note	A major variant found in one of the patients throughout study period.

Variant ID.	`630`
Epitope Seq.	`ELRSLYNTV`
Variant Seq.	`ELRSLfNTi`
Mutations	Y/F V/I
Epitope Location	Y6F V9I
HXB2 Location	Y79F V82I
Mutation Type	OV: observed variant
Note	A major variant found in one of the patients throughout study period.

Variant ID.	`631`
Epitope Seq.	`ELRSLYNTV`
Variant Seq.	`ELRSLcNTi`
Mutations	Y/C V/I
Epitope Location	Y6C V9I
HXB2 Location	Y79C V82I
Mutation Type	OV: observed variant
Note	Minor variant found in one of the patients at week 63.

Variant ID.	`632`
Epitope Seq.	`ELRSLYNTV`
Variant Seq.	`ELRSLYNai`
Mutations	T/A V/I
Epitope Location	T8A V9I
HXB2 Location	T81A V82I
Mutation Type	OV: observed variant
Note	Minor variant found in one of the patients at week 39.

References

Displaying record number 54556

HXB2 Location Gag(77-85) Gag Epitope Map
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Epitope

SLYNTVATL

Epitope Alignment

Variants

`SLYNTiATL`		susceptible form
`SLfNTiATL`		diminished response; escape documented in this paper
`SLYNaiATL`		inferred escape
`SLcNTiATL`		inferred escape

Epitope Name SL9

Species (MHC/HLA) human(A*02)

Variant Details

Showing all: 4 variant(s).

Variant ID.	`633`
Epitope Seq.	`SLYNTVATL`
Variant Seq.	`SLYNTiATL`
Mutations	V/I
Epitope Location	V6I
HXB2 Location	V82I
Mutation Type	SF: susceptible form
Method	CD8 T-cell Elispot - IFNy
Note	A major variant detected by week 39 in one of the patients that induced a CTL response.

Variant ID.	`634`
Epitope Seq.	`SLYNTVATL`
Variant Seq.	`SLfNTiATL`
Mutations	Y/F V/I
Epitope Location	Y3F V6I
HXB2 Location	Y79F V82I
Mutation Type	DR: diminished response E: escape documented in this paper
Method	CD8 T-cell Elispot - IFNy
Note	Variant detected by week 63. Lower magnitude responses than wt and V/I mutant. Positive selection. Seen with upstream changes E62G/V/A, where the 62A mutation persisted and is suggested to reduce fitness cost of the Y/F escape mutation.

Variant ID.	`635`
Epitope Seq.	`SLYNTVATL`
Variant Seq.	`SLYNaiATL`
Mutations	T/A V/I
Epitope Location	T5A V6I
HXB2 Location	T81A V82I
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant detected in 1/14 clones at week 39 in patients. OP428 as viral escape. No CTL response detected.

Variant ID.	`636`
Epitope Seq.	`SLYNTVATL`
Variant Seq.	`SLcNTiATL`
Mutations	Y/C V/I
Epitope Location	Y3C V6I
HXB2 Location	Y79C V82I
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant as a viral escape, detected in 1/12 clones at week 63 in patient OP428. No CTL response detected.

References

Displaying record number 54579

HXB2 Location Gag(93-101) Gag Epitope Map
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Epitope

EVKDTKEAL

Epitope Alignment

Variants

`dVKDTKEAL`		diminished response
`EiKDTKEAL`		inferred escape
`kVKDTKEAL`		inferred escape
`EVKDTKgAL`		inferred escape

Epitope Name EL9

Species (MHC/HLA) human(B*08)

Variant Details

Showing all: 4 variant(s).

Variant ID.	`637`
Epitope Seq.	`EVKDTKEAL`
Variant Seq.	`dVKDTKEAL`
Mutations	E/D
Epitope Location	E1D
HXB2 Location	E93D
Mutation Type	DR: diminished response
Method	CD8 T-cell Elispot - IFNy
Note	Variant found in one patient at week 63. A minor response to this variant, but the variant was eliminated by CTLs. R91G upstream mutation affects processing.

Variant ID.	`638`
Epitope Seq.	`EVKDTKEAL`
Variant Seq.	`EiKDTKEAL`
Mutations	V/I
Epitope Location	V2I
HXB2 Location	V94I
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant detected in 9/14 clones at week 39 in patient OP428 as viral escape. No CTL response detected.

Variant ID.	`639`
Epitope Seq.	`EVKDTKEAL`
Variant Seq.	`kVKDTKEAL`
Mutations	E/K
Epitope Location	E1K
HXB2 Location	E93K
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant detected in 1/11 clones at week 139 in patient OP428 as viral escape. No CTL response detected.

Variant ID.	`640`
Epitope Seq.	`EVKDTKEAL`
Variant Seq.	`EVKDTKgAL`
Mutations	E/G
Epitope Location	E7G
HXB2 Location	E99G
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant detected in 1/16 clones at week 15 in patient OP428 as viral escape. No CTL response detected.

References

Displaying record number 54576

HXB2 Location Gag(147-155) Gag Epitope Map
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Epitope

ISPRTLNAW

Epitope Alignment

Variants

lSPRTLNAW observed variant

Epitope Name IW9

Species (MHC/HLA) human(B*57)

Variant Details

Showing all: 1 variant(s).

Variant ID.	`641`
Epitope Seq.	`ISPRTLNAW`
Variant Seq.	`lSPRTLNAW`
Mutations	I/L
Epitope Location	I1L
HXB2 Location	I147L
Mutation Type	OV: observed variant
Note	Variant detected at week 106 in one of the patients, but not in association with antigen processing altering mutation A146P.

References

Displaying record number 54570

HXB2 Location Pol(188-196) Pol Epitope Map
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Epitope

ALVEICTEM

Epitope Alignment

Variants

`ALiEICTEM`		diminished response
`ALmEICTEM`		susceptible form
`ALtEICTEM`		observed variant
`ALiEICTEt`		observed variant
`ALiEICTdM`		observed variant
`ALmkICTEM`		observed variant
`ALmEICaEM`		observed variant

Species (MHC/HLA) human(A*02)

Variant Details

Showing all: 7 variant(s).

Variant ID.	`642`
Epitope Seq.	`ALVEICTEM`
Variant Seq.	`ALiEICTEM`
Mutations	V/I
Epitope Location	V3I
HXB2 Location	V190I
Mutation Type	DR: diminished response
Method	CD8 T-cell Elispot - IFNy
Note	Weaker responses to this variant. Variant found at the start of infection.

Variant ID.	`643`
Epitope Seq.	`ALVEICTEM`
Variant Seq.	`ALmEICTEM`
Mutations	V/M
Epitope Location	V3M
HXB2 Location	V190M
Mutation Type	SF: susceptible form
Method	CD8 T-cell Elispot - IFNy
Note	Strongest responses to this variant that emerged after the first variant. Eventually it reverted back to the wt sequence.

Variant ID.	`644`
Epitope Seq.	`ALVEICTEM`
Variant Seq.	`ALtEICTEM`
Mutations	V/T
Epitope Location	V3T
HXB2 Location	V190T
Mutation Type	OV: observed variant
Note	Variant found in 1/17 clones at week 39.

Variant ID.	`645`
Epitope Seq.	`ALVEICTEM`
Variant Seq.	`ALiEICTEt`
Mutations	V/I M/T
Epitope Location	V3I M9T
HXB2 Location	V190I M196T
Mutation Type	OV: observed variant
Note	Variant found in 1/17 clones at week 39.

Variant ID.	`646`
Epitope Seq.	`ALVEICTEM`
Variant Seq.	`ALiEICTdM`
Mutations	V/I E/D
Epitope Location	V3I E8D
HXB2 Location	V190I E195D
Mutation Type	OV: observed variant
Note	Variant found in 1/12 clones at week 88.

Variant ID.	`647`
Epitope Seq.	`ALVEICTEM`
Variant Seq.	`ALmkICTEM`
Mutations	V/M E/K
Epitope Location	V3M E4K
HXB2 Location	V190M E191K
Mutation Type	OV: observed variant
Note	Variant found in 1/12 clones at week 88.

Variant ID.	`648`
Epitope Seq.	`ALVEICTEM`
Variant Seq.	`ALmEICaEM`
Mutations	V/M T/A
Epitope Location	V3M T7A
HXB2 Location	V190M T194A
Mutation Type	OV: observed variant
Note	Variant found in 1/13 clones at week 156.

References

Displaying record number 54564

HXB2 Location Nef(83-91) Nef Epitope Map
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Epitope

AAVDLSHFL

Epitope Alignment

Variants

`AAVDiSHFL`		diminished response
`AAVDirHFL`		inferred escape
`gAlDLSHFL`		diminished response; escape documented in this paper
`gArDLSHFL`		escape documented in this paper
`gAfDLSfFL`		escape documented in this paper
`AAlDLSHFL`		escape documented in this paper
`AAiDLSHFL`		escape documented in this paper
`AAlDiSHFL`		diminished response
`AAlDiSHlL`		inferred escape
`kAlDLSHFL`		inferred escape
`gAVDLSHFL`		escape documented in this paper

Epitope Name AL9

Species (MHC/HLA) human(A*02)

Variant Details

Showing all: 11 variant(s).

Variant ID.	`649`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`AAVDiSHFL`
Mutations	L/I
Epitope Location	L5I
HXB2 Location	L87I
Mutation Type	DR: diminished response
Method	CD8 T-cell Elispot - IFNy
Note	Variant found as a minor population at week 10 (5/16 clones) and dominated viral population at later timepoint. A less intense CTL response targeted this variant than the wt epitope and an increase in viral load was observed. Position under positive selection.

Variant ID.	`650`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`AAVDirHFL`
Mutations	L/I S/R
Epitope Location	L5I S6R
HXB2 Location	L87I S88R
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 61 in 1/14 clones from patient OP177 as viral escape. No CTL response detected against the variant.

Variant ID.	`651`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`gAlDLSHFL`
Mutations	A/G V/L
Epitope Location	A1G V3L
HXB2 Location	A83G V85L
Mutation Type	DR: diminished response E: escape documented in this paper
Method	CD8 T-cell Elispot - IFNy
Note	Variant found as a major population at week 158 in one of the patients, and a less prevalent CTL response against it could be detected. Positions under positive selection. Variant was found in many of the HLA-A2 positive and HLA-A2 negative patients at baseline and follow up timepoints. None of the patients were able to generate a CTL response against autologous virus.

Variant ID.	`652`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`gArDLSHFL`
Mutations	A/G V/R
Epitope Location	A1G V3R
HXB2 Location	A83G V85R
Mutation Type	E: escape documented in this paper
Method	CD8 T-cell Elispot - IFNy
Note	Variant was found in one of the HLA-A2 positive patients at baseline and follow up timepoints. The patient was not able to generate a CTL response against autologous virus.

Variant ID.	`653`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`gAfDLSfFL`
Mutations	A/G V/F H/F
Epitope Location	A1G V3F H7F
HXB2 Location	A83G V85F H89F
Mutation Type	E: escape documented in this paper
Method	CD8 T-cell Elispot - IFNy
Note	Variant was found in one of the HLA-A2 negative patients at baseline and follow up timepoints. The patient was not able to generate a CTL response against autologous virus.

Variant ID.	`654`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`AAlDLSHFL`
Mutations	V/L
Epitope Location	V3L
HXB2 Location	V85L
Mutation Type	E: escape documented in this paper
Method	CD8 T-cell Elispot - IFNy
Note	Variant found at week 109 in 1/13 clones in one of the patients. No CTL response detected against the variant. Variant was also found in two HLA-A2 negative patients at baseline and follow up timepoints. None of the patients were able to generate a CTL response against autologous virus.

Variant ID.	`655`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`AAiDLSHFL`
Mutations	V/I
Epitope Location	V3I
HXB2 Location	V85I
Mutation Type	E: escape documented in this paper
Method	CD8 T-cell Elispot - IFNy
Note	Variant was found in one of the HLA-A2 negative patients at baseline and follow up timepoints. The patient was not able to generate a CTL response against autologous virus.

Variant ID.	`656`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`AAlDiSHFL`
Mutations	V/L L/I
Epitope Location	V3L L5I
HXB2 Location	V85L L87I
Mutation Type	DR: diminished response
Method	CD8 T-cell Elispot - IFNy
Note	Variant found at weeks 109 and 158. A less intense CTL response targeted this variant than the wt epitope and an increase in viral load was observed.

Variant ID.	`657`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`AAlDiSHlL`
Mutations	V/L L/I F/L
Epitope Location	V3L L5I F8L
HXB2 Location	V85L L87I F90L
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 109 in 1/13 clones in patient OP177 as viral escape. No CTL response detected against the variant.

Variant ID.	`658`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`kAlDLSHFL`
Mutations	A/K V/L
Epitope Location	A1K V3L
HXB2 Location	A83K V85L
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 109 in 1/13 clones from patient OP177 as viral escape. No CTL response detected against the variant.

Variant ID.	`659`
Epitope Seq.	`AAVDLSHFL`
Variant Seq.	`gAVDLSHFL`
Mutations	A/G
Epitope Location	A1G
HXB2 Location	A83G
Mutation Type	E: escape documented in this paper
Method	CD8 T-cell Elispot - IFNy
Note	Variant found in two HLA-A2 positive patients at baseline timepoint and none of the patients were able to generate a CTL response against autologous virus.

References

Displaying record number 54578

HXB2 Location Nef(92-100) Nef Epitope Map
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Epitope

KEKGGLEGL

Epitope Alignment

Variants

`KEKGGLdGL`		diminished response
`KEKGGLEeL`		inferred escape

Epitope Name KL9

Species (MHC/HLA) human(B*40)

Variant Details

Showing all: 2 variant(s).

Variant ID.	`660`
Epitope Seq.	`KEKGGLEGL`
Variant Seq.	`KEKGGLdGL`
Mutations	E/D
Epitope Location	E7D
HXB2 Location	E98D
Mutation Type	DR: diminished response
Method	CD8 T-cell Elispot - IFNy
Note	Variant found at weeks 109 and 158. A less intense CTL response targeted this variant than the wt epitope.

Variant ID.	`661`
Epitope Seq.	`KEKGGLEGL`
Variant Seq.	`KEKGGLEeL`
Mutations	G/E
Epitope Location	G8E
HXB2 Location	G99E
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 158 in 1/14 clones as viral escape. No CTL response detected against the variant.

References

Displaying record number 54566

HXB2 Location Nef(180-189) Nef Epitope Map
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Epitope

VLEWRFDSRL

Epitope Alignment

Variants

`VLEWRFDSsL`		inferred escape
`VLEWRFgSRL`		inferred escape
`VLEWkFDSRL`		diminished response

Epitope Name VL10

Species (MHC/HLA) human(A*02)

Variant Details

Showing all: 3 variant(s).

Variant ID.	`662`
Epitope Seq.	`VLEWRFDSRL`
Variant Seq.	`VLEWRFDSsL`
Mutations	R/S
Epitope Location	R9S
HXB2 Location	R188S
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 10 in 2/16 clones from patient OP177 as viral escape. No CTL response detected against the variant.

Variant ID.	`663`
Epitope Seq.	`VLEWRFDSRL`
Variant Seq.	`VLEWRFgSRL`
Mutations	D/G
Epitope Location	D7G
HXB2 Location	D186G
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 13 in 1/26 clones from patient OP177 as viral escape. No CTL response detected against the variant.

Variant ID.	`664`
Epitope Seq.	`VLEWRFDSRL`
Variant Seq.	`VLEWkFDSRL`
Mutations	R/K
Epitope Location	R5K
HXB2 Location	R184K
Mutation Type	DR: diminished response
Method	CD8 T-cell Elispot - IFNy
Note	Variant found at week 158 in 4/14 clones. A less intense CTL response targeted this variant than the wt epitope.

References

Displaying record number 54581

HXB2 Location Nef(183-191) Nef Epitope Map
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Epitope

WRFDSRLAF

Epitope Alignment

Variants

`WkFDSRLAF`		susceptible form
`WRFgSRLAF`		inferred escape
`WRFDSsLAF`		inferred escape
`WRFDSRLAc`		inferred escape
`WRFDSRLAl`		inferred escape

Epitope Name WF9

Species (MHC/HLA) human(B*15)

Variant Details

Showing all: 5 variant(s).

Variant ID.	`665`
Epitope Seq.	`WRFDSRLAF`
Variant Seq.	`WkFDSRLAF`
Mutations	R/K
Epitope Location	R2K
HXB2 Location	R184K
Mutation Type	SF: susceptible form
Method	CD8 T-cell Elispot - IFNy
Note	Variant found at week 158 in 4/14 clones. Variant elicited a potent HLA-B15 restricted immune response.

Variant ID.	`666`
Epitope Seq.	`WRFDSRLAF`
Variant Seq.	`WRFgSRLAF`
Mutations	D/G
Epitope Location	D4G
HXB2 Location	D186G
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 13 in 1/26 clones from patient OP177 as viral escape. No CTL response detected against the variant.

Variant ID.	`667`
Epitope Seq.	`WRFDSRLAF`
Variant Seq.	`WRFDSsLAF`
Mutations	R/S
Epitope Location	R6S
HXB2 Location	R188S
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 10 in 2/16 clones from patient OP177 as viral escape. No CTL response detected against the variant.

Variant ID.	`668`
Epitope Seq.	`WRFDSRLAF`
Variant Seq.	`WRFDSRLAc`
Mutations	F/C
Epitope Location	F9C
HXB2 Location	F191C
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 13 in 1/26 clones from patient OP177 as viral escape. No CTL response detected against the variant.

Variant ID.	`669`
Epitope Seq.	`WRFDSRLAF`
Variant Seq.	`WRFDSRLAl`
Mutations	F/L
Epitope Location	F9L
HXB2 Location	F191L
Mutation Type	IE: inferred escape
Method	CD8 T-cell Elispot - IFNy
Note	Author tabulates this variant found at week 13 in 1/26 clones from patient OP177 as viral escape. No CTL response detected against the variant.