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Found 5 matching records:

Displaying record number 53629

HXB2 Location Gag(19-27) Gag Epitope Map
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Epitope

IRLRPGGKK

Epitope Alignment

Variants

IRLRPGGrK susceptible form

Species (MHC/HLA) human(B27)

Variant Details

Showing all: 1 variant(s).

Variant ID.	`113`
Epitope Seq.	`IRLRPGGKK`
Variant Seq.	`IRLRPGGrK`
Mutations	K/R
Epitope Location	K8R
HXB2 Location	K26R
Mutation Type	SF: susceptible form
Method	Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Note	The dominant viral sequence was irlrpggRk, found in 12/15 clones, while the screening sequence IRLRPGGKK was found in 3/15 clones. The least frequent variant stimulated the strongest response.

References

Casazza2005a Joseph P. Casazza, Michael R. Betts, Brenna J. Hill, Jason M. Brenchley, David A. Price, Daniel C. Douek, and Richard A. Koup. Immunologic Pressure within Class I-Restricted Cognate Human Immunodeficiency Virus Epitopes during Highly Active Antiretroviral Therapy. J. Virol., 79(6):3653-3663, Mar 2005. PubMed ID: 15731259. Show all entries for this paper.

Displaying record number 53633

HXB2 Location Gag(20-28) Gag Epitope Map
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Epitope

RLRPGGKKK

Epitope Alignment

Variants

`RLRPGGKKq`		diminished response; susceptible form
`RLRPGGKKr`		susceptible form

Species (MHC/HLA) human(A3, A30, B42, B62)

Variant Details

Showing all: 2 variant(s).

Variant ID.	`114`
Epitope Seq.	`RLRPGGKKK`
Variant Seq.	`RLRPGGKKq`
Mutations	K/Q
Epitope Location	K9Q
HXB2 Location	K28Q
Mutation Type	DR: diminished response SF: susceptible form
Method	Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Note	The majority of viral sequences prior to therapy were rlrpggkkQ. At week 14 of therapy a major change in the viral quasispecies occurred: the variants present were found to be rlrpggkkK (14/16 clones) and rlrpggkkR (2/16 clones), both well recognized by HIV-specific CD8 T cells. At week 19, the quasispecies reverted back to the less well-recognized rlrpggkkQ variant.

Variant ID.	`115`
Epitope Seq.	`RLRPGGKKK`
Variant Seq.	`RLRPGGKKr`
Mutations	K/R
Epitope Location	K9R
HXB2 Location	K28R
Mutation Type	SF: susceptible form
Method	Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Note	The majority of viral sequences prior to therapy were rlrpggkkQ. At week 14 of therapy a major change in the viral quasispecies occurred: the variants present were found to be rlrpggkkK (14/16 clones) and rlrpggkkR (2/16 clones), both well recognized by HIV-specific CD8 T cells. At week 19, the quasispecies reverted back to the less well-recognized rlrpggkkQ variant.

References

Displaying record number 53630

HXB2 Location Gag(260-267) Gag Epitope Map
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Epitope

EIYKRWII

Epitope Alignment

Variants

`dIYKRWII`		non-susceptible form
`EvYKRWII`		susceptible form

Species (MHC/HLA) human(B8)

Variant Details

Showing all: 2 variant(s).

Variant ID.	`116`
Epitope Seq.	`EIYKRWII`
Variant Seq.	`dIYKRWII`
Mutations	E/D
Epitope Location	E1D
HXB2 Location	E260D
Mutation Type	NSF: non-susceptible form
Method	Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Note	Diykrwii sequence was found in 12/17 clones after the initiation of therapy, while eVykrwii sequence was found in 5/17, and the peptide used to initially detect the response was not found, EIYKRWII. The less frequent clone was most often recognized. No dramatic shift towards escape was observed after the initiation of therapy.

Variant ID.	`117`
Epitope Seq.	`EIYKRWII`
Variant Seq.	`EvYKRWII`
Mutations	I/V
Epitope Location	I2V
HXB2 Location	I261V
Mutation Type	SF: susceptible form
Method	Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Note	Diykrwii sequence was found in 12/17 clones after the initiation of therapy, while eVykrwii sequence was found in 5/17, and the peptide used to initially detect the response was not found, EIYKRWII. The less frequent clone was most often recognized. No dramatic shift towards escape was observed after the initiation of therapy.

References

Displaying record number 53634

HXB2 Location Pol(283-290) Pol Epitope Map
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Epitope

TAFTIPSI

Epitope Alignment

Variants

`TAFTIPSt`		diminished response; susceptible form
`TAFTIPSm`		diminished response; susceptible form

Species (MHC/HLA) human(B51)

Variant Details

Showing all: 2 variant(s).

Variant ID.	`118`
Epitope Seq.	`TAFTIPSI`
Variant Seq.	`TAFTIPSt`
Mutations	I/T
Epitope Location	I8T
HXB2 Location	I290T
Mutation Type	DR: diminished response SF: susceptible form
Method	Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Note	Prior to the initiation of therapy, taftipsT variant was found in 24/24 clones. At week 14 of therapy, this variant was completely replaced with taftipsI. By week 19, a complete replacement occurred again, this time to taftipsM. The change at nucleotide level suggests a stepwise progression from ACA to ATA to ATG. The taftipsT and taftipsM variants had lower avidity than the taftipsI variant, but this wasn't evident at saturating conditions; only careful titrations revealed the difference. HLA-B51 stabilization studies revealed the increased stabilization with the taftipsI form. Also, CD3 down-regulation was larger in response to taftipsI. The viral shift to the taftipsM variant during HAART was predicted to have minimal or undetectable effect on drug sensitivity.

Variant ID.	`119`
Epitope Seq.	`TAFTIPSI`
Variant Seq.	`TAFTIPSm`
Mutations	I/M
Epitope Location	I8M
HXB2 Location	I290M
Mutation Type	DR: diminished response SF: susceptible form
Method	Flow cytometric T-cell cytokine assay, Intracellular cytokine staining
Note	Prior to the initiation of therapy, taftipsT variant was found in 24/24 clones. At week 14 of therapy, this variant was completely replaced with taftipsI. By week 19, a complete replacement occurred again, this time to taftipsM. The change at nucleotide level suggests a stepwise progression from ACA to ATA to ATG. The taftipsT and taftipsM variants had lower avidity than the taftipsI variant, but this wasn't evident at saturating conditions; only careful titrations revealed the difference. HLA-B51 stabilization studies revealed the increased stabilization with the taftipsI form. Also, CD3 down-regulation was larger in response to taftipsI. The viral shift to the taftipsM variant during HAART was predicted to have minimal or undetectable effect on drug sensitivity.

References

Displaying record number 53628

HXB2 Location Nef(135-143) Nef Epitope Map
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Epitope

YPLTFGWCY

Epitope Alignment

Variants

YPLTFGWCf susceptible form

Species (MHC/HLA) human(B18, B35, B49, B53, B7)

Variant Details

Showing all: 1 variant(s).

Variant ID.	`120`
Epitope Seq.	`YPLTFGWCY`
Variant Seq.	`YPLTFGWCf`
Mutations	Y/F
Epitope Location	Y9F
HXB2 Location	Y143F
Mutation Type	SF: susceptible form
Note	A predominant sequence of ypltfgwcF was found in 2 patients (in 11/11 and 15/15 sequences) that cross-recognized the peptide used for screening, YPLTFGWCY. In patient B, CD8 T-cell response of 0.95% was found for the dominant variant, while the response for the screening epitope ypltfgwcy was 0.58%. In patient F, the frequency of response did not differ significantly between the 2 variants. Assays for both patients were done immediately prior to the initiation of therapy.