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Found 5 matching records:

Displaying record number 53629

HXB2 Location  Gag(19-27)   Gag Epitope Map
View variants at this location
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
View variants at this location
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

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 53630

HXB2 Location  Gag(260-267)   Gag Epitope Map
View variants at this location
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

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 53634

HXB2 Location  Pol(283-290)   Pol Epitope Map
View variants at this location
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

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 53628

HXB2 Location  Nef(135-143)   Nef Epitope Map
View variants at this location
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.

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.


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