HIV molecular immunology database

 

Search the Epitope Variant and Escape Mutation Database

Help


Found 23 matching records:

Displaying record number 56630

HXB2 Location  Gag(147-155)   Gag Epitope Map
View variants at this location
Epitope ISPRTLNAW   Epitope Alignment
Variants
lSPRTLNAW   escape documented in this paper
Epitope Name IW9
Species (MHC/HLA human(B*57:01)

Variant Details

Showing all: 1 variant(s).


Variant ID.  1980
Epitope Seq.  ISPRTLNAW
Variant Seq.  lSPRTLNAW
Mutations I/L
Epitope Location I1L
HXB2 Location I147L
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note A simple but atypical pattern of escape was seen with this variant in one patient, CH77 where the variant completely replaced the index epitope. In patient CH58, no significant change with respect to selection in this epitope was detected. For CH58, positive ELISpot from the full proteome scan but with not statistical evidence for selection for change was seen. For CH77, known T cell response from the full proteome scan with evidence for variation and escape by positive ELISpot was seen.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56673

HXB2 Location  Gag(240-249)   Gag Epitope Map
View variants at this location
Epitope TSTLQEQIGW   Epitope Alignment
Variants
TnTLQEQIGW   observed variant
TSTLQEQIeW   observed variant
Species (MHC/HLA human(B*57:01)

Variant Details

Showing all: 2 variant(s).


Variant ID.  2128
Epitope Seq.  TSTLQEQIGW
Variant Seq.  TnTLQEQIGW
Mutations S/N
Epitope Location S2N
HXB2 Location S241N
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH58 carried this mutant. By day 85, two mutants, TnTLQEQIGW (22%) and TSTLQEQIeW (67%) dominated; pooled mutants were reactive to the same extent as the transmitted form.


Variant ID.  2129
Epitope Seq.  TSTLQEQIGW
Variant Seq.  TSTLQEQIeW
Mutations G/E
Epitope Location G9E
HXB2 Location G248E
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH58 carried this mutant. By day 85, two mutants, TnTLQEQIGW (22%) and TSTLQEQIeW (67%) dominated; pooled mutants were reactive to the same extent as the transmitted form.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56633

HXB2 Location  Gag(240-249)   Gag Epitope Map
View variants at this location
Epitope TSTLQEQVGW   Epitope Alignment
Variants
TSTLQEQiGW   observed variant
TSTLQEQVeW   observed variant
TSnLQEQiaW   inferred escape
Epitope Name TW10
Species (MHC/HLA human(B*57:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  1987
Epitope Seq.  TSTLQEQVGW
Variant Seq.  TSTLQEQiGW
Mutations V/I
Epitope Location V8I
HXB2 Location V247I
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note In patient 77 at day 159, the transmitted epitope disappeared and was substituted by two variants, TSTLQEQiGW (89%) and TSTLQEQVeW (11%). At the same time, response was high.


Variant ID.  1988
Epitope Seq.  TSTLQEQVGW
Variant Seq.  TSTLQEQVeW
Mutations G/E
Epitope Location G9E
HXB2 Location G248E
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note In patient 77 at day 159, the transmitted epitope disappeared and was substituted by two variants, TSTLQEQiGW (89%) and TSTLQEQVeW (11%). At the same time, response was high.


Variant ID.  2332
Epitope Seq.  TSTLQEQVGW
Variant Seq.  TSnLQEQiaW
Mutations T/N V/I G/A
Epitope Location T3N V8I G9A
HXB2 Location T242N V247I G248A
Mutation Type IE: inferred escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining
Note In patient CH77 at 592 days, this variant predominated and the authors infer escape.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56638

HXB2 Location  Gag(395-403)   Gag Epitope Map
View variants at this location
Epitope CGKEGHIAR   Epitope Alignment
Variants
CGKEGHIAk   escape documented in this paper
CGKEGHlAR   escape documented in this paper
Species (MHC/HLA human(A*31:01)

Variant Details

Showing all: 2 variant(s).


Variant ID.  2004
Epitope Seq.  CGKEGHIAR
Variant Seq.  CGKEGHIAk
Mutations R/K
Epitope Location R9K
HXB2 Location R403K
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note CGKEGHIAR was strongly recognized by T cells, whereas CGKEGHIAk was not.


Variant ID.  2005
Epitope Seq.  CGKEGHIAR
Variant Seq.  CGKEGHlAR
Mutations I/L
Epitope Location I7L
HXB2 Location I401L
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note CGKEGHIAR was strongly recognized by T cells, whereas the mutant was not.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56654

HXB2 Location  Gag(481-498)   Gag Epitope Map
View variants at this location
Epitope KELYPLASLRSLFGNDPS   Epitope Alignment
Variants
qELYPLASLRSLFGNDPS   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  2081
Epitope Seq.  KELYPLASLRSLFGNDPS
Variant Seq.  qELYPLASLRSLFGNDPS
Mutations K/Q
Epitope Location K1Q
HXB2 Location K481Q
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant in Patient CH40 gave a positive ELISpot from the full proteome scan but was not associated with statistical evidence of positive selection.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56639

HXB2 Location  Pol(81-98)   Pol Epitope Map
View variants at this location
Epitope DTGADDTVLEEMNLPGRW   Epitope Alignment
Variants
{rEALL}DTGADDTVLEEMNLPGRW   calculated escape; processing
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  2330
Epitope Seq.  {KEALL}DTGADDTVLEEMNLPGRW
Variant Seq.  {rEALL}DTGADDTVLEEMNLPGRW
Mutations K/R
Epitope Location K-5R
HXB2 Location K76R
Mutation Type CE: calculated escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining
Note The mutation seen proximal to DTGADDTVLEEMNLPGRW was {GQLrEAL}DTGADDTVLEEMNLPGRW where K/R, and it was predicted to be a processing escape.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56658

HXB2 Location  Vif(119-127)   Vif Epitope Map
View variants at this location
Epitope AIRKAILGR   Epitope Alignment
Variants
AIRKAlLGR   inferred escape
AIRKAIvGR   inferred escape
AIRtAILGR   inferred escape
AIReAILGR   inferred escape
{dS}AIReAILGR   inferred escape; processing
Species (MHC/HLA human

Variant Details

Showing all: 5 variant(s).


Variant ID.  2083
Epitope Seq.  AIRKAILGR
Variant Seq.  AIRKAlLGR
Mutations I/L
Epitope Location I6L
HXB2 Location I124L
Mutation Type IE: inferred escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH40 carried this mutant, and at the same time lost response to the original epitope.


Variant ID.  2084
Epitope Seq.  AIRKAILGR
Variant Seq.  AIRKAIvGR
Mutations L/V
Epitope Location L7V
HXB2 Location L125V
Mutation Type IE: inferred escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH40 carried this mutant, and at the same time lost response to the original epitope.


Variant ID.  2085
Epitope Seq.  AIRKAILGR
Variant Seq.  AIRtAILGR
Mutations K/T
Epitope Location K4T
HXB2 Location K122T
Mutation Type IE: inferred escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH40 carried this mutant, and at the same time lost response to the original epitope.


Variant ID.  2086
Epitope Seq.  AIRKAILGR
Variant Seq.  AIReAILGR
Mutations K/E
Epitope Location K4E
HXB2 Location K122E
Mutation Type IE: inferred escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH40 carried this mutant, and at the same time lost response to the original epitope.


Variant ID.  2329
Epitope Seq.  {ES}AIRKAILGR
Variant Seq.  {dS}AIReAILGR
Mutations E/D K/E
Epitope Location E-2D K4E
HXB2 Location E117D K122E
Mutation Type IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH40 carried this mutant, and at the same time lost response to the original epitope.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56636

HXB2 Location  Vpr(73-90)   Vpr Epitope Map
View variants at this location
Epitope RIGCQHSRIGISQRRRAR   Epitope Alignment
Variants
RIGCQHSRIGIrQRRRAR   reversion
RIGCQrSRIGIrQRRRAR   calculated escape
RIGCQHSRIGIrhRRRAR   calculated escape
RIGCQHSRIGIgQRRRAR   calculated escape
RIGCQHSRIGlgQRRRAR   calculated escape
Species (MHC/HLA human

Variant Details

Showing all: 5 variant(s).


Variant ID.  1998
Epitope Seq.  RIGCQHSRIGISQRRRAR
Variant Seq.  RIGCQHSRIGIrQRRRAR
Mutations S/R
Epitope Location S12R
HXB2 Location S84R
Mutation Type R: reversion
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This S84R substitution to the Clade B consensus persisted and was inferred to be a case of reversion. While there was no ELISpot evidence, there was evidence for positive selection.


Variant ID.  1999
Epitope Seq.  RIGCQHSRIGISQRRRAR
Variant Seq.  RIGCQrSRIGIrQRRRAR
Mutations S/R H/R
Epitope Location S12R H6R
HXB2 Location S84R H78R
Mutation Type CE: calculated escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Substitution seen in Patient CH40. While there was no ELISpot evidence, there was evidence for positive selection.


Variant ID.  2000
Epitope Seq.  RIGCQHSRIGISQRRRAR
Variant Seq.  RIGCQHSRIGIrhRRRAR
Mutations S/R Q/H
Epitope Location S12R Q13H
HXB2 Location S84R Q85H
Mutation Type CE: calculated escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Substitution seen in Patient CH40. While there was no ELISpot evidence, there was evidence for positive selection.


Variant ID.  2001
Epitope Seq.  RIGCQHSRIGISQRRRAR
Variant Seq.  RIGCQHSRIGIgQRRRAR
Mutations S/G
Epitope Location S12G
HXB2 Location S84G
Mutation Type CE: calculated escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Substitution seen in Patient CH40. While there was no ELISpot evidence, there was evidence for positive selection.


Variant ID.  2002
Epitope Seq.  RIGCQHSRIGISQRRRAR
Variant Seq.  RIGCQHSRIGlgQRRRAR
Mutations I/L S/G
Epitope Location I11L S12G
HXB2 Location I83L S84G
Mutation Type CE: calculated escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Substitution seen in Patient CH40. While there was no ELISpot evidence, there was evidence for positive selection.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 57343

HXB2 Location  Rev(9-26)   Rev Epitope Map
View variants at this location
Epitope DEDLLKTVRLIKRLYQSS   Epitope Alignment
Variants
DEnLLKTVRLIKRLYQSS   observed variant
DEDLLKaVRLIKRLYQSS   observed variant
DEDLLKiVRLIKRLYQSS   observed variant
DEDLLKTVgiIKRLYQSS   observed variant
DEDLLKTVRvIKRLYQSS   observed variant
DEDLLKTVRiIKRLYQSS   observed variant
DEDLLrTVRLIKRLYQSS   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 7 variant(s).


Variant ID.  2050
Epitope Seq.  DEDLLKTVRLIKRLYQSS
Variant Seq.  DEnLLKTVRLIKRLYQSS
Mutations D/N
Epitope Location D3N
HXB2 Location D11N
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant seen in Patient CH77. Response not measured.


Variant ID.  2051
Epitope Seq.  DEDLLKTVRLIKRLYQSS
Variant Seq.  DEDLLKaVRLIKRLYQSS
Mutations T/A
Epitope Location T7A
HXB2 Location T15A
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant seen in Patient CH77. Response not measured.


Variant ID.  2052
Epitope Seq.  DEDLLKTVRLIKRLYQSS
Variant Seq.  DEDLLKiVRLIKRLYQSS
Mutations T/I
Epitope Location T7I
HXB2 Location T15I
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant seen in Patient CH77. Response not measured.


Variant ID.  2053
Epitope Seq.  DEDLLKTVRLIKRLYQSS
Variant Seq.  DEDLLKTVgiIKRLYQSS
Mutations L/I R/G
Epitope Location L10I R9G
HXB2 Location L18I R17G
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant seen in Patient CH77. Response not measured.


Variant ID.  2054
Epitope Seq.  DEDLLKTVRLIKRLYQSS
Variant Seq.  DEDLLKTVRvIKRLYQSS
Mutations L/V
Epitope Location L10V
HXB2 Location L18V
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant seen in Patient CH77. Response not measured.


Variant ID.  2055
Epitope Seq.  DEDLLKTVRLIKRLYQSS
Variant Seq.  DEDLLKTVRiIKRLYQSS
Mutations L/I
Epitope Location L10I
HXB2 Location L18I
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant seen in Patient CH77. Response not measured.


Variant ID.  2056
Epitope Seq.  DEDLLKTVRLIKRLYQSS
Variant Seq.  DEDLLrTVRLIKRLYQSS
Mutations K/R
Epitope Location K6R
HXB2 Location K14R
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant seen in Patient CH77. Response not measured.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56634

HXB2 Location  Rev(47-55)   Rev Epitope Map
View variants at this location
Epitope QRQRQIQSL   Epitope Alignment
Variants
QkQRQIQSL   diminished response
QRQRhIQSL   escape documented in this paper
QRQRQIrSL   diminished response
QRQRQIQSi   diminished response; susceptible form
QRQRQIQlL   diminished response; escape documented in this paper
Species (MHC/HLA human

Variant Details

Showing all: 5 variant(s).


Variant ID.  1990
Epitope Seq.  QRQRQIQSL
Variant Seq.  QkQRQIQSL
Mutations R/K
Epitope Location R2K
HXB2 Location R48K
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy, Sequence
Note Patient SUMA0874 developed this nonsynonymous substitution that diminished CTL response measured by ELISpot.


Variant ID.  1991
Epitope Seq.  QRQRQIQSL
Variant Seq.  QRQRhIQSL
Mutations Q/H
Epitope Location Q5H
HXB2 Location Q51H
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Sequence
Note Patient SUMA0874 developed this nonsynonymous substitution that abrogated ELISpot response.


Variant ID.  1992
Epitope Seq.  QRQRQIQSL
Variant Seq.  QRQRQIrSL
Mutations Q/R
Epitope Location Q7R
HXB2 Location Q53R
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy, Sequence
Note Patient SUMA0874 developed this nonsynonymous substitution that diminished CTL response measured by ELISpot.


Variant ID.  1993
Epitope Seq.  QRQRQIQSL
Variant Seq.  QRQRQIQSi
Mutations L/I
Epitope Location L9I
HXB2 Location L55I
Mutation Type DR: diminished response
SF: susceptible form
Method CD8 T-cell Elispot - IFNy, Sequence
Note Patient SUMA0874 developed this nonsynonymous substitution that had a robust EliSpot response, but somewhat diminished.


Variant ID.  2207
Epitope Seq.  QRQRQIQSL
Variant Seq.  QRQRQIQlL
Mutations S/L
Epitope Location S8L
HXB2 Location S54L
Mutation Type DR: diminished response
E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Sequence
Note Patient SUMA0874 developed this nonsynonymous substitution that severely diminished CTL response measured by ELISpot.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56659

HXB2 Location  Rev(49-66)   Rev Epitope Map
View variants at this location
Epitope QRQIRSISERILSTYLER   Epitope Alignment
Variants
QRQIRSISERILnTYLER   inferred escape
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  2088
Epitope Seq.  QRQIRSISERILSTYLER
Variant Seq.  QRQIRSISERILnTYLER
Mutations S/N
Epitope Location S13N
HXB2 Location S61N
Mutation Type IE: inferred escape
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH40 responded to the epitope until day 412 when this mutant dominated the sequenced population.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56647

HXB2 Location  gp160(334-351)   gp160 Epitope Map
View variants at this location
Epitope SGEDWNKTLSHVVDKLRE   Epitope Alignment
Variants
SGEDWNKTLSyVVDKLRE   observed variant
SGEDWNKTLSHVVnKLRE   observed variant
SGEDWNKTLnHVVDKLRE   observed variant
SGEDWNKTLSHVVaKLRE   observed variant
SGEDWNKTLgHVVDKLRE   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 5 variant(s).


Variant ID.  2061
Epitope Seq.  SGEDWNKTLSHVVDKLRE
Variant Seq.  SGEDWNKTLSyVVDKLRE
Mutations H/Y
Epitope Location H11Y
HXB2 Location H344Y
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant sequence was observed but not documented as an escape mutant.


Variant ID.  2062
Epitope Seq.  SGEDWNKTLSHVVDKLRE
Variant Seq.  SGEDWNKTLSHVVnKLRE
Mutations D/N
Epitope Location D14N
HXB2 Location D347N
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant sequence was observed but not documented as an escape mutant.


Variant ID.  2064
Epitope Seq.  SGEDWNKTLSHVVDKLRE
Variant Seq.  SGEDWNKTLnHVVDKLRE
Mutations S/N
Epitope Location S10N
HXB2 Location S343N
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant sequence was observed but not documented as an escape mutant.


Variant ID.  2065
Epitope Seq.  SGEDWNKTLSHVVDKLRE
Variant Seq.  SGEDWNKTLSHVVaKLRE
Mutations D/A
Epitope Location D14A
HXB2 Location D347A
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant sequence was observed but not documented as an escape mutant.


Variant ID.  2273
Epitope Seq.  SGEDWNKTLSHVVDKLRE
Variant Seq.  SGEDWNKTLgHVVDKLRE
Mutations S/G
Epitope Location S10G
HXB2 Location S343G
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant sequence was observed but not documented as an escape mutant.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56642

HXB2 Location  gp160(352-361)   gp160 Epitope Map
View variants at this location
Epitope QFRNKTIVF   Epitope Alignment
Variants
QFkNKTIVF   escape documented in this paper
QFsNKTIVF   observed variant
QFnNKTIVF   observed variant
QFRNKaIVF   observed variant
QFkNKaIVF   observed variant
QFkdKTIVF   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 6 variant(s).


Variant ID.  2033
Epitope Seq.  QFRNKTIVF
Variant Seq.  QFkNKTIVF
Mutations R/K
Epitope Location R3K
HXB2 Location R354K
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly described epitope showed escape early on in Patient CH77. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2034
Epitope Seq.  QFRNKTIVF
Variant Seq.  QFsNKTIVF
Mutations R/S
Epitope Location R3S
HXB2 Location R354S
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly described epitope showed escape early on in Patient CH77. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2035
Epitope Seq.  QFRNKTIVF
Variant Seq.  QFnNKTIVF
Mutations R/N
Epitope Location R3N
HXB2 Location R354N
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly described epitope showed escape early on in Patient CH77. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2036
Epitope Seq.  QFRNKTIVF
Variant Seq.  QFRNKaIVF
Mutations T/A
Epitope Location T6A
HXB2 Location T357A
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly described epitope showed escape early on in Patient CH77. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2037
Epitope Seq.  QFRNKTIVF
Variant Seq.  QFkNKaIVF
Mutations R/K T/A
Epitope Location R3K T6A
HXB2 Location R354K T357A
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly described epitope showed escape early on in Patient CH77. There was no response to the R3K mutant; R3K, T6A was not tested.


Variant ID.  2038
Epitope Seq.  QFRNKTIVF
Variant Seq.  QFkdKTIVF
Mutations R/K N/D
Epitope Location R3K N4D
HXB2 Location R354K N355D
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly described epitope showed escape early on in Patient CH77. There was no response to the R3K mutant; R3K, N4D was not tested.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56649

HXB2 Location  gp160(584-592)   gp160 Epitope Map
View variants at this location
Epitope ERYLRDQQL   Epitope Alignment
Variants
ERYLgDQQL   observed variant
ERhLRDQQL   escape documented in this paper
ERYLkDQQL   observed variant
ERYLsDQQL   escape documented in this paper
Species (MHC/HLA human(B*14:01)

Variant Details

Showing all: 4 variant(s).


Variant ID.  2066
Epitope Seq.  ERYLRDQQL
Variant Seq.  ERYLgDQQL
Mutations R/G
Epitope Location R5G
HXB2 Location R588G
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant arose in longitudinal study of Patient CH58, but loss of response not documented.


Variant ID.  2067
Epitope Seq.  ERYLRDQQL
Variant Seq.  ERhLRDQQL
Mutations Y/H
Epitope Location Y3H
HXB2 Location Y586H
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Decrease in response to this epitope was documented in Patient CH58.


Variant ID.  2068
Epitope Seq.  ERYLRDQQL
Variant Seq.  ERYLkDQQL
Mutations R/K
Epitope Location R5K
HXB2 Location R588K
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant arose in longitudinal study of Patient CH58, but loss of response not documented.


Variant ID.  2069
Epitope Seq.  ERYLRDQQL
Variant Seq.  ERYLsDQQL
Mutations R/S
Epitope Location R5S
HXB2 Location R588S
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Decrease in response to this epitope was documented in Patient CH58.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 57344

HXB2 Location  gp160(597-622)   gp160 Epitope Map
View variants at this location
Epitope GCSGRVICTTTVPWNVSWSNKSLNEI   Epitope Alignment
Variants
dCSGRVICTTTVPWNVSWSNKSLNEI   observed variant
GCSGRVICTTTVPWNsSWSNKSLNEI   observed variant
GCSGRVICTTTVPWNtSWSNKSLsEI   observed variant
GCSGRVICTTTVPWNtSWSNKSLNEI   observed variant
Species (MHC/HLA human(B*57:01)

Variant Details

Showing all: 4 variant(s).


Variant ID.  2057
Epitope Seq.  GCSGRVICTTTVPWNVSWSNKSLNEI
Variant Seq.  dCSGRVICTTTVPWNVSWSNKSLNEI
Mutations G/D
Epitope Location G1D
HXB2 Location G597D
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note The peptide containing epitope TTVPWNVSW showed this variant in Patient CH77.


Variant ID.  2058
Epitope Seq.  GCSGRVICTTTVPWNVSWSNKSLNEI
Variant Seq.  GCSGRVICTTTVPWNsSWSNKSLNEI
Mutations V/S
Epitope Location V16S
HXB2 Location V612S
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note The peptide containing epitope TTVPWNVSW showed this variant in Patient CH77.


Variant ID.  2059
Epitope Seq.  GCSGRVICTTTVPWNVSWSNKSLNEI
Variant Seq.  GCSGRVICTTTVPWNtSWSNKSLsEI
Mutations V/T N/S
Epitope Location V16T N24S
HXB2 Location V612T N620S
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note The peptide containing epitope TTVPWNVSW showed this variant in Patient CH77.


Variant ID.  2060
Epitope Seq.  GCSGRVICTTTVPWNVSWSNKSLNEI
Variant Seq.  GCSGRVICTTTVPWNtSWSNKSLNEI
Mutations V/T
Epitope Location V16T
HXB2 Location V612T
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note The peptide containing epitope TTVPWNVSW showed this variant in Patient CH77.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56657

HXB2 Location  gp160(765-782)   gp160 Epitope Map
View variants at this location
Epitope LFSYHRLRDLLLIVTRIV   Epitope Alignment
Variants
LFrYHRLRDLLLIVTRIV   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  2082
Epitope Seq.  LFSYHRLRDLLLIVTRIV
Variant Seq.  LFrYHRLRDLLLIVTRIV
Mutations S/R
Epitope Location S3R
HXB2 Location S767R
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This variant in Patient CH40 gave a positive ELISpot from the full proteome scan but was not associated with statistical evidence of positive selection.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56684

HXB2 Location  gp160(822-836)   gp160 Epitope Map
View variants at this location
Epitope VAEGTDRVIEELQRA   Epitope Alignment
Variants
VAEGTgRVIEgLQRA   observed variant
VAEGTDRVIEgLQRA   observed variant
VAEGTDRVIEEsQRA   observed variant
VAEGTDRiIEEsQRA   observed variant
VAEGTDRVIEaLQRA   observed variant
{t}VAEGTDRVIEELQRA   compensatory mutation; inferred escape; processing
{t}VAEGTDRVIEgLQRA   compensatory mutation; inferred escape; processing
{t}VAEGTDRiIEgLQRA   compensatory mutation; inferred escape; processing
{v}VAEGTDRiIEgLQRv   compensatory mutation; inferred escape; processing
{v}VAEGTDRiIEgLQRA   compensatory mutation; inferred escape; processing
Species (MHC/HLA human

Variant Details

Showing all: 10 variant(s).


Variant ID.  2130
Epitope Seq.  VAEGTDRVIEELQRA
Variant Seq.  VAEGTgRVIEgLQRA
Mutations E/G D/G
Epitope Location E11G D6G
HXB2 Location E832G D827G
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this variant.


Variant ID.  2131
Epitope Seq.  VAEGTDRVIEELQRA
Variant Seq.  VAEGTDRVIEgLQRA
Mutations E/G
Epitope Location E11G
HXB2 Location E832G
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this variant.


Variant ID.  2132
Epitope Seq.  VAEGTDRVIEELQRA
Variant Seq.  VAEGTDRVIEEsQRA
Mutations L/S
Epitope Location L12S
HXB2 Location L833S
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this variant.


Variant ID.  2133
Epitope Seq.  VAEGTDRVIEELQRA
Variant Seq.  VAEGTDRiIEEsQRA
Mutations L/S V/I
Epitope Location L12S V8I
HXB2 Location L833S V829I
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this variant.


Variant ID.  2134
Epitope Seq.  VAEGTDRVIEELQRA
Variant Seq.  VAEGTDRVIEaLQRA
Mutations E/A
Epitope Location E11A
HXB2 Location E832A
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this variant.


Variant ID.  2318
Epitope Seq.  {A}VAEGTDRVIEELQRA
Variant Seq.  {t}VAEGTDRVIEELQRA
Mutations A/T
Epitope Location A-1T
HXB2 Location A821T
Mutation Type CM: compensatory mutation
IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2319
Epitope Seq.  {A}VAEGTDRVIEELQRA
Variant Seq.  {t}VAEGTDRVIEgLQRA
Mutations A/T E/G
Epitope Location A-1T E11G
HXB2 Location A821T E832G
Mutation Type CM: compensatory mutation
IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2320
Epitope Seq.  {A}VAEGTDRVIEELQRA
Variant Seq.  {t}VAEGTDRiIEgLQRA
Mutations A/T E/G V/I
Epitope Location A-1T E11G V8I
HXB2 Location A821T E832G V829I
Mutation Type CM: compensatory mutation
IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2321
Epitope Seq.  {A}VAEGTDRVIEELQRA
Variant Seq.  {v}VAEGTDRiIEgLQRv
Mutations A/V E/G A/V V/I
Epitope Location A-1V E11G A15V V8I
HXB2 Location A821V E832G A836V V829I
Mutation Type CM: compensatory mutation
IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2322
Epitope Seq.  {A}VAEGTDRVIEELQRA
Variant Seq.  {v}VAEGTDRiIEgLQRA
Mutations A/V E/G V/I
Epitope Location A-1V E11G V8I
HXB2 Location A821V E832G V829I
Mutation Type CM: compensatory mutation
IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Patient CH77 carried this proximal variant (from {LLNTIAIA}VAEGTDRVIEELQRA) that may impact processing or be a compensatory mutation .

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56661

HXB2 Location  gp160(830-847)   gp160 Epitope Map
View variants at this location
Epitope IEVVQRACRAILHIPRRI   Epitope Alignment
Variants
IEVVQRACRAILHIPRkI   observed variant
IEiVQRACRAILHIPRRI   observed variant
IEVVQRACRAIcHIPRRI   observed variant
IEVVQRACRAIrHIPRRI   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 4 variant(s).


Variant ID.  2090
Epitope Seq.  IEVVQRACRAILHIPRRI
Variant Seq.  IEVVQRACRAILHIPRkI
Mutations R/K
Epitope Location R17K
HXB2 Location R846K
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note The authors suggested this as an escape mutation by statistical evidence, but the variant was transient, infrequent, and there was no loss of EliSpot response to the original epitope.


Variant ID.  2091
Epitope Seq.  IEVVQRACRAILHIPRRI
Variant Seq.  IEiVQRACRAILHIPRRI
Mutations V/I
Epitope Location V3I
HXB2 Location V832I
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note The authors suggested this as an escape mutation by statistical evidence, but the variant was transient, infrequent, and there was no loss of EliSpot response to the original epitope.


Variant ID.  2092
Epitope Seq.  IEVVQRACRAILHIPRRI
Variant Seq.  IEVVQRACRAIcHIPRRI
Mutations L/C
Epitope Location L12C
HXB2 Location L841C
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note The authors suggested this as an escape mutation by statistical evidence, but the variant was transient, infrequent, and there was no loss of EliSpot response to the original epitope.


Variant ID.  2093
Epitope Seq.  IEVVQRACRAILHIPRRI
Variant Seq.  IEVVQRACRAIrHIPRRI
Mutations L/R
Epitope Location L12R
HXB2 Location L841R
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note The authors suggested this as an escape mutation by statistical evidence, but the variant was transient, infrequent, and there was no loss of EliSpot response to the original epitope.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56686

HXB2 Location  gp160(838-855)   gp160 Epitope Map
View variants at this location
Epitope RAVLNIPTRIRQGLERAL   Epitope Alignment
Variants
RAVLNvPTRIRQGLERAL   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  2135
Epitope Seq.  RAVLNIPTRIRQGLERAL
Variant Seq.  RAVLNvPTRIRQGLERAL
Mutations I/V
Epitope Location I6V
HXB2 Location I843V
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This transmitted peptide sequence RAVLNIPTRIRQGLERAL was recognized in patient CH77 by week 24. A mutation was seen at RAVLNvPTRIRQGLERAL.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56640

HXB2 Location  Nef(17-34)   Nef Epitope Map
View variants at this location
Epitope RERRRRDEPAAVGVGPAS   Epitope Alignment
Variants
RERRRRnEPAAVGVGPAS   escape documented in this paper
RERRRRnEPAAVGVGsAS   escape documented in this paper
RERRRkDEPAAVGVGPAS   escape documented in this paper
RERRRkDEPAAVGVGPvS   escape documented in this paper
RERRkRDEPAAVGVGPAS   escape documented in this paper
RERgkRDEPAAVGVGPAS   observed variant
RERR....PAAVGVGPAS   observed variant
RERRRReEPAAVGVGPAS   escape documented in this paper
kERRRReEPAAVGVGPAS   escape documented in this paper
RERRRReEPAAVGVGPvS   escape documented in this paper
RERRRgDEPAAVGVGPAS   escape documented in this paper
RERRRgDEPAAVGVGtAS   escape documented in this paper
RERRRtDEPAAVGVGPAS   escape documented in this paper
RERRgRDEPAAVGVGPAS   escape documented in this paper
RERRRRDEsAAVGVGPAS   observed variant
REgaRerrPAAVGVGPAS   observed variant
RERRgRDEPAAVGVGPAS|r   escape documented in this paper
RERRgkDEPAAVGVGPAS|r   observed variant
RERRRtDEPAAVGVGPAS|r   escape documented in this paper
RERRRReEPAAVGVGPAS   observed variant
RERRRgDEPA.......S   escape documented in this paper
Species (MHC/HLA human

Variant Details

Showing all: 21 variant(s).


Variant ID.  2006
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRRnEPAAVGVGPAS
Mutations D/N
Epitope Location D7N
HXB2 Location D23N
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. Variant occurred at day 14, when pooled mutants were negative for response.


Variant ID.  2007
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRRnEPAAVGVGsAS
Mutations P/S D/N
Epitope Location P16S D7N
HXB2 Location P32S D23N
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.


Variant ID.  2008
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRkDEPAAVGVGPAS
Mutations R/K
Epitope Location R6K
HXB2 Location R22K
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 14. Loss of response to this specific variant was clearly documented.


Variant ID.  2009
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRkDEPAAVGVGPvS
Mutations A/V R/K
Epitope Location A17V R6K
HXB2 Location A33V R22K
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.


Variant ID.  2010
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRkRDEPAAVGVGPAS
Mutations R/K
Epitope Location R5K
HXB2 Location R21K
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at several time points, and loss of response was clearly documented.


Variant ID.  2011
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERgkRDEPAAVGVGPAS
Mutations R/G R/K
Epitope Location R4G R5K
HXB2 Location R20G R21K
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 592.


Variant ID.  2012
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERR....PAAVGVGPAS
Mutations R/. R/. D/. E/.
Epitope Location R5. R6. D7. E8.
HXB2 Location R21. R22. D23. E24.
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 32.


Variant ID.  2013
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRReEPAAVGVGPAS
Mutations D/E
Epitope Location D7E
HXB2 Location D23E
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at several time points and lack of response to variant was clearly demonstrated.


Variant ID.  2014
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  kERRRReEPAAVGVGPAS
Mutations R/K D/E
Epitope Location R1K D7E
HXB2 Location R17K D23E
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159, when patient response had been lost.


Variant ID.  2015
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRReEPAAVGVGPvS
Mutations A/V D/E
Epitope Location A17V D7E
HXB2 Location A33V D23E
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.


Variant ID.  2016
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRgDEPAAVGVGPAS
Mutations R/G
Epitope Location R6G
HXB2 Location R22G
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.


Variant ID.  2017
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRgDEPAAVGVGtAS
Mutations P/T R/G
Epitope Location P16T R6G
HXB2 Location P32T R22G
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.


Variant ID.  2018
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRtDEPAAVGVGPAS
Mutations R/T
Epitope Location R6T
HXB2 Location R22T
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.


Variant ID.  2019
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRgRDEPAAVGVGPAS
Mutations R/G
Epitope Location R5G
HXB2 Location R21G
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 159.


Variant ID.  2020
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRRDEsAAVGVGPAS
Mutations P/S
Epitope Location P9S
HXB2 Location P25S
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This newly defined epitope-containing peptide escaped CTL recognition rapidly in Patient 77. This variant occurred at day 32 when patient response was unknown.


Variant ID.  2021
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  REgaRerrPAAVGVGPAS
Mutations R/G R/A R/E D/R E/R
Epitope Location R3G R4A R6E D7R E8R
HXB2 Location R19G R20A R22E D23R E24R
Mutation Type OV: observed variant
Method Sequence
Note This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant was found at day 32.


Variant ID.  2024
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRgRDEPAAVGVGPAS|r
Mutations Q/R R/G
Epitope Location Q19R R5G
HXB2 Location Q35R R21G
Mutation Type E: escape documented in this paper
Method Sequence
Note This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.


Variant ID.  2025
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRgkDEPAAVGVGPAS|r
Mutations Q/R R/G R/K
Epitope Location Q19R R5G R6K
HXB2 Location Q35R R21G R22K
Mutation Type OV: observed variant
Method Sequence
Note This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 592.


Variant ID.  2026
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRtDEPAAVGVGPAS|r
Mutations S/R R/T
Epitope Location S18R R6T
HXB2 Location S34R R22T
Mutation Type E: escape documented in this paper
Method Sequence
Note This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.


Variant ID.  2272
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRReEPAAVGVGPAS
Mutations R/E
Epitope Location R6E
HXB2 Location R22E
Mutation Type OV: observed variant
Method Sequence
Note This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 32; escape was not documented.


Variant ID.  2334
Epitope Seq.  RERRRRDEPAAVGVGPAS
Variant Seq.  RERRRgDEPA.......S
Mutations A/. V/. G/. V/. G/. P/. A/. R/G
Epitope Location A11. V12. G13. V14. G15. P16. A17. R6G
HXB2 Location A27. V28. G29. V30. G31. P32. A33. R22G
Mutation Type E: escape documented in this paper
Method Sequence
Note This newly defined epitope-containing peptide varied rapidly in Patient 77. This variant occurred at day 159 when patient had lost EliSpot response.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56632

HXB2 Location  Nef(82-90)   Nef Epitope Map
View variants at this location
Epitope KAALDLSHF   Epitope Alignment
Variants
KgALDLSHF   diminished response
qAALDLSHF   diminished response
tAALDLSHF   observed variant
pAALDLSHF   observed variant
KAAhDLSHF   observed variant
KAALDiSHF   observed variant
{l*****}qAALDLSHF   compensatory mutation; inferred escape; processing
{*****}KgALDLSHF   compensatory mutation; inferred escape; processing
{**}KAALDLSHF   compensatory mutation; inferred escape; processing
Species (MHC/HLA human(B*57:01)

Variant Details

Showing all: 9 variant(s).


Variant ID.  1981
Epitope Seq.  KAALDLSHF
Variant Seq.  KgALDLSHF
Mutations A/G
Epitope Location A2G
HXB2 Location A83G
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Documented reduced response to this variant.


Variant ID.  1982
Epitope Seq.  KAALDLSHF
Variant Seq.  qAALDLSHF
Mutations K/Q
Epitope Location K1Q
HXB2 Location K82Q
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Documented reduced response to this variant.


Variant ID.  1983
Epitope Seq.  KAALDLSHF
Variant Seq.  tAALDLSHF
Mutations K/T
Epitope Location K1T
HXB2 Location K82T
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant arose on day 32; response unknown.


Variant ID.  1984
Epitope Seq.  KAALDLSHF
Variant Seq.  pAALDLSHF
Mutations K/P
Epitope Location K1P
HXB2 Location K82P
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant arose on day 32; response unknown.


Variant ID.  1985
Epitope Seq.  KAALDLSHF
Variant Seq.  KAAhDLSHF
Mutations L/H
Epitope Location L4H
HXB2 Location L85H
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant arose on day 32; response unknown.


Variant ID.  1986
Epitope Seq.  KAALDLSHF
Variant Seq.  KAALDiSHF
Mutations L/I
Epitope Location L6I
HXB2 Location L87I
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note Variant arose on day 32; response unknown.


Variant ID.  2326
Epitope Seq.  {V*****}KAALDLSHF
Variant Seq.  {l*****}qAALDLSHF
Mutations K/Q V/L
Epitope Location K1Q V-6L
HXB2 Location K82Q V76L
Mutation Type CM: compensatory mutation
IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This flanking substitution is predicted to be either a processing escape or a compensatory mutation.


Variant ID.  2327
Epitope Seq.  {V*****}KAALDLSHF
Variant Seq.  {*****}KgALDLSHF
Mutations A/G V/L
Epitope Location A2G V-6L
HXB2 Location A83G V76L
Mutation Type CM: compensatory mutation
IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This flanking substitution is predicted to be either a processing escape or a compensatory mutation.


Variant ID.  2328
Epitope Seq.  {M**}KAALDLSHF
Variant Seq.  {**}KAALDLSHF
Mutations M/I
Epitope Location M-3I
HXB2 Location M79I
Mutation Type CM: compensatory mutation
IE: inferred escape
P: processing
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This flanking substitution is predicted to be either a processing escape or a compensatory mutation.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56652

HXB2 Location  Nef(105-115)   Nef Epitope Map
View variants at this location
Epitope KRQDILDLWVY   Epitope Alignment
Variants
rRQDILDLWVY   diminished response
KRQeILDLWVY   diminished response
Species (MHC/HLA human(C*07:01)

Variant Details

Showing all: 2 variant(s).


Variant ID.  2070
Epitope Seq.  KRQDILDLWVY
Variant Seq.  rRQDILDLWVY
Mutations K/R
Epitope Location K1R
HXB2 Location K105R
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This nonsynonymous change, K110R showed 50% CTL response compared to index epitope sequence in Patient CH58. It could also affect processing of the downstream epitope HTQGYFPDWQ. Known T cell response from the full proteome scan with evidence for variation and escape was seen.


Variant ID.  2071
Epitope Seq.  KRQDILDLWVY
Variant Seq.  KRQeILDLWVY
Mutations D/E
Epitope Location D4E
HXB2 Location D108E
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This nonsynonymous change, K110R showed 50% CTL response compared to wild index epitope in Patient CH58. It could also affect processing of the downstream epitope HTQGYFPDWQ. Known T cell response from the full proteome scan with evidence for variation and escape was seen.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Displaying record number 56635

HXB2 Location  Nef(188-196)   Nef Epitope Map
View variants at this location
Epitope SLAFRHVAR   Epitope Alignment
Variants
nLAFRHVAR   escape documented in this paper
SLAFRHVAq   escape documented in this paper
Species (MHC/HLA human(A*31:01)

Variant Details

Showing all: 2 variant(s).


Variant ID.  1997
Epitope Seq.  SLAFRHVAR
Variant Seq.  nLAFRHVAR
Mutations S/N
Epitope Location S1N
HXB2 Location S188N
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This S188N substitution was a dominating variant in Patient CH40. The variant was not recognized by EliSpot.


Variant ID.  2271
Epitope Seq.  SLAFRHVAR
Variant Seq.  SLAFRHVAq
Mutations R/Q
Epitope Location R9Q
HXB2 Location R196Q
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy, Intracellular cytokine staining, Sequence
Note This R196Q substitution was a dominating variant in Patient CH40. The variant was not recognized by EliSpot.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.


Questions or comments? Contact us at immuno@lanl.gov
 
Managed by Triad National Security, LLC for the U.S. Department of Energy’s National Nuclear Security Administration
Copyright © 2022 Triad National Security, LLC | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health