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Found 6 matching records:

Displaying record number 57875

HXB2 Location  Gag(20-29)   Gag Epitope Map
View variants at this location
Epitope RLRPGGKKHY   Epitope Alignment
Variants
kLRPGGKKHY   inferred escape
kLRPGGKKrY   inferred escape
RLRPGGKKrY   inferred escape
RLRPGGKKqY   inferred escape
Species (MHC/HLA human(B*42:01)

Variant Details

Showing all: 4 variant(s).


Variant ID.  2944
Epitope Seq.  RLRPGGKKHY
Variant Seq.  kLRPGGKKHY
Mutations R/K
Epitope Location R1K
HXB2 Location R20K
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject CAP 274 carried this escape in 9/9 sequences 2.4 months post-infection (Mo.PI) and in 7/7 sequences 5.1 Mo.PI.


Variant ID.  2945
Epitope Seq.  RLRPGGKKHY
Variant Seq.  kLRPGGKKrY
Mutations R/K H/R
Epitope Location R1K H9R
HXB2 Location R20K H28R
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject CAP 274 carried this escape in 19/19 sequences 13.9 months post-infection.


Variant ID.  2946
Epitope Seq.  RLRPGGKKHY
Variant Seq.  RLRPGGKKrY
Mutations H/R
Epitope Location H9R
HXB2 Location H28R
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject CAP 239 carried this escape in 4/9 sequences 18.2 months post-infection.


Variant ID.  2947
Epitope Seq.  RLRPGGKKHY
Variant Seq.  RLRPGGKKqY
Mutations H/Q
Epitope Location H9Q
HXB2 Location H28Q
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject CAP 239 carried this escape in 5/9 sequences 18.2 months post-infection.

References

Chopera2011 D. R. Chopera, M. Mlotshwa, Z. Woodman, K. Mlisana, D. de Assis Rosa, D. P. Martin, S. Abdool Karim, C. M. Gray, C. Williamson, and CAPRISA 002 Study Team. Virological and Immunological Factors Associated with HIV-1 Differential Disease Progression in HLA-B*58:01-Positive Individuals. J. Virol., 85(14):7070-7080, Jul 2011. PubMed ID: 21613398. Show all entries for this paper.


Displaying record number 57877

HXB2 Location  Gag(76-86)   Gag Epitope Map
View variants at this location
Epitope RSLYNTVATLY   Epitope Alignment
Variants
kSLYNTVATLY   inferred escape
kSLYNTVAvLY   inferred escape
Species (MHC/HLA human(A*30:02)

Variant Details

Showing all: 2 variant(s).


Variant ID.  2948
Epitope Seq.  RSLYNTVATLY
Variant Seq.  kSLYNTVATLY
Mutations R/K
Epitope Location R1K
HXB2 Location R76K
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject CAP270 carried mutation kSLYNTVATLY in 6/6 sequences 1.8 months post-infection (Mo.PI), 7/7 sequences 2.9 Mo.PI, 9/9 sequences 6.6 Mo.PI, 17/29 sequences 13.3 Mo.PI.


Variant ID.  2949
Epitope Seq.  RSLYNTVATLY
Variant Seq.  kSLYNTVAvLY
Mutations R/K T/V
Epitope Location R1K T9V
HXB2 Location R76K T84V
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject CAP270 carried mutation kSLYNTVAvLY in 12/29 sequences 13.3 months post-infection.

References

Chopera2011 D. R. Chopera, M. Mlotshwa, Z. Woodman, K. Mlisana, D. de Assis Rosa, D. P. Martin, S. Abdool Karim, C. M. Gray, C. Williamson, and CAPRISA 002 Study Team. Virological and Immunological Factors Associated with HIV-1 Differential Disease Progression in HLA-B*58:01-Positive Individuals. J. Virol., 85(14):7070-7080, Jul 2011. PubMed ID: 21613398. Show all entries for this paper.


Displaying record number 57873

HXB2 Location  Gag(240-249)   Gag Epitope Map
View variants at this location
Epitope TSTLQEQIAW   Epitope Alignment
Variants
TSTLpEQIAW   unclear
TSTLQEeIAW   unclear
TSTLQEQIAW{i}   observed variant; susceptible form
TSTLQEQItW   unclear
TSnLQEQItW   observed variant; susceptible form
TSnLQEQvAW   observed variant; susceptible form
TSTLQEQvAW   observed variant
TSTiQEQvtW   unclear
TSnLQEQvtW   susceptible form
TSTLhEQvqW   non-susceptible form
TSnLQEQvqW   non-susceptible form
TSTLtEQIAW   unclear
TSnLQEQIAW   unclear; observed variant; susceptible form
Epitope Name TW10
Species (MHC/HLA human(B*58:01)

Variant Details

Showing all: 13 variant(s).


Variant ID.  2714
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSTLpEQIAW
Mutations Q/P
Epitope Location Q5P
HXB2 Location Q244P
Mutation Type ?: unclear
Epitope Subtype C
Variant Subtype C
Method Sequence
Note 4/18 and 4/12 sampled viral sequences in subject CAP217 carried this variant, TSTLpEQIAW, 3.4 and 3.8 months post infection.


Variant ID.  2715
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSTLQEeIAW
Mutations Q/E
Epitope Location Q7E
HXB2 Location Q246E
Mutation Type ?: unclear
Epitope Subtype C
Variant Subtype C
Method Sequence
Note 1/18 sampled viral sequences in subject CAP217 carried this variant, TSTLQEeIAW, 3.4 months post infection.


Variant ID.  2716
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSTLQEQIAW{i}
Mutations M/I
Epitope Location M+1I
HXB2 Location M250I
Mutation Type OV: observed variant
SF: susceptible form
Epitope Subtype C
Variant Subtype C
Method CD8 T-cell Elispot - IFNy, Sequence
Note All sampled viral sequences in subject CAP268 carried this flanking mutation, TSTLQEQIAW{i}, 1.8, 5.5, 12.3, 19.8 and 31.4 months post infection. While this subject responded to TW10, not surprisingly no epitopic escapes were found as the M250I mutation here has been previously associated with reduced frequency of escape in TW10.


Variant ID.  2717
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSTLQEQItW
Mutations A/T
Epitope Location A9T
HXB2 Location A248T
Mutation Type ?: unclear
Epitope Subtype C
Variant Subtype C
Method Sequence
Note 2/10 sampled viral sequences in subject CAP229 carried this variant, TSTLQEQItW, 1.8 months post infection.


Variant ID.  2718
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSnLQEQItW
Mutations T/N A/T
Epitope Location T3N A9T
HXB2 Location T242N A248T
Mutation Type OV: observed variant
SF: susceptible form
Epitope Subtype C
Variant Subtype C
Method CD8 T-cell Elispot - IFNy, Sequence
Note 2/10, 6/6, 3/3, 23/23, 15/15, 24/24, 15/15 and 16/16 sampled viral sequences in subject CAP229 carried this variant, TSTLQEQItW, 1.8, 2.1, 4.8, 5.8, 18.4, 21.2, 24.2 and 28.1 months post infection. At 2.1 months post-infection, CTL response was reduced.


Variant ID.  2719
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSnLQEQvAW
Mutations T/N I/V
Epitope Location T3N I8V
HXB2 Location T242N I247V
Mutation Type OV: observed variant
SF: susceptible form
Epitope Subtype C
Variant Subtype C
Method CD8 T-cell Elispot - IFNy, Sequence
Note 9/9 and 9/9 sampled viral sequences in subject CAP239 carried this variant, TSnLQEQvAW, 5.1 and 18.2 months post infection. At 5.1 months post-infection, CTL response was reduced.


Variant ID.  2720
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSTLQEQvAW
Mutations I/V
Epitope Location I8V
HXB2 Location I247V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note 20/21 sampled viral sequences in subject CAP239 carried this variant, TSTLQEQvAW, 0.5 months post infection.


Variant ID.  2721
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSTiQEQvtW
Mutations L/I I/V A/T
Epitope Location L4I I8V A9T
HXB2 Location L243I I247V A248T
Mutation Type ?: unclear
Epitope Subtype C
Variant Subtype C
Method Sequence
Note 1/21 sampled viral sequences in subject CAP239 carried this variant, TSTiQEQvtW, 0.5 months post infection.


Variant ID.  2722
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSnLQEQvtW
Mutations T/N I/V A/T
Epitope Location T3N I8V A9T
HXB2 Location T242N I247V A248T
Mutation Type SF: susceptible form
Epitope Subtype C
Variant Subtype C
Method CD8 T-cell Elispot - IFNy, Sequence
Note 27/27 and 19/19 sampled viral sequences in subject CAP239 carried this variant, TSnLQEQvtW, 1.2 and 1.4 months post infection and CTL response when tested, was reduced.


Variant ID.  2723
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSTLhEQvqW
Mutations Q/H I/V A/Q
Epitope Location Q5H I8V A9Q
HXB2 Location Q244H I247V A248Q
Mutation Type NSF: non-susceptible form
Epitope Subtype C
Variant Subtype C
Method CD8 T-cell Elispot - IFNy, Sequence
Note 2/9 sampled viral sequences in subject CAP274 carried this variant, TSTLhEQvqW, 2.4 months post infection.


Variant ID.  2724
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSnLQEQvqW
Mutations T/N I/V A/Q
Epitope Location T3N I8V A9Q
HXB2 Location T242N I247V A248Q
Mutation Type NSF: non-susceptible form
Epitope Subtype C
Variant Subtype C
Method CD8 T-cell Elispot - IFNy, Sequence
Note All viral sequences sampled in subject CAP274 carried this variant, TSnLQEQvqW, 2.4, 5.1 and 13.9 months post infection.


Variant ID.  2725
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSTLtEQIAW
Mutations Q/T
Epitope Location Q5T
HXB2 Location Q244T
Mutation Type ?: unclear
Epitope Subtype C
Variant Subtype C
Method Sequence
Note 1/9 sampled viral sequences in subject CAP217 carried this variant, TSTLtEQIAW, 5.2 months post infection.


Variant ID.  2726
Epitope Seq.  TSTLQEQIAW
Variant Seq.  TSnLQEQIAW
Mutations T/N
Epitope Location T3N
HXB2 Location T242N
Mutation Type ?: unclear
OV: observed variant
SF: susceptible form
Epitope Subtype C
Variant Subtype C
Method CD8 T-cell Elispot - IFNy, Sequence
Note This variant at position 3, TSnLQEQIAW, was seen in subject CAP217. 6/12, 12/12, 7/9, 10/10 and 14/14 sequences carried the variant at 3.8, 4.3, 5.2, 6.2 and 13.8 months post-infection. At 4.3 months post-infection, CTL response was reduced.

References

Chopera2011 D. R. Chopera, M. Mlotshwa, Z. Woodman, K. Mlisana, D. de Assis Rosa, D. P. Martin, S. Abdool Karim, C. M. Gray, C. Williamson, and CAPRISA 002 Study Team. Virological and Immunological Factors Associated with HIV-1 Differential Disease Progression in HLA-B*58:01-Positive Individuals. J. Virol., 85(14):7070-7080, Jul 2011. PubMed ID: 21613398. Show all entries for this paper.


Displaying record number 57878

HXB2 Location  Nef(13-20)   Nef Epitope Map
View variants at this location
Epitope WPAVRERI   Epitope Alignment
Variants
WPdVRERm   inferred escape
WPnVRERm   inferred escape
WPeVRERm   inferred escape
WPnVREgm   inferred escape
WPdVREkm   inferred escape
WPdVgERm   inferred escape
Species (MHC/HLA human(B*08:01)

Variant Details

Showing all: 6 variant(s).


Variant ID.  2951
Epitope Seq.  WPAVRERI
Variant Seq.  WPdVRERm
Mutations A/D I/M
Epitope Location A3D I8M
HXB2 Location A15D I20M
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject 270 carried this mutation in 11/24 sequences 2.9 months post-infection.


Variant ID.  2952
Epitope Seq.  WPAVRERI
Variant Seq.  WPnVRERm
Mutations A/N I/M
Epitope Location A3N I8M
HXB2 Location A15N I20M
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject 270 carried this mutation 1.8 months post-infection (Mo.PI) in 24/24 sequences and in 11/24 sequences 2.9 Mo.PI.


Variant ID.  2953
Epitope Seq.  WPAVRERI
Variant Seq.  WPeVRERm
Mutations A/E I/M
Epitope Location A3E I8M
HXB2 Location A15E I20M
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject 270 carried this mutation in 21/22 sequences 13.3 months post-infection.


Variant ID.  2954
Epitope Seq.  WPAVRERI
Variant Seq.  WPnVREgm
Mutations A/N R/G I/M
Epitope Location A3N R7G I8M
HXB2 Location A15N R19G I20M
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject 270 carried this mutation in 1/24 sequences 2.9 months post-infection.


Variant ID.  2955
Epitope Seq.  WPAVRERI
Variant Seq.  WPdVREkm
Mutations A/D R/K I/M
Epitope Location A3D R7K I8M
HXB2 Location A15D R19K I20M
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject 270 carried this mutation in 1/22 sequences 13.3 months post-infection.


Variant ID.  2956
Epitope Seq.  WPAVRERI
Variant Seq.  WPdVgERm
Mutations A/D R/G I/M
Epitope Location A3D R5G I8M
HXB2 Location A15D R17G I20M
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject 270 carried this mutation in 1/24 sequences 2.9 months post-infection.

References

Chopera2011 D. R. Chopera, M. Mlotshwa, Z. Woodman, K. Mlisana, D. de Assis Rosa, D. P. Martin, S. Abdool Karim, C. M. Gray, C. Williamson, and CAPRISA 002 Study Team. Virological and Immunological Factors Associated with HIV-1 Differential Disease Progression in HLA-B*58:01-Positive Individuals. J. Virol., 85(14):7070-7080, Jul 2011. PubMed ID: 21613398. Show all entries for this paper.


Displaying record number 57876

HXB2 Location  Nef(71-79)   Nef Epitope Map
View variants at this location
Epitope RPQVPLRPM   Epitope Alignment
Variants
kPQVPLRPM   inferred escape
Species (MHC/HLA human(B*07:02)

Variant Details

Showing all: 1 variant(s).


Variant ID.  2950
Epitope Seq.  RPQVPLRPM
Variant Seq.  kPQVPLRPM
Mutations R/K
Epitope Location R1K
HXB2 Location R71K
Mutation Type IE: inferred escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Subject CAP268 carried this mutation as detected by population sequencing 5.5 months post-infection.

References

Chopera2011 D. R. Chopera, M. Mlotshwa, Z. Woodman, K. Mlisana, D. de Assis Rosa, D. P. Martin, S. Abdool Karim, C. M. Gray, C. Williamson, and CAPRISA 002 Study Team. Virological and Immunological Factors Associated with HIV-1 Differential Disease Progression in HLA-B*58:01-Positive Individuals. J. Virol., 85(14):7070-7080, Jul 2011. PubMed ID: 21613398. Show all entries for this paper.


Displaying record number 57874

HXB2 Location  Nef(82-90)   Nef Epitope Map
View variants at this location
Epitope KAAFDLSFF   Epitope Alignment
Variants
KeAFDLSFF   escape documented in this paper
{f}KAAFDLgFF   escape documented in this paper
KgAFDLSFF   escape documented in this paper
KgAvDLSFF   escape documented in this paper
rAAFDLSFF   escape documented in this paper
KAAvDLSFF   escape documented in this paper
{f}KAAFDLSFF   escape documented in this paper
-----LSFF   escape documented in this paper
Epitope Name KF9
Species (MHC/HLA human(B*58:01)

Variant Details

Showing all: 8 variant(s).


Variant ID.  2651
Epitope Seq.  KAAFDLSFF
Variant Seq.  KeAFDLSFF
Mutations A/E
Epitope Location A2E
HXB2 Location A83E
Mutation Type E: escape documented in this paper
Epitope Subtype C
Variant Subtype C
Method Longitudinal study
Note This variant, KeAFDLSFF, was seen in subject CAP217. 1/24, 13/24 and 22/22 sequences carried the variant 2.2, 5.2 and 13.8 months post-infection thus the variant reached KeAFDLSFF reached fixation by 14 months in 1/6 patients.


Variant ID.  2652
Epitope Seq.  {Y}KAAFDLSFF
Variant Seq.  {f}KAAFDLgFF
Mutations -/F S/G
Epitope Location --1F S7G
HXB2 Location -81F S88G
Mutation Type E: escape documented in this paper
Epitope Subtype C
Variant Subtype C
Method Longitudinal study, Sequence
Note This variant, from {Y}KAAFDLSFF to {f}KAAFDLgFF, was seen in subject CAP270. 1/24 and 22/22 sequences carried the variant at 2.9 and 13.3 months post-infection, the variant thus reaching fixation by 14 months.


Variant ID.  2653
Epitope Seq.  KAAFDLSFF
Variant Seq.  KgAFDLSFF
Mutations A/G
Epitope Location A2G
HXB2 Location A83G
Mutation Type E: escape documented in this paper
Epitope Subtype C
Variant Subtype C
Method Longitudinal study
Note This variant, KgAFDLSFF, was seen in 3 subjects. In subject CAP217 1/24 sequences carried the variant 5.2 months post-infection; subject CAP229 had all 24/24 sequences with the variant 18.4 months post-infection and subject CAP239 carried the variant in 6/23 sequences 18.2 months post-infection. Thus KgAFDLSFF reached fixation by 19 months in 2/6 patients.


Variant ID.  2748
Epitope Seq.  KAAFDLSFF
Variant Seq.  KgAvDLSFF
Mutations A/G F/V
Epitope Location A2G F4V
HXB2 Location A83G F85V
Mutation Type E: escape documented in this paper
Epitope Subtype C
Variant Subtype C
Method Longitudinal study
Note This variant, KgAvDLSFF, was seen in subject CAP239. 22/24 and 27/23 sequences carried the variant 5.1 and 18.2 months post-infection.


Variant ID.  2749
Epitope Seq.  KAAFDLSFF
Variant Seq.  rAAFDLSFF
Mutations K/R
Epitope Location K1R
HXB2 Location K82R
Mutation Type E: escape documented in this paper
Epitope Subtype C
Variant Subtype C
Method Longitudinal study
Note This variant, rAAFDLSFF, was seen in subject CAP229. 1/24 sequences carried the variant 5.8 months post-infection.


Variant ID.  2750
Epitope Seq.  KAAFDLSFF
Variant Seq.  KAAvDLSFF
Mutations F/V
Epitope Location F4V
HXB2 Location F85V
Mutation Type E: escape documented in this paper
Epitope Subtype C
Variant Subtype C
Method Longitudinal study
Note This variant, KAAvDLSFF, was seen in 2 subjects. In subject CAP217 2/24 sequences carried the variant 2.2 months after infection. In subject CAP239, all (i.e. 24/24 and 23/23) sequences carried the variant at 0.5 and 1.2 months post-infection.


Variant ID.  2751
Epitope Seq.  {Y}KAAFDLSFF
Variant Seq.  {f}KAAFDLSFF
Mutations Y/F
Epitope Location Y-1F
HXB2 Location Y81F
Mutation Type E: escape documented in this paper
Epitope Subtype C
Variant Subtype C
Method Longitudinal study
Note This variant in flanking sequence of KF9, {f}KAAFDLSFF, was seen in subject CAP270. 24/24 and 23/24 sequences carried the variant 1.8 and 2.9 months post-infection.


Variant ID.  2753
Epitope Seq.  KAAFDLSFF
Variant Seq.  -----LSFF
Mutations K/- A/- A/- F/- D/-
Epitope Location K1- A2- A3- F4- D5-
HXB2 Location K82- A83- A84- F85- D86-
Mutation Type E: escape documented in this paper
Epitope Subtype C
Variant Subtype C
Method Longitudinal study, Sequence
Note This deletion variant,-----LSFF, was seen in subject CAP217. 1/24 sequences carried the variant at 2.2 months post-infection.

References

Chopera2011 D. R. Chopera, M. Mlotshwa, Z. Woodman, K. Mlisana, D. de Assis Rosa, D. P. Martin, S. Abdool Karim, C. M. Gray, C. Williamson, and CAPRISA 002 Study Team. Virological and Immunological Factors Associated with HIV-1 Differential Disease Progression in HLA-B*58:01-Positive Individuals. J. Virol., 85(14):7070-7080, Jul 2011. PubMed ID: 21613398. Show all entries for this paper.


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