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Found 6 matching records:

Displaying record number 57875

HXB2 Location Gag(20-29) Gag Epitope Map
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RLRPGGKKHY

`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
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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

Displaying record number 57873

HXB2 Location Gag(240-249) Gag Epitope Map
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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

Displaying record number 57878

HXB2 Location Nef(13-20) Nef Epitope Map
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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

Displaying record number 57876

HXB2 Location Nef(71-79) Nef Epitope Map
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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

Displaying record number 57874

HXB2 Location Nef(82-90) Nef Epitope Map
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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.