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Found 45 matching records:

Displaying record number 63007

HXB2 Location  Gag(113-130)   Gag Epitope Map
View variants at this location
Epitope KKAQQAAADTGNSSQVSQ   Epitope Alignment
Variants
KKAQQAAADTGNSrQVSQ   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5124
Epitope Seq.  KKAQQAAADTGNSSQVSQ
Variant Seq.  KKAQQAAADTGNSrQVSQ
Mutations S/R
Epitope Location S14R
HXB2 Location S126R
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant KKAQQAAADTGNSrQVSQ was observed, along with index peptide, at 6 mo following onset of symptoms, although response was no longer detected by 2 mo FOSx.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53223

HXB2 Location  Gag(119-127)   Gag Epitope Map
View variants at this location
Epitope AADTGNSSQ   Epitope Alignment
Variants
AADTGNgSQ   escape documented in this paper
eADTGNSSQ   escape documented in this paper
AADTkNSSQ   escape documented in this paper
AADTrNSSQ   escape documented in this paper
eADTGkSSQ   escape documented in this paper
AADTGNSSk   escape documented in this paper
AADTGsSSQ   escape documented in this paper
tADTGNSns   escape documented in this paper
AADTGNnnQ   escape documented in this paper
A-DTGNSSQ   observed variant
AAgTGNSSQ   observed variant
AADTeNSSQ   observed variant
AADTGN-S-(ss)   escape documented in this paper
tADTGN-Sn(s)   escape documented in this paper
AADTGNnS(ns)Q   observed variant
AADTGN-S(ss)Q   escape documented in this paper
Epitope Name Gag AQ9
Species (MHC/HLA human

Variant Details

Showing all: 16 variant(s).


Variant ID.  507
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTGNgSQ
Mutations S/G
Epitope Location S7G
HXB2 Location S125G
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  508
Epitope Seq.  AADTGNSSQ
Variant Seq.  eADTGNSSQ
Mutations A/E
Epitope Location A1E
HXB2 Location A119E
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  509
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTkNSSQ
Mutations G/K
Epitope Location G5K
HXB2 Location G123K
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  510
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTrNSSQ
Mutations G/R
Epitope Location G5R
HXB2 Location G123R
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  511
Epitope Seq.  AADTGNSSQ
Variant Seq.  eADTGkSSQ
Mutations A/E N/K
Epitope Location A1E N6K
HXB2 Location A119E N124K
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  512
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTGNSSk
Mutations Q/K
Epitope Location Q9K
HXB2 Location Q127K
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  513
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTGsSSQ
Mutations N/S
Epitope Location N6S
HXB2 Location N124S
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  514
Epitope Seq.  AADTGNSSQ
Variant Seq.  tADTGNSns
Mutations A/T S/N Q/S
Epitope Location A1T S8N Q9S
HXB2 Location A119T S126N Q127S
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  515
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTGNnnQ
Mutations S/N S/N
Epitope Location S7N S8N
HXB2 Location S125N S126N
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  516
Epitope Seq.  AADTGNSSQ
Variant Seq.  A-DTGNSSQ
Mutations A/-
Epitope Location A2-
HXB2 Location A120-
Mutation Type OV: observed variant
Note 1/15 clones at time point 35.


Variant ID.  517
Epitope Seq.  AADTGNSSQ
Variant Seq.  AAgTGNSSQ
Mutations D/G
Epitope Location D3G
HXB2 Location D121G
Mutation Type OV: observed variant
Note 1/15 clones at time point 55.


Variant ID.  518
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTeNSSQ
Mutations G/E
Epitope Location G5E
HXB2 Location G123E
Mutation Type OV: observed variant
Note 2/15 clones at time point 55 and 1/15 clones at time point 65.


Variant ID.  2285
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTGN-S-(ss)
Mutations S/- Q/- -/S -/S
Epitope Location S7- Q9- -(9.1)S -(9.2)S
HXB2 Location S125- Q127- -(127.1)S -(127.2)S
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  2287
Epitope Seq.  AADTGNSSQ
Variant Seq.  tADTGN-Sn(s)
Mutations A/T S/- Q/N -/S
Epitope Location A1T S7- Q9N -(9.1)S
HXB2 Location A119T S125- Q127N -(127.1)S
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.


Variant ID.  2288
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTGNnS(ns)Q
Mutations S/N -/N -/S
Epitope Location S7N -(8.1)N -(8.2)S
HXB2 Location S125N -(126.1)N -(126.2)S
Mutation Type OV: observed variant
Note 1/15 clones at time point 556.


Variant ID.  2299
Epitope Seq.  AADTGNSSQ
Variant Seq.  AADTGN-S(ss)Q
Mutations S/- -/S -/S
Epitope Location S7- -(8.1)S -(8.2)S
HXB2 Location S125- -(126.1)S -(126.2)S
Mutation Type E: escape documented in this paper
Note Variant dramatically reduced CTL recognition.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53224

HXB2 Location  Gag(124-133)   Gag Epitope Map
View variants at this location
Epitope NSSQVSQNYP   Epitope Alignment
Variants
NgSQVSQNYP   diminished response
NSSQaSQNYP   diminished response
sSSQVSQNYP   diminished response
NSSQdSQNYP   diminished response
NSSQgSQNYP   diminished response
kSSQVSQNYP   diminished response
NSSkVSQNYP   diminished response
NmnQVSQNYP   diminished response
NSS(s)QVSQNYP   diminished response
NS(n)SQVSQNYP   diminished response
NnS(ns)QVSQNYP   diminished response
Epitope Name Gag NP10
Species (MHC/HLA human

Variant Details

Showing all: 11 variant(s).


Variant ID.  519
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NgSQVSQNYP
Mutations S/G
Epitope Location S2G
HXB2 Location S125G
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  520
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NSSQaSQNYP
Mutations V/A
Epitope Location V5A
HXB2 Location V128A
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  521
Epitope Seq.  NSSQVSQNYP
Variant Seq.  sSSQVSQNYP
Mutations N/S
Epitope Location N1S
HXB2 Location N124S
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  522
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NSSQdSQNYP
Mutations V/D
Epitope Location V5D
HXB2 Location V128D
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  523
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NSSQgSQNYP
Mutations V/G
Epitope Location V5G
HXB2 Location V128G
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  524
Epitope Seq.  NSSQVSQNYP
Variant Seq.  kSSQVSQNYP
Mutations N/K
Epitope Location N1K
HXB2 Location N124K
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  525
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NSSkVSQNYP
Mutations Q/K
Epitope Location Q4K
HXB2 Location Q127K
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  526
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NmnQVSQNYP
Mutations S/M S/N
Epitope Location S2M S3N
HXB2 Location S125M S126N
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  2289
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NSS(s)QVSQNYP
Mutations -/S
Epitope Location -(3.1)S
HXB2 Location -(126.1)S
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  2290
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NS(n)SQVSQNYP
Mutations -/N
Epitope Location -(2.1)N
HXB2 Location -(125.1)N
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.


Variant ID.  2291
Epitope Seq.  NSSQVSQNYP
Variant Seq.  NnS(ns)QVSQNYP
Mutations S/N -/N -/S
Epitope Location S2N -(3.1)N -(3.2)S
HXB2 Location S125N -(126.1)N -(126.2)S
Mutation Type DR: diminished response
Note Confirmed some degree of escape by diminishing CTL response.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 62978

HXB2 Location  Gag(138-156)   Gag Epitope Map
View variants at this location
Epitope LQGQMVHQALSPRTLNAWV   Epitope Alignment
Variants
LQGQMVHQAiSPRTLNAWV   susceptible form
LQGQMVHQAipPRTLNAWV   observed variant
LQGQMVHrAiSPRTLNAWV   observed variant
LQGQMVHQAiSlRTLNAWV   observed variant
LQGQMiHQAiSPRTLNAWV   observed variant
Epitope Name Gag 138-156
Species (MHC/HLA human

Variant Details

Showing all: 5 variant(s).


Variant ID.  5089
Epitope Seq.  LQGQMVHQALSPRTLNAWV
Variant Seq.  LQGQMVHQAiSPRTLNAWV
Mutations L/I
Epitope Location L10I
HXB2 Location L147I
Mutation Type SF: susceptible form
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Chromium-release assay, Longitudinal study
Note Autologous susceptible form LQGQMVHQAiSPRTLNAWV was first observed in 9/15 clones at 17 days from the onset of symptoms (DFOSx) and persisted at frequencies of 13-15 per 15 clones through 556 DFOSx.


Variant ID.  5090
Epitope Seq.  LQGQMVHQALSPRTLNAWV
Variant Seq.  LQGQMVHQAipPRTLNAWV
Mutations L/I S/P
Epitope Location L10I S11P
HXB2 Location L147I S148P
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant LQGQMVHQAipPRTLNAWV was observed in 1/15 clones on 17 & 556 days from the onset of symptoms but was not observed in 5 intervening timepoints.


Variant ID.  5091
Epitope Seq.  LQGQMVHQALSPRTLNAWV
Variant Seq.  LQGQMVHrAiSPRTLNAWV
Mutations L/I Q/R
Epitope Location L10I Q8R
HXB2 Location L147I Q145R
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant LQGQMVHrAiSPRTLNAWV was observed in 1/15 clones in 1/6 sampled timepoints (35 days from the onset of symptoms).


Variant ID.  5092
Epitope Seq.  LQGQMVHQALSPRTLNAWV
Variant Seq.  LQGQMVHQAiSlRTLNAWV
Mutations L/I P/L
Epitope Location L10I P12L
HXB2 Location L147I P149L
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant LQGQMVHQAiSlRTLNAWV was observed in 1/15 clones in 1/6 sampled timepoints (65 days from the onset of symptoms).


Variant ID.  5093
Epitope Seq.  LQGQMVHQALSPRTLNAWV
Variant Seq.  LQGQMiHQAiSPRTLNAWV
Mutations L/I V/I
Epitope Location L10I V6I
HXB2 Location L147I V143I
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant LQGQMiHQAiSPRTLNAWV was observed in 1/15 clones on the last of 6 sampled timepoints (556 days from the onset of symptoms).

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 57555

HXB2 Location  Gag(240-249)   Gag Epitope Map
View variants at this location
Epitope TSTLQEQIGW   Epitope Alignment
Variants
TSnLQEQIGW   escape documented in this paper
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  2527
Epitope Seq.  TSTLQEQIGW
Variant Seq.  TSnLQEQIGW
Mutations T/N
Epitope Location T3N
HXB2 Location T242N
Mutation Type E: escape documented in this paper
Epitope Subtype B
Variant Subtype B
Method CD4 T-cell Elispot - IFNy
Note The variant TSnLQEQIGW evolved to dominate the quasispecies, and was not recognized compared to the index peptide TSTLQEQIGW by the PBMC from time points around the time of response decline, indicating escape.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63010

HXB2 Location  Gag(429-446)   Gag Epitope Map
View variants at this location
Epitope RQANFLGKIWPPHKGRPG   Epitope Alignment
Variants
RQANFLGKIWsPHKGRPG   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5139
Epitope Seq.  RQANFLGKIWPPHKGRPG
Variant Seq.  RQANFLGKIWsPHKGRPG
Mutations P/S
Epitope Location P11S
HXB2 Location P439S
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Note Autologous variant RQANFLGKIWsPHKGRPG was observed at 6 months following onset of symptoms in patient MM43.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63040

HXB2 Location  Pol(81-98)   Pol Epitope Map
View variants at this location
Epitope DTGADDTVLEEMNLPGRW   Epitope Alignment
Variants
DTGADDTVLEdMNLPGRW   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5123
Epitope Seq.  DTGADDTVLEEMNLPGRW
Variant Seq.  DTGADDTVLEdMNLPGRW
Mutations E/D
Epitope Location E11D
HXB2 Location E91D
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant DTGADDTVLEdMNLPGRW was observed at 6 months following symptom onset in patient MM33.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63043

HXB2 Location  Pol(417-434)   Pol Epitope Map
View variants at this location
Epitope GKLNWASQIYAGIKVKQL   Epitope Alignment
Variants
GKLNWASQIYAGIKVrQL   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5147
Epitope Seq.  GKLNWASQIYAGIKVKQL
Variant Seq.  GKLNWASQIYAGIKVrQL
Mutations K/R
Epitope Location K16R
HXB2 Location K432R
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note In MM33, autologous variant GKLNWASQIYAGIKVrQL was observed at 6 mo following onset of symptoms.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63026

HXB2 Location  Pol(825-842)   Pol Epitope Map
View variants at this location
Epitope VKAIHTDNGSNFTSAAVK   Epitope Alignment
Variants
VKAIHTDNGSNFiSAAVK   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5122
Epitope Seq.  VKAIHTDNGSNFTSAAVK
Variant Seq.  VKAIHTDNGSNFiSAAVK
Mutations T/I
Epitope Location T13I
HXB2 Location T837I
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant VKAIHTDNGSNFiSAAVK was observed at 6 months following onset of symptoms in patient MM33.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63091

HXB2 Location  Vif(111-130)   Vif Epitope Map
View variants at this location
Epitope YFDCFSESAIRNAILGHIVS   Epitope Alignment
Variants
DCFSESAIRgAILGHIVS   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5109
Epitope Seq.  YFDCFSESAIRNAILGHIVS
Variant Seq.  DCFSESAIRgAILGHIVS
Mutations N/G
Epitope Location N10G
HXB2 Location N120G
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note Autologous variant DCFSESAIRgAILGHIVS, with a 2 AA truncation on the N-terminus relative to B cons, elicited a response in B-subtype acutely-infected patient MM43.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63081

HXB2 Location  Vif(113-130)   Vif Epitope Map
View variants at this location
Epitope DCFSESAIRGAILGHIVS   Epitope Alignment
Variants
YFDCFSESAIRnAILGHIVS   observed variant
DCFSdSAIRGAILGHIVS   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 2 variant(s).


Variant ID.  5110
Epitope Seq.  DCFSESAIRGAILGHIVS
Variant Seq.  YFDCFSESAIRnAILGHIVS
Mutations G/N
Epitope Location G10N
HXB2 Location G122N
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note B cons variant (YF)DCFSESAIRnAILGHIVS, with a 2 AA N-terminus extension relative to B cons indicated by parentheses, elicited a response in B-subtype acutely infected patient MM50.


Variant ID.  5137
Epitope Seq.  DCFSESAIRGAILGHIVS
Variant Seq.  DCFSdSAIRGAILGHIVS
Mutations E/D
Epitope Location E5D
HXB2 Location E117D
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note Autologous variant DCFSdSAIRGAILGHIVS was observed at 6 mo following onset of symptoms in patient MM43.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63082

HXB2 Location  Vpr(9-26)   Vpr Epitope Map
View variants at this location
Epitope GPQREPFNEWTLELLEEL   Epitope Alignment
Variants
GPQRgPFNEWTLELLEEL   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5133
Epitope Seq.  GPQREPFNEWTLELLEEL
Variant Seq.  GPQRgPFNEWTLELLEEL
Mutations E/G
Epitope Location E5G
HXB2 Location E13G
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant GPQRgPFNEWTLELLEEL was observed, along with the index sequence, at 6 months following onset of symptoms.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63083

HXB2 Location  Vpr(73-90)   Vpr Epitope Map
View variants at this location
Epitope RIGCQHSRIGIIQRRRAR   Epitope Alignment
Variants
RIGCQHSRIGvIQRRRAR   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5132
Epitope Seq.  RIGCQHSRIGIIQRRRAR
Variant Seq.  RIGCQHSRIGvIQRRRAR
Mutations I/V
Epitope Location I11V
HXB2 Location I83V
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant RIGCQHSRIGvIQRRRAR was observed at 6 months following onset of symptoms.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53225

HXB2 Location  Tat(24-32)   Tat Epitope Map
View variants at this location
Epitope NCYCKKCCY   Epitope Alignment
Variants
kCYCKKCCY   escape documented in this paper
kCYCKrCCY   escape documented in this paper
kCYCKqCCY   escape documented in this paper
NCYCKKyCY   observed variant
NCYCKKCCc   observed variant
NCYCKrCCf   susceptible form
Epitope Name Tat NY9
Species (MHC/HLA human(A*29:02)

Variant Details

Showing all: 6 variant(s).


Variant ID.  527
Epitope Seq.  NCYCKKCCY
Variant Seq.  kCYCKKCCY
Mutations N/K
Epitope Location N1K
HXB2 Location N24K
Mutation Type E: escape documented in this paper
Note Variant appeared by day 31, dramatically reduced CTL recognition.


Variant ID.  528
Epitope Seq.  NCYCKKCCY
Variant Seq.  kCYCKrCCY
Mutations N/K K/R
Epitope Location N1K K6R
HXB2 Location N24K K29R
Mutation Type E: escape documented in this paper
Note Variant appeared by day 218, dramatically reduced CTL recognition.


Variant ID.  529
Epitope Seq.  NCYCKKCCY
Variant Seq.  kCYCKqCCY
Mutations N/K K/Q
Epitope Location N1K K6Q
HXB2 Location N24K K29Q
Mutation Type E: escape documented in this paper
Note Variant appeared by day 556, dramatically reduced CTL recognition.


Variant ID.  530
Epitope Seq.  NCYCKKCCY
Variant Seq.  NCYCKKyCY
Mutations C/Y
Epitope Location C7Y
HXB2 Location C30Y
Mutation Type OV: observed variant
Note 1/23 clones, transiently present at day 55.


Variant ID.  531
Epitope Seq.  NCYCKKCCY
Variant Seq.  NCYCKKCCc
Mutations Y/C
Epitope Location Y9C
HXB2 Location Y32C
Mutation Type OV: observed variant
Note 2/23 clones, transiently present at day 55.


Variant ID.  5094
Epitope Seq.  NCYCKKCCY
Variant Seq.  NCYCKrCCf
Mutations K/R Y/F
Epitope Location K6R Y9F
HXB2 Location K29R Y32F
Mutation Type SF: susceptible form
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Chromium-release assay
Note Please see CTL record #53233 for mutations in corresponding autologous variant NCYCKrCCf observed in subtype B-infected patient WEAU.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53233

HXB2 Location  Tat(24-32)   Tat Epitope Map
View variants at this location
Epitope NCYCKRCCF   Epitope Alignment
Variants
kCYCKRCCF   escape documented in this paper
NCYCKkCCF   observed variant
tCYCKRCCF   observed variant
kCYCKsCCF   observed variant
kCYCKkCCF   observed variant
NCYCKkCCy   susceptible form
Epitope Name Tat NF9
Species (MHC/HLA human(A*29:02)

Variant Details

Showing all: 6 variant(s).


Variant ID.  532
Epitope Seq.  NCYCKRCCF
Variant Seq.  kCYCKRCCF
Mutations N/K
Epitope Location N1K
HXB2 Location N24K
Mutation Type E: escape documented in this paper
Note The CTL response diminished in vivo as this variant appeared. The variant was evident by day 72.


Variant ID.  533
Epitope Seq.  NCYCKRCCF
Variant Seq.  NCYCKkCCF
Mutations R/K
Epitope Location R6K
HXB2 Location R29K
Mutation Type OV: observed variant
Note 1/7 clones, variant evident in samples taken at day 391.


Variant ID.  534
Epitope Seq.  NCYCKRCCF
Variant Seq.  tCYCKRCCF
Mutations N/T
Epitope Location N1T
HXB2 Location N24T
Mutation Type OV: observed variant
Note 5/7 clones, variant evident in samples taken at day 772.


Variant ID.  535
Epitope Seq.  NCYCKRCCF
Variant Seq.  kCYCKsCCF
Mutations N/K R/S
Epitope Location N1K R6S
HXB2 Location N24K R29S
Mutation Type OV: observed variant
Note 1/9 clones, variant evident in samples taken at day 772.


Variant ID.  536
Epitope Seq.  NCYCKRCCF
Variant Seq.  kCYCKkCCF
Mutations N/K R/K
Epitope Location N1K R6K
HXB2 Location N24K R29K
Mutation Type OV: observed variant
Note 1/9 clones, variant evident in samples taken at day 772.


Variant ID.  5095
Epitope Seq.  NCYCKRCCF
Variant Seq.  NCYCKkCCy
Mutations R/K F/Y
Epitope Location R6K F9Y
HXB2 Location R29K F32Y
Mutation Type SF: susceptible form
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note Please see CTL record #53225 for mutations in corresponding autologous variant NCYCKkCCy observed in subtype B-infected patient BORI.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63078

HXB2 Location  Tat(31-50)   Tat Epitope Map
View variants at this location
Epitope CFHCQVCFITKGLGISYGRK   Epitope Alignment
Variants
HCQVCFIsKGLGISYGRK   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5111
Epitope Seq.  CFHCQVCFITKGLGISYGRK
Variant Seq.  HCQVCFIsKGLGISYGRK
Mutations T/S
Epitope Location T10S
HXB2 Location T40S
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note Autologous variant HCQVCFIsKGLGISYGRK, with a 2 AA N-terminus truncation, elicited a CTL response in subtype B acutely-infected patient MM39.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53235

HXB2 Location  Tat(32-41)   Tat Epitope Map
View variants at this location
Epitope FHCQVCFMTK   Epitope Alignment
Variants
FHCQVCFtTK   escape documented in this paper
FHCQVCFtTe   observed variant
lHCQVCFMkK   escape documented in this paper
Epitope Name Tat FK10
Species (MHC/HLA human

Variant Details

Showing all: 3 variant(s).


Variant ID.  537
Epitope Seq.  FHCQVCFMTK
Variant Seq.  FHCQVCFtTK
Mutations M/T
Epitope Location M8T
HXB2 Location M39T
Mutation Type E: escape documented in this paper
Note The variant was evident during acute phase of infection. The substitution abrogated responses to the epitope.


Variant ID.  538
Epitope Seq.  FHCQVCFMTK
Variant Seq.  FHCQVCFtTe
Mutations K/E M/T
Epitope Location K10E M8T
HXB2 Location K41E M39T
Mutation Type OV: observed variant
Note 1/20 clones, variant found at time point 20.


Variant ID.  539
Epitope Seq.  FHCQVCFMTK
Variant Seq.  lHCQVCFMkK
Mutations F/L T/K
Epitope Location F1L T9K
HXB2 Location F32L T40K
Mutation Type E: escape documented in this paper
Note The double mutation was evident at day 69 and the variant was not recognized.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63080

HXB2 Location  Tat(33-50)   Tat Epitope Map
View variants at this location
Epitope HCQVCFISKGLGISYGRK   Epitope Alignment
Variants
CFHCQVCFItKGLGISYGRK   observed variant
HCQVCFISKGLGIpYGRK   observed variant
HCQVCFISKGLGIn-GRK   observed variant
HCQVCFISKGLGIS-GRK   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 4 variant(s).


Variant ID.  5112
Epitope Seq.  HCQVCFISKGLGISYGRK
Variant Seq.  CFHCQVCFItKGLGISYGRK
Mutations S/T
Epitope Location S8T
HXB2 Location S40T
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note B cons variant (CF)HCQVCFItKGLGISYGRK, with a 2 AA N-terminus extension relative to B cons indicated by parentheses, elicited a CTL response in patient MM48 with mutational escape within the nested epitope ITKGLGISY suggested by Fig. 5 of Turnbull2009.


Variant ID.  5126
Epitope Seq.  HCQVCFISKGLGISYGRK
Variant Seq.  HCQVCFISKGLGIpYGRK
Mutations S/P
Epitope Location S14P
HXB2 Location S46P
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant HCQVCFISKGLGIpYGRK was observed in MM39 at 6 mo following onset of symptoms.


Variant ID.  5127
Epitope Seq.  HCQVCFISKGLGISYGRK
Variant Seq.  HCQVCFISKGLGIn-GRK
Mutations S/N Y/-
Epitope Location S14N Y15-
HXB2 Location S46N Y47-
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant HCQVCFISKGLGIn-GRK was observed in MM39 at 6 mo following onset of symptoms.


Variant ID.  5128
Epitope Seq.  HCQVCFISKGLGISYGRK
Variant Seq.  HCQVCFISKGLGIS-GRK
Mutations Y/-
Epitope Location Y15-
HXB2 Location Y47-
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant HCQVCFISKGLGIS-GRK was observed in MM39 at 6 mo following onset of symptoms.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53236

HXB2 Location  Tat(36-45)   Tat Epitope Map
View variants at this location
Epitope VCFMTKGLGI   Epitope Alignment
Variants
VCFtTKGLGI   escape documented in this paper
VCFtTeGLGI   observed variant
VCFMkKGLGI   escape documented in this paper
Epitope Name Tat VI10
Species (MHC/HLA human(B*15:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  540
Epitope Seq.  VCFMTKGLGI
Variant Seq.  VCFtTKGLGI
Mutations M/T
Epitope Location M4T
HXB2 Location M39T
Mutation Type E: escape documented in this paper
Note The variant was evident during acute phase of infection. The substitution abrogated responses to the epitope.


Variant ID.  541
Epitope Seq.  VCFMTKGLGI
Variant Seq.  VCFtTeGLGI
Mutations M/T K/E
Epitope Location M4T K6E
HXB2 Location M39T K41E
Mutation Type OV: observed variant
Note 1/20 clones, variant found at time point 20.


Variant ID.  542
Epitope Seq.  VCFMTKGLGI
Variant Seq.  VCFMkKGLGI
Mutations T/K
Epitope Location T5K
HXB2 Location T40K
Mutation Type E: escape documented in this paper
Note The mutation was evident at day 69 and the variant was not recognized.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53237

HXB2 Location  Tat(39-47)   Tat Epitope Map
View variants at this location
Epitope MTKGLGISY   Epitope Alignment
Variants
tTKGLGISY   susceptible form
tTeGLGISY   observed variant
MkKGLGISY   inferred escape; processing
Epitope Name Tat MY9
Species (MHC/HLA human(B*15:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  543
Epitope Seq.  MTKGLGISY
Variant Seq.  tTKGLGISY
Mutations M/T
Epitope Location M1T
HXB2 Location M39T
Mutation Type SF: susceptible form
Note The variant was evident during acute phase of infection. The substitution did not abrogate responses to the epitope.


Variant ID.  544
Epitope Seq.  MTKGLGISY
Variant Seq.  tTeGLGISY
Mutations M/T K/E
Epitope Location M1T K3E
HXB2 Location M39T K41E
Mutation Type OV: observed variant
Note 1/20 clones, variant found at time point 20.


Variant ID.  545
Epitope Seq.  MTKGLGISY
Variant Seq.  MkKGLGISY
Mutations T/K
Epitope Location T2K
HXB2 Location T40K
Mutation Type IE: inferred escape
P: processing
Note This mutation was evident at day 69. CTL response was strong to the variant, but the substitution seemed to impact processing of the epitope.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63079

HXB2 Location  Rev(65-82)   Rev Epitope Map
View variants at this location
Epitope GRPAEPVPLQLPPLERLT   Epitope Alignment
Variants
GRPtEPVPLQLPPLERLT   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5148
Epitope Seq.  GRPAEPVPLQLPPLERLT
Variant Seq.  GRPtEPVPLQLPPLERLT
Mutations A/T
Epitope Location A4T
HXB2 Location A68T
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note At 6 mo FOSx, autologous variant GRPtEPVPLQLPPLERLT was observed, along with index peptide, in patient MM45.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 57556

HXB2 Location  Rev(66-75)   Rev Epitope Map
View variants at this location
Epitope RPAELVLQL   Epitope Alignment
Variants
RstELVLQL   escape documented in this paper
RPtAELVLQL   escape documented in this paper
Species (MHC/HLA human

Variant Details

Showing all: 2 variant(s).


Variant ID.  2528
Epitope Seq.  RPAELVLQL
Variant Seq.  RstELVLQL
Mutations P/S A/T
Epitope Location P2S A3T
HXB2 Location P67S A68T
Mutation Type E: escape documented in this paper
Epitope Subtype B
Variant Subtype B
Method CD4 T-cell Elispot - IFNy
Note The variants RstELVLQL and RPtAELVLQL evolved to dominate the quasispecies, and were less well recognized than the index peptide by the PBMC from time points around the time of response decline, indicating escape.


Variant ID.  2529
Epitope Seq.  RPAELVLQL
Variant Seq.  RPtAELVLQL
Mutations -/T
Epitope Location -2T
HXB2 Location -67T
Mutation Type E: escape documented in this paper
Epitope Subtype B
Variant Subtype B
Method CD4 T-cell Elispot - IFNy
Note The variants RstELVLQL and RPtAELVLQL evolved to dominate the quasispecies, and were less well recognized than the index peptide by the PBMC from time points around the time of response decline, indicating escape.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 62955

HXB2 Location  gp160(1-19)   gp160 Epitope Map
View variants at this location
Epitope MKVKGIRKNWHNLGKWGS   Epitope Alignment
Variants
MKVrGIRKNWHNLGKWGS   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5131
Epitope Seq.  MKVKGIRKNWHNLGKWGS
Variant Seq.  MKVrGIRKNWHNLGKWGS
Mutations K/R
Epitope Location K4R
HXB2 Location K4R
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant MKVrGIRKNWHNLGKWGS was observed at 6 mo following onset of symptoms in patient MM43.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 62981

HXB2 Location  gp160(6-20)   gp160 Epitope Map
View variants at this location
Epitope NYQHLWRGGIMLLWRGIM   Epitope Alignment
Variants
NYQHLWRGGIsLLWRGIM   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5138
Epitope Seq.  NYQHLWRGGIMLLWRGIM
Variant Seq.  NYQHLWRGGIsLLWRGIM
Mutations M/S
Epitope Location M11S
HXB2 Location M16S
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note Autologous variant NYQHLWRGGIsLLWRGIM was observed at 6 months following onset of symptoms in patient MM43.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53226

HXB2 Location  gp160(31-39)   gp160 Epitope Map
View variants at this location
Epitope AENLWVTVY   Epitope Alignment
Variants
AaNLWVTaY   diminished response
AEkLWVTVY   diminished response
AENLgVTVY   diminished response
tENLWVTVY   susceptible form
vENsWVTVY   diminished response
tEkLWVTVY   diminished response
AgNLWVTVY   diminished response
AaNLWVTVY   escape documented in this paper
AkNLWVTVY   escape documented in this paper
tENLWVTiY   susceptible form
Epitope Name gp160 AY9
Species (MHC/HLA human(B*44:03)

Variant Details

Showing all: 10 variant(s).


Variant ID.  546
Epitope Seq.  AENLWVTVY
Variant Seq.  AaNLWVTaY
Mutations E/A V/A
Epitope Location E2A V8A
HXB2 Location E32A V38A
Mutation Type DR: diminished response
Note Confirmed some degree of escape by reduction of CTL response.


Variant ID.  547
Epitope Seq.  AENLWVTVY
Variant Seq.  AEkLWVTVY
Mutations N/K
Epitope Location N3K
HXB2 Location N33K
Mutation Type DR: diminished response
Note Confirmed some degree of escape by reduction of CTL response.


Variant ID.  548
Epitope Seq.  AENLWVTVY
Variant Seq.  AENLgVTVY
Mutations W/G
Epitope Location W5G
HXB2 Location W35G
Mutation Type DR: diminished response
Note Confirmed some degree of escape by reduction of CTL response.


Variant ID.  549
Epitope Seq.  AENLWVTVY
Variant Seq.  tENLWVTVY
Mutations A/T
Epitope Location A1T
HXB2 Location A31T
Mutation Type SF: susceptible form
Note Variant did not diminish CTL response.


Variant ID.  550
Epitope Seq.  AENLWVTVY
Variant Seq.  vENsWVTVY
Mutations A/V L/S
Epitope Location A1V L4S
HXB2 Location A31V L34S
Mutation Type DR: diminished response
Note Confirmed some degree of escape by reduction of CTL response.


Variant ID.  551
Epitope Seq.  AENLWVTVY
Variant Seq.  tEkLWVTVY
Mutations A/T N/K
Epitope Location A1T N3K
HXB2 Location A31T N33K
Mutation Type DR: diminished response
Note Confirmed some degree of escape by reduction of CTL response.


Variant ID.  552
Epitope Seq.  AENLWVTVY
Variant Seq.  AgNLWVTVY
Mutations E/G
Epitope Location E2G
HXB2 Location E32G
Mutation Type DR: diminished response
Note Confirmed some degree of escape by reduction of CTL response.


Variant ID.  553
Epitope Seq.  AENLWVTVY
Variant Seq.  AaNLWVTVY
Mutations E/A
Epitope Location E2A
HXB2 Location E32A
Mutation Type E: escape documented in this paper
Note Confirmed escape by dramatic decrease in CTL response.


Variant ID.  554
Epitope Seq.  AENLWVTVY
Variant Seq.  AkNLWVTVY
Mutations E/K
Epitope Location E2K
HXB2 Location E32K
Mutation Type E: escape documented in this paper
Note Confirmed escape by dramatic decrease in CTL response.


Variant ID.  555
Epitope Seq.  AENLWVTVY
Variant Seq.  tENLWVTiY
Mutations A/T V/I
Epitope Location A1T V8I
HXB2 Location A31T V38I
Mutation Type SF: susceptible form
Note Elicited strong CTL response

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53219

HXB2 Location  gp160(209-217)   gp160 Epitope Map
View variants at this location
Epitope SFEPIPIHY   Epitope Alignment
Variants
SFdPIPIHY   diminished response
SFEPIPIHf   diminished response
SiEPIPIHf   diminished response
tFEPIPIHY   diminished response
SsEPIPIHY   observed variant
SFEPIPInY   observed variant
SFEPIPIdf   observed variant
Epitope Name gp160 SY9
Species (MHC/HLA human(A*29:02)

Variant Details

Showing all: 7 variant(s).


Variant ID.  556
Epitope Seq.  SFEPIPIHY
Variant Seq.  SFdPIPIHY
Mutations E/D
Epitope Location E3D
HXB2 Location E211D
Mutation Type DR: diminished response
Note Confirmed some degree of escape by reduction of CTL response.


Variant ID.  557
Epitope Seq.  SFEPIPIHY
Variant Seq.  SFEPIPIHf
Mutations Y/F
Epitope Location Y9F
HXB2 Location Y217F
Mutation Type DR: diminished response
Note Variant found in two patients, somewhat reduced CTL response.


Variant ID.  558
Epitope Seq.  SFEPIPIHY
Variant Seq.  SiEPIPIHf
Mutations F/I Y/F
Epitope Location F2I Y9F
HXB2 Location F210I Y217F
Mutation Type DR: diminished response
Note Rare form found at day 218. Weakest CTL response.


Variant ID.  559
Epitope Seq.  SFEPIPIHY
Variant Seq.  tFEPIPIHY
Mutations S/T
Epitope Location S1T
HXB2 Location S209T
Mutation Type DR: diminished response
Note Confirmed some degree of escape by reduction of CTL response.


Variant ID.  560
Epitope Seq.  SFEPIPIHY
Variant Seq.  SsEPIPIHY
Mutations F/S
Epitope Location F2S
HXB2 Location F210S
Mutation Type OV: observed variant
Note 1/10 clones present at time point 41.


Variant ID.  561
Epitope Seq.  SFEPIPIHY
Variant Seq.  SFEPIPInY
Mutations H/N
Epitope Location H8N
HXB2 Location H216N
Mutation Type OV: observed variant
Note 7/34 clones present at time point 212 and 4/14 clones at time point 295.


Variant ID.  562
Epitope Seq.  SFEPIPIHY
Variant Seq.  SFEPIPIdf
Mutations H/D Y/F
Epitope Location H8D Y9F
HXB2 Location H216D Y217F
Mutation Type OV: observed variant
Note 1/11 clones present at time point 136.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63072

HXB2 Location  gp160(213-230)   gp160 Epitope Map
View variants at this location
Epitope IPIHYCAPAGFAILKCNN   Epitope Alignment
Variants
IPIHYCAPAGFAILKCNdKK   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5102
Epitope Seq.  IPIHYCAPAGFAILKCNN
Variant Seq.  IPIHYCAPAGFAILKCNdKK
Mutations N/D
Epitope Location N18D
HXB2 Location N230D
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note B cons peptide IPIHYCAPAGFAILKCNd(KK), with a 2 AA C-terminus extension, elicited a CTL response in 1/14 patients (MM48) assessed for B cons peptides.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 62952

HXB2 Location  gp160(213-232)   gp160 Epitope Map
View variants at this location
Epitope IPIHYCAPAGFAILKCNDKK   Epitope Alignment
Variants
IPIHYCAPAGFAILKCNn   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5088
Epitope Seq.  IPIHYCAPAGFAILKCNDKK
Variant Seq.  IPIHYCAPAGFAILKCNn
Mutations D/N
Epitope Location D18N
HXB2 Location D230N
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Other
Note Autologous variant IPIHYCAPAGFAILKCNn, truncated by 2 AA vs. B cons peptide IPIHYCAPAGFAILKCNDKK, is 1/15 immunogenic peptides targeted by HIV-specific sub-dominant T-cell responses in patient MM43.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53220

HXB2 Location  gp160(239-247)   gp160 Epitope Map
View variants at this location
Epitope CKNVSTVQC   Epitope Alignment
Variants
CeNVSTVQC   inferred escape
CeNVSTVhC   inferred escape
CgNVSTVQC   observed variant
Epitope Name gp160 CC9
Species (MHC/HLA human(C*08:02)

Variant Details

Showing all: 3 variant(s).


Variant ID.  563
Epitope Seq.  CKNVSTVQC
Variant Seq.  CeNVSTVQC
Mutations K/E
Epitope Location K2E
HXB2 Location K240E
Mutation Type IE: inferred escape
Note 4 variants found in the patient. This one and cCeNVSTVhC came up first, at day 6. This variant persisted. Not tested for impact on escape.


Variant ID.  564
Epitope Seq.  CKNVSTVQC
Variant Seq.  CeNVSTVhC
Mutations K/E Q/H
Epitope Location K2E Q8H
HXB2 Location K240E Q246H
Mutation Type IE: inferred escape
Note 4 variants found in the patient. This one and CeNVSTVQC came up first, at day 6. Not tested for impact on escape.


Variant ID.  565
Epitope Seq.  CKNVSTVQC
Variant Seq.  CgNVSTVQC
Mutations K/G
Epitope Location K2G
HXB2 Location K240G
Mutation Type OV: observed variant
Note Rare variant present at day 35. Not tested for impact on escape.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 53221

HXB2 Location  gp160(584-592)   gp160 Epitope Map
View variants at this location
Epitope ERYLKDQQL   Epitope Alignment
Variants
ERYLKeQQp   observed variant
ERYLrDQQL   susceptible form
ERYLtDQQL   diminished response
ERYLqDQQL   diminished response
ERYLsDQQL   diminished response
ERYLmDQQL   diminished response
ERYLmDQrL   observed variant
ERYLmDrQL   observed variant
ERYLmDQlL   observed variant
ERYLtDQrL   observed variant
ERYrtDQrL   observed variant
Epitope Name gp160 EL9
Species (MHC/HLA human

Variant Details

Showing all: 11 variant(s).


Variant ID.  578
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLKeQQp
Mutations D/E L/P
Epitope Location D6E L9P
HXB2 Location D589E L592P
Mutation Type OV: observed variant
Note Came up at day 17. Not tested for escape.


Variant ID.  579
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLrDQQL
Mutations K/R
Epitope Location K5R
HXB2 Location K588R
Mutation Type SF: susceptible form
Note Came up at day 31, did not confer escape.


Variant ID.  580
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLtDQQL
Mutations K/T
Epitope Location K5T
HXB2 Location K588T
Mutation Type DR: diminished response
Note One of the three variants found at day 218, gave diminished CTL response.


Variant ID.  581
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLqDQQL
Mutations K/Q
Epitope Location K5Q
HXB2 Location K588Q
Mutation Type DR: diminished response
Note One of the three variants found at day 218, gave diminished CTL response. Also found in another patient.


Variant ID.  582
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLsDQQL
Mutations K/S
Epitope Location K5S
HXB2 Location K588S
Mutation Type DR: diminished response
Note One of the three variants found at day 218, gave diminished CTL response.


Variant ID.  583
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLmDQQL
Mutations K/M
Epitope Location K5M
HXB2 Location K588M
Mutation Type DR: diminished response
Note Found at day 556, gave a further reduction of CTL response.


Variant ID.  584
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLmDQrL
Mutations K/M Q/R
Epitope Location K5M Q8R
HXB2 Location K588M Q591R
Mutation Type OV: observed variant
Note Double mutant found at day 556. Not tested for escape.


Variant ID.  585
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLmDrQL
Mutations K/M Q/R
Epitope Location K5M Q7R
HXB2 Location K588M Q590R
Mutation Type OV: observed variant
Note Double mutant found at day 556. Not tested for escape.


Variant ID.  586
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLmDQlL
Mutations K/M Q/L
Epitope Location K5M Q8L
HXB2 Location K588M Q591L
Mutation Type OV: observed variant
Note Double mutant found at day 556. Not tested for escape.


Variant ID.  587
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYLtDQrL
Mutations K/T Q/R
Epitope Location K5T Q8R
HXB2 Location K588T Q591R
Mutation Type OV: observed variant
Note Double mutant found at day 556. Not tested for escape.


Variant ID.  588
Epitope Seq.  ERYLKDQQL
Variant Seq.  ERYrtDQrL
Mutations L/R K/T Q/R
Epitope Location L4R K5T Q8R
HXB2 Location L587R K588T Q591R
Mutation Type OV: observed variant
Note Double mutant found at day 556. Not tested for escape.

References

Jones2004 Nicola A. Jones, Xiping Wei, Darren R. Flower, MaiLee Wong, Franziska Michor, Michael S. Saag, Beatrice H. Hahn, Martin A. Nowak, George M. Shaw, and Persephone Borrow. Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response. J. Exp. Med., 200(10):1243-1256, 15 Nov 2004. PubMed ID: 15545352. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 62970

HXB2 Location  gp160(701-718)   gp160 Epitope Map
View variants at this location
Epitope VLSIVNRVRQGYSPLSLQ   Epitope Alignment
Variants
VLSIVkRVRkGYSPLSLQ   observed variant
VLSIVkRVRQGYSPLSLQ   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 2 variant(s).


Variant ID.  5135
Epitope Seq.  VLSIVNRVRQGYSPLSLQ
Variant Seq.  VLSIVkRVRkGYSPLSLQ
Mutations Q/K N/K
Epitope Location Q10K N6K
HXB2 Location Q710K N706K
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note Autologous variant VLSIVkRVRkGYSPLSLQ was observed at 6 months following onset of symptoms in patient MM42.


Variant ID.  5136
Epitope Seq.  VLSIVNRVRQGYSPLSLQ
Variant Seq.  VLSIVkRVRQGYSPLSLQ
Mutations N/K
Epitope Location N6K
HXB2 Location N706K
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note Autologous variant VLSIVkRVRQGYSPLSLQ was observed at 6 months following onset of symptoms in patient MM42.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 62947

HXB2 Location  gp160(837-856)   gp160 Epitope Map
View variants at this location
Epitope CRAILHIPRRIRQGLERALL   Epitope Alignment
Variants
RAILHIPRRIRQGLERsL   observed variant
RAILHIPtRIRQGLERcL   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 2 variant(s).


Variant ID.  5086
Epitope Seq.  CRAILHIPRRIRQGLERALL
Variant Seq.  RAILHIPRRIRQGLERsL
Mutations A/S
Epitope Location A17S
HXB2 Location A853S
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Other
Note Autologous variant RAILHIPRRIRQGLERsL was 1/10 peptides targeted by HIV-specific T-cell response in acutely infected patient MM45. Corresponding B cons peptide, CRAILHIPRRIRQGLERALL, is extended 1 AA on both ends.


Variant ID.  5087
Epitope Seq.  CRAILHIPRRIRQGLERALL
Variant Seq.  RAILHIPtRIRQGLERcL
Mutations A/C R/T
Epitope Location A17C R8T
HXB2 Location A853C R844T
Mutation Type OV: observed variant
Method CD8 T-cell Elispot - IFNy, Other
Note Autologous variant RAILHIPtRIRQGLERcL is 1/3 immunogenic peptides targeted by the HIV-specific T-cell response in the first PBMC sample after symptoms onset & 1/10 targets throughout entire study for patient MM33. During the 6 months following symptom onset, sequence variation was not observed and RAILHIPtRIRQGLERcL-specific T cell response was initially subdominant but became dominant by 1-2 months. Corresponding B cons peptide, CRAILHIPRRIRQGLERALL, is extended 1 AA on both ends.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63070

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

Variant Details

Showing all: 2 variant(s).


Variant ID.  5098
Epitope Seq.  RAILHIPRRIRQGLERSL
Variant Seq.  RAILHIPtRIRQGLERcL
Mutations S/C R/T
Epitope Location S17C R8T
HXB2 Location S854C R845T
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant RAILHIPtRIRQGLERcL is 1/3 immunogenic peptides targeted by the HIV-specific T-cell response in the first PBMC sample after symptoms onset & 1/10 targets throughout entire study for patient MM33. During the 6 months following symptom onset, sequence variation was not observed and RAILHIPtRIRQGLERcL-specific T cell response was initially subdominant but became dominant by 1-2 months.


Variant ID.  5099
Epitope Seq.  RAILHIPRRIRQGLERSL
Variant Seq.  CRAILHIPRRIRQGLERALL
Mutations S/A
Epitope Location S17A
HXB2 Location S854A
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note B cons peptide CRAILHIPRRIRQGLERALL is extended 1 AA on both ends & elicited CTL responses in 3/14 patients (MM28, MM46, MM50) assessed for B consensus peptides.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63071

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

Variant Details

Showing all: 2 variant(s).


Variant ID.  5100
Epitope Seq.  RAILHIPTRIRQGLERCL
Variant Seq.  CRAILHIPrRIRQGLERaLL
Mutations C/A T/R
Epitope Location C17A T8R
HXB2 Location C854A T845R
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note B cons peptide CRAILHIPRRIRQGLERALL is extended 1 AA on both ends & elicited CTL responses in 3/14 patients (MM28, MM46, MM50) assessed for B consensus peptides.


Variant ID.  5101
Epitope Seq.  RAILHIPTRIRQGLERCL
Variant Seq.  RAILHIPrRIRQGLERsL
Mutations C/S T/R
Epitope Location C17S T8R
HXB2 Location C854S T845R
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note Autologous variant RAILHIPrRIRQGLERsL was 1/10 peptides targeted by HIV-specific T-cell response in acutely infected patient MM45.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63055

HXB2 Location  Nef(41-58)   Nef Epitope Map
View variants at this location
Epitope GALTSSNTPSNNATCAWL   Epitope Alignment
Variants
GAiTSSNTaaNNAdCAWLEA   observed variant
GALTSSNTPStNATCAWL   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 2 variant(s).


Variant ID.  5097
Epitope Seq.  GALTSSNTPSNNATCAWL
Variant Seq.  GAiTSSNTaaNNAdCAWLEA
Mutations S/A T/D L/I P/A
Epitope Location S10A T14D L3I P9A
HXB2 Location S50A T54D L43I P49A
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note B cons variant GAiTSSNTaaNNAdCAWL(EA) elicited a CTL response in 1/14 patients, MM55, assessed for B cons peptides responses and has a 2 AA extended C-terminus (indicated by parentheses) compared to immunogenic autologous peptide GALTSSNTPSNNATCAWL observed in patient MM43.


Variant ID.  5134
Epitope Seq.  GALTSSNTPSNNATCAWL
Variant Seq.  GALTSSNTPStNATCAWL
Mutations N/T
Epitope Location N11T
HXB2 Location N51T
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note In patient MM43, autologous variant GALTSSNTPStNATCAWL was observed at 6 months following onset of symptoms.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63058

HXB2 Location  Nef(41-60)   Nef Epitope Map
View variants at this location
Epitope GAITSSNTAANNADCAWLEA   Epitope Alignment
Variants
GAlTSSNTpsNNAtCAWL   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5096
Epitope Seq.  GAITSSNTAANNADCAWLEA
Variant Seq.  GAlTSSNTpsNNAtCAWL
Mutations A/S D/T I/L A/P
Epitope Location A10S D14T I3L A9P
HXB2 Location A50S D54T I43L A49P
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note Autologous variant GAlTSSNTpsNNAtCAWL elicited a CTL response in patient MM43 and has a 2 AA truncation (indicated by parentheses) compared to B cons peptide GAITSSNTAANNADCAWL(EA) which was targeted in 1/14 patients, MM55, assessed for B cons peptide responses.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63051

HXB2 Location  Nef(65-82)   Nef Epitope Map
View variants at this location
Epitope EVGFPVRPQVPLRPMTYK   Epitope Alignment
Variants
EVGFPVtPQVPLRPMTYK   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5125
Epitope Seq.  EVGFPVRPQVPLRPMTYK
Variant Seq.  EVGFPVtPQVPLRPMTYK
Mutations R/T
Epitope Location R7T
HXB2 Location R71T
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant EVGFPVtPQVPLRPMTYK was observed at 6 mo following onset of symptoms in patient MM33.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63056

HXB2 Location  Nef(81-98)   Nef Epitope Map
View variants at this location
Epitope YKGAVDLSHFLKEKGGLE   Epitope Alignment
Variants
YKaAVDLSHFLKEKGGLEGL   observed variant
YKaAVDLSHFLKEKGGLE   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 2 variant(s).


Variant ID.  5103
Epitope Seq.  YKGAVDLSHFLKEKGGLE
Variant Seq.  YKaAVDLSHFLKEKGGLEGL
Mutations G/A
Epitope Location G3A
HXB2 Location G83A
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note B cons variant YKaAVDLSHFLKEKGGLE(GL), with a 2 AA extended C-terminus as indicated by parentheses, was a CTL target in 2 other patients: MM23 & MM46.


Variant ID.  5119
Epitope Seq.  YKGAVDLSHFLKEKGGLE
Variant Seq.  YKaAVDLSHFLKEKGGLE
Mutations G/A
Epitope Location G3A
HXB2 Location G83A
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant YKaAVDLSHFLKEKGGLE was observed in patient MM33 at 6 months following onset of symptoms.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63069

HXB2 Location  Nef(81-100)   Nef Epitope Map
View variants at this location
Epitope YKAAVDLSHFLKEKGGLEGL   Epitope Alignment
Variants
YKgAVDLSHFLKEKGGLE   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5121
Epitope Seq.  YKAAVDLSHFLKEKGGLEGL
Variant Seq.  YKgAVDLSHFLKEKGGLE
Mutations A/G
Epitope Location A3G
HXB2 Location A83G
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant YKgAVDLSHFLKEKGGLE, with a 2 AA C-terminus truncation, was observed as a CTL target in patient MM33.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63054

HXB2 Location  Nef(121-138)   Nef Epitope Map
View variants at this location
Epitope FPDWQNYTPGPGIRYPLT   Epitope Alignment
Variants
FPDWQNYTPGPGtRYPLT   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5129
Epitope Seq.  FPDWQNYTPGPGIRYPLT
Variant Seq.  FPDWQNYTPGPGtRYPLT
Mutations I/T
Epitope Location I13T
HXB2 Location I133T
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant FPDWQNYTPGPGtRYPLT was observed at 6 mo following onset o symptoms in patient MM39.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 57557

HXB2 Location  Nef(134-143)   Nef Epitope Map
View variants at this location
Epitope RYPLTFGWCF   Epitope Alignment
Variants
RYPLTFGWCy   observed variant
Species (MHC/HLA human(A*24)

Variant Details

Showing all: 1 variant(s).


Variant ID.  5108
Epitope Seq.  RYPLTFGWCF
Variant Seq.  RYPLTFGWCy
Mutations F/Y
Epitope Location F10Y
HXB2 Location F143Y
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype C
Method Tetramer binding
Note Variant RYPLTFGWCy elicited a response in subtype C-acutely infected patient MM47.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63067

HXB2 Location  Nef(134-143)   Nef Epitope Map
View variants at this location
Epitope RYPLTFGWCY   Epitope Alignment
Variants
RYPLTFGWCf   observed variant
Species (MHC/HLA human(A*24)

Variant Details

Showing all: 1 variant(s).


Variant ID.  5107
Epitope Seq.  RYPLTFGWCY
Variant Seq.  RYPLTFGWCf
Mutations Y/F
Epitope Location Y10F
HXB2 Location Y143F
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype B
Method Tetramer binding
Note Variant RYPLTFGWCf elicited a response in subtype B-acutely infected patient MM40.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63050

HXB2 Location  Nef(177-194)   Nef Epitope Map
View variants at this location
Epitope EKEVLEWRFDITLAHHHR   Epitope Alignment
Variants
EgEVLqWkFDsrLAfHHm   observed variant
EKEVLqWRFDITLAHHHR   observed variant
EKEVLpWRFDITLAHHHR   observed variant
EKEVLaWRFDITLAHHHR   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 4 variant(s).


Variant ID.  5106
Epitope Seq.  EKEVLEWRFDITLAHHHR
Variant Seq.  EgEVLqWkFDsrLAfHHm
Mutations I/S T/R H/F R/M K/G E/Q R/K
Epitope Location I11S T12R H15F R18M K2G E6Q R8K
HXB2 Location I187S T188R H191F R194M K178G E182Q R184K
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note Autologous variant EgEVLqWkFDsrLAfHHm was a CTL target in patient MM33.


Variant ID.  5144
Epitope Seq.  EKEVLEWRFDITLAHHHR
Variant Seq.  EKEVLqWRFDITLAHHHR
Mutations E/Q
Epitope Location E6Q
HXB2 Location E182Q
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note At 6 mo following onset of symptoms, 3 autologous variants (EKEVLqWRFDITLAHHHR, EKEVLpWRFDITLAHHHR, EKEVLaWRFDITLAHHHR) & index peptide were observed in MM45.


Variant ID.  5145
Epitope Seq.  EKEVLEWRFDITLAHHHR
Variant Seq.  EKEVLpWRFDITLAHHHR
Mutations E/P
Epitope Location E6P
HXB2 Location E182P
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note At 6 mo following onset of symptoms, 3 autologous variants (EKEVLqWRFDITLAHHHR, EKEVLpWRFDITLAHHHR, EKEVLaWRFDITLAHHHR) & index peptide were observed in MM45.


Variant ID.  5146
Epitope Seq.  EKEVLEWRFDITLAHHHR
Variant Seq.  EKEVLaWRFDITLAHHHR
Mutations E/A
Epitope Location E6A
HXB2 Location E182A
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method Longitudinal study
Note At 6 mo following onset of symptoms, 3 autologous variants (EKEVLqWRFDITLAHHHR, EKEVLpWRFDITLAHHHR, EKEVLaWRFDITLAHHHR) & index peptide were observed in MM45.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63049

HXB2 Location  Nef(177-194)   Nef Epitope Map
View variants at this location
Epitope EGEVLQWKFDSRLAFHHM   Epitope Alignment
Variants
EkEVLeWrFDitLAhHHr   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5105
Epitope Seq.  EGEVLQWKFDSRLAFHHM
Variant Seq.  EkEVLeWrFDitLAhHHr
Mutations S/I R/T F/H M/R G/K Q/E K/R
Epitope Location S11I R12T F15H M18R G2K Q6E K8R
HXB2 Location S187I R188T F191H M194R G178K Q182E K184R
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy
Note Autologous variant EkEVLeWrFDitLAhHHr was identified as a CTL target in patient MM43.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


Displaying record number 63052

HXB2 Location  Nef(185-202)   Nef Epitope Map
View variants at this location
Epitope FDSRLAFHHIARELHPEY   Epitope Alignment
Variants
FDSlLAFHHIARELHPEY   observed variant
Species (MHC/HLA human

Variant Details

Showing all: 1 variant(s).


Variant ID.  5130
Epitope Seq.  FDSRLAFHHIARELHPEY
Variant Seq.  FDSlLAFHHIARELHPEY
Mutations R/L
Epitope Location R4L
HXB2 Location R188L
Mutation Type OV: observed variant
Epitope Subtype B
Variant Subtype B
Method CD8 T-cell Elispot - IFNy, Longitudinal study
Note Autologous variant FDSlLAFHHIARELHPEY was observed at 6 mo following onset of symptoms in patient MM42.

References

Turnbull2009 Emma L. Turnbull, MaiLee Wong, Shuyi Wang, Xiping Wei, Nicola A. Jones, Karen E. Conrod, Diana Aldam, Jo Turner, Pierre Pellegrino, Brandon F. Keele, Ian Williams, George M. Shaw, and Persephone Borrow. Kinetics of Expansion of Epitope-Specific T Cell Responses During primary HIV-1 Infection. J. Immunol., 182(11):7131-7145, 1 Jun 2009. PubMed ID: 19454710. Show all entries for this paper.

Yang2019 Yiding Yang, and Vitaly V. Ganusov. Defining Kinetic Properties of HIV-Specific CD8(+) T-Cell Responses in Acute Infection. Microorganisms, 7(3):microorganisms7030069 doi, Mar 2019. PubMed ID: 30836625 Show all entries for this paper.


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