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Found 28 matching records:

Displaying record number 61685

HXB2 Location  Gag(6-15)   Gag Epitope Map
View variants at this location
Epitope SILRGGKLDK   Epitope Alignment
Variants
SILRGeKLDK   observed variant
SvLRGGKLDK   observed variant
SILRGGnLDK   literature escape
Epitope Name Gag-SK10
Species (MHC/HLA human(A*74:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  4230
Epitope Seq.  SILRGGKLDK
Variant Seq.  SILRGeKLDK
Mutations G/E
Epitope Location G6E
HXB2 Location G11E
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Variant SILRGeKLDK was found in maternal subject 133-M but not in her child, 133-C, as 100% of the circulating virus at 1.1 years post


Variant ID.  4231
Epitope Seq.  SILRGGKLDK
Variant Seq.  SvLRGGKLDK
Mutations I/V
Epitope Location I2V
HXB2 Location I7V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note Variant SvLRGGKLDK was first observed, and recorded as fixed at 100%, in maternal subject 133-M when her child 133-C was at 7yr of age. 133-M is A*74- (which is the restricting HLA for SK10) and this I7V mutation was always observed as a co-variant with G11E. While the I7V mutation does not appear to have been transmitted to 133-C from the mother, it arose in the child before 2.7yr. In 133-C, A*74+, the I7V mutation was always observed as co-variant with G11E and K12N.


Variant ID.  4232
Epitope Seq.  SILRGGKLDK
Variant Seq.  SILRGGnLDK
Mutations K/N
Epitope Location K7N
HXB2 Location K12N
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SILRGGnLDK is a known escape variant. While SILRGGnLDK does not appear to have been transmitted to 133-C from the A*74- (which is the restricting HLA for SK10) mother, it arose in the child and was observed to be at a frequency of 100% at 0.3yr. In 133-C, A*74+, the K12N mutation was always observed as a co-variant with G11E and sometimes covariant with I7V.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62248

HXB2 Location  Gag(76-86)   Gag Epitope Map
View variants at this location
Epitope RSLYNTVATLY   Epitope Alignment
Variants
RSLfNTVATLY   observed variant
kSLYNTVATLY   literature escape
RSLYNTVAvLY   observed variant
RSLYNTiATLY   observed variant
RSLYNTVvTLY   observed variant
Epitope Name Gag-RY11
Species (MHC/HLA human(A*30)

Variant Details

Showing all: 5 variant(s).


Variant ID.  4289
Epitope Seq.  RSLYNTVATLY
Variant Seq.  RSLfNTVATLY
Mutations Y/F
Epitope Location Y4F
HXB2 Location Y79F
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RSLfNTVATLY (Y79F) was observed in A*30+ (which is a restricting HLA for RY11) subject 517-M and her A*30+ child, 517-C. It was present at all sampling time points and was always observed as a covariant with T84V and R76K. Sometimes it was also observed with A83V or V82I.


Variant ID.  4290
Epitope Seq.  RSLYNTVATLY
Variant Seq.  kSLYNTVATLY
Mutations R/K
Epitope Location R1K
HXB2 Location R76K
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note kSLYNTVATLY (R76K) is a documented escape variant. It was observed in A*30+ (which is a restricting HLA for RY11) subject 517-M and her A*30+ child, 517-C. It was present at all sampling time points and was always observed as a covariant with T84V. Sometimes it was also observed with A83V, Y79F, or V82I.


Variant ID.  4291
Epitope Seq.  RSLYNTVATLY
Variant Seq.  RSLYNTVAvLY
Mutations T/V
Epitope Location T9V
HXB2 Location T84V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RSLYNTVAvLY (T84V) was observed in A*30+ (which is a restricting HLA for RY11) subject 517-M and her A*30+ child, 517-C. It was present at all sampling time points and was always observed as a covariant with Y79F and R76K. Sometimes it was also observed with A83V or V82I.


Variant ID.  4292
Epitope Seq.  RSLYNTVATLY
Variant Seq.  RSLYNTiATLY
Mutations V/I
Epitope Location V7I
HXB2 Location V82I
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RSLYNTiATLY (V82I) was observed to arise in A*30+ (which is a restricting HLA for RY11) subject 517-C between 2.5 and 5 years. It was always observed as a covariant with Y79F, T84V, and R76K. Sometimes it was also observed with A83V.


Variant ID.  4293
Epitope Seq.  RSLYNTVATLY
Variant Seq.  RSLYNTVvTLY
Mutations A/V
Epitope Location A8V
HXB2 Location A83V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RSLYNTVvTLY (A83V) was observed to arise in A*30+ (which is a restricting HLA for RY11) subject 517-C between 2.5 and 5 years. It was always observed as a covariant with Y79F, T84V, and R76K. Sometimes it was also observed with V82I.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62220

HXB2 Location  Gag(180-188)   Gag Epitope Map
View variants at this location
Epitope TPQDLNTML   Epitope Alignment
Variants
TPtDLNTML   literature escape
TPaDLNTML   observed variant
TPsDLNTML   observed variant
Epitope Name Gag-TL9
Species (MHC/HLA human(B*42:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  4252
Epitope Seq.  TPQDLNTML
Variant Seq.  TPtDLNTML
Mutations Q/T
Epitope Location Q3T
HXB2 Location Q182T
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Other
Note TPtDLNTML (Q182T) is documented escape variant. It was observed to arise in B*42+ (which is a restricting HLA for TL9) subject 133-M when her B*42- child, 133-C, was at age 7. Q182T was also observed in B*42+ subject 517-M when her B*42+ child, 517-C, was 0.25yrs old. However, it was not observed in 517-C. In B*42+ subject 021-M, the Q182T variant was observed starting at 0.1yr before the birth of her child, 021-C. However it was not observed 021-C, who is B*42+, until 4.9yrs.


Variant ID.  4253
Epitope Seq.  TPQDLNTML
Variant Seq.  TPaDLNTML
Mutations Q/A
Epitope Location Q3A
HXB2 Location Q182A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Other
Note TPaDLNTML (Q182A) was observed in B*42+ (which is a restricting HLA for TL9) subject 517-M when her B*42+ child, 517-C, was 0.25yrs old. However, it was not observed in 517-C.


Variant ID.  4349
Epitope Seq.  TPQDLNTML
Variant Seq.  TPsDLNTML
Mutations Q/S
Epitope Location Q3S
HXB2 Location Q182S
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Other
Note TPsDLNTML (Q182S) was observed in B*8101+ (which is a restricting HLA for TL9) subject K-3046-C at age 7.8. K-3046-C was a subject in the Pediatric Early HAART and Strategic Treatment Interruption Study.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 61683

HXB2 Location  Gag(180-188)   Gag Epitope Map
View variants at this location
Epitope TPQDLNTML   Epitope Alignment
Variants
TPQDLNmML   literature escape
TPgDLNTML   observed variant
TPQDLNsML   observed variant
TPsDLNTML   observed variant
Epitope Name Gag-TL9
Species (MHC/HLA human(B*81:01)

Variant Details

Showing all: 4 variant(s).


Variant ID.  4251
Epitope Seq.  TPQDLNTML
Variant Seq.  TPQDLNmML
Mutations T/M
Epitope Location T7M
HXB2 Location T186M
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note TPQDLNmML (T186X) is a documented escape variant. It was observed to arise between 0.7 and 1.3yrs in B*81+ (which is a restricting HLA for TL9) subject 133-C.


Variant ID.  4346
Epitope Seq.  TPQDLNTML
Variant Seq.  TPgDLNTML
Mutations Q/G
Epitope Location Q3G
HXB2 Location Q182G
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note TPgDLNTML (Q182G) was observed in B*8101+ (which is a restricting HLA for TL9) subject K-004-C at 12.8 years and in B*8101+ subject K-044-C at 8 years. All were subjects in the Pediatric Early HAART and Strategic Treatment Interruption Study.


Variant ID.  4347
Epitope Seq.  TPQDLNTML
Variant Seq.  TPQDLNsML
Mutations T/S
Epitope Location T7S
HXB2 Location T186S
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note TPQDLNsML (T186S) was observed in B*8101+ (which is a restricting HLA for TL9) subjects K-047-C (6.3 years), K-073-C (10.1 years), K-075-C (7.5 years), K-136-C (9.1 years), and K-146-C (3 years). All were subjects in the Pediatric Early HAART and Strategic Treatment Interruption Study.


Variant ID.  4348
Epitope Seq.  TPQDLNTML
Variant Seq.  TPsDLNTML
Mutations Q/S
Epitope Location Q3S
HXB2 Location Q182S
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note TPsDLNTML (Q182S) was observed in B*8101+ (which is a restricting HLA for TL9) subject K-158-C at age 1.7. K-158-C was a subject in the Pediatric Early HAART and Strategic Treatment Interruption Study.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62219

HXB2 Location  Gag(296-304)   Gag Epitope Map
View variants at this location
Epitope YVDRFFKTL   Epitope Alignment
Variants
YVDRFFrTL   observed variant
YVDRFFKvL   literature escape
YVDRFFKaL   literature escape
Epitope Name Gag-YL9
Species (MHC/HLA human(C*03)

Variant Details

Showing all: 3 variant(s).


Variant ID.  4248
Epitope Seq.  YVDRFFKTL
Variant Seq.  YVDRFFrTL
Mutations K/R
Epitope Location K7R
HXB2 Location K302R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note YVDRFFrTL was observed in the Cw*03+ (which is the restricting HLA for RM9) child, 517-C. It arose between 0.2 and 2.5yrs.


Variant ID.  4249
Epitope Seq.  YVDRFFKTL
Variant Seq.  YVDRFFKvL
Mutations T/V
Epitope Location T8V
HXB2 Location T303V
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note YVDRFFKvL (T303X) is a known escape variant. It arose in the Cw*03+ (which is the restricting HLA for RM9) child, 517-C, between 2.5 and 5yrs.


Variant ID.  4250
Epitope Seq.  YVDRFFKTL
Variant Seq.  YVDRFFKaL
Mutations T/A
Epitope Location T8A
HXB2 Location T303A
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note YVDRFFKaL (T303X) is a known escape variant. It arose in the Cw*03+ (which is the restricting HLA for RM9) child, 517-C, between 5 and 8.5yrs.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 61686

HXB2 Location  Pol(158-167)   Pol Epitope Map
View variants at this location
Epitope SPIETVPVKL   Epitope Alignment
Variants
SPIdTVPVKL   literature escape
SPIEpVPVKL   observed variant
SPIkTVPVKL   literature escape
SsIETVPVKL   literature escape
StIETVPVKL   observed variant
Epitope Name Pol-SL10
Species (MHC/HLA human(B*81:01)

Variant Details

Showing all: 5 variant(s).


Variant ID.  4233
Epitope Seq.  SPIETVPVKL
Variant Seq.  SPIdTVPVKL
Mutations E/D
Epitope Location E4D
HXB2 Location E161D
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SPIdTVPVKL (E161X) is a known escape variant. SPIdTVPVKL does not appear to have been transmitted to child 133-C from the B*81- (which is the restricting HLA for SL10) mother, 133-M. The E161D mutation arose in the B*81+ child 133-C by 0.3yr.


Variant ID.  4234
Epitope Seq.  SPIETVPVKL
Variant Seq.  SPIEpVPVKL
Mutations T/P
Epitope Location T5P
HXB2 Location T162P
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SPIEpVPVKL does not appear to have been transmitted to child 133-C from the B*81- (which is the restricting HLA for SL10) mother, 133-M. The T162P mutation arose in the B*81+ child 133-C and was only observed at the 0.3yr sampling time point at a frequency of 2%.


Variant ID.  4235
Epitope Seq.  SPIETVPVKL
Variant Seq.  SPIkTVPVKL
Mutations E/K
Epitope Location E4K
HXB2 Location E161K
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SPIkTVPVKL (E161X) is a known escape variant. SPIkTVPVKL does not appear to have been transmitted to child 133-C from the B*81- (which is the restricting HLA for SL10) mother, 133-M. The E161K mutation arose in the B*81+ child 133-C by 0.3yr.


Variant ID.  4236
Epitope Seq.  SPIETVPVKL
Variant Seq.  SsIETVPVKL
Mutations P/S
Epitope Location P2S
HXB2 Location P159S
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SsIETVPVKL (P159S) is a known escape variant. SsIETVPVKL does not appear to have been transmitted to child 133-C from the B*81- (which is the restricting HLA for SL10) mother, 133-M. The P159S mutation arose in the B*81+ child 133-C between 0.3 and 2.7yr.


Variant ID.  4237
Epitope Seq.  SPIETVPVKL
Variant Seq.  StIETVPVKL
Mutations P/T
Epitope Location P2T
HXB2 Location P159T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note StIETVPVKL does not appear to have been transmitted to child 133-C from the B*81- (which is the restricting HLA for SL10) mother, 133-M. The P159T mutation arose in the B*81+ child 133-C between 4.9 and 7.7yr.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62241

HXB2 Location  Pol(282-290)   Pol Epitope Map
View variants at this location
Epitope YTAFTIPSI   Epitope Alignment
Variants
YTAFTIPSv   observed variant
Epitope Name Pol-YI9
Species (MHC/HLA human(A*02)

Variant Details

Showing all: 1 variant(s).


Variant ID.  4335
Epitope Seq.  YTAFTIPSI
Variant Seq.  YTAFTIPSv
Mutations I/V
Epitope Location I9V
HXB2 Location I290V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note YTAFTIPSv (I290V) was observed in A*02+ (which is a restricting HLA for YI9) subject 021-M five years after the birth of her child, 021-C.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62222

HXB2 Location  Pol(328-336)   Pol Epitope Map
View variants at this location
Epitope AQNPEIVIY   Epitope Alignment
Variants
ArNPEIVIY   observed variant
AkNPEIVIY   observed variant
AQNPEIVIc   observed variant
AQNPElVIY   observed variant
tQNPEIVIY   observed variant
Epitope Name Pol-AY9
Species (MHC/HLA human(A*30)

Variant Details

Showing all: 5 variant(s).


Variant ID.  4254
Epitope Seq.  AQNPEIVIY
Variant Seq.  ArNPEIVIY
Mutations Q/R
Epitope Location Q2R
HXB2 Location Q329R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note ArNPEIVIY (Q329R) was observed in A*30+ (which is a restricting HLA for AY9) subject 517-M when her A*30+ child, 517-C, was 6 yrs old. It was not observed in 517-C.


Variant ID.  4255
Epitope Seq.  AQNPEIVIY
Variant Seq.  AkNPEIVIY
Mutations Q/K
Epitope Location Q2K
HXB2 Location Q329K
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note AkNPEIVIY (Q329K) was observed in A*30+ (which is a restricting HLA for AY9) subject 517-M when her A*30+ child, 517-C, was 6 yrs old. It was not observed in 517-C.


Variant ID.  4256
Epitope Seq.  AQNPEIVIY
Variant Seq.  AQNPEIVIc
Mutations Y/C
Epitope Location Y9C
HXB2 Location Y336C
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note AQNPEIVIc (Y336C) was observed in A*30+ (which is a restricting HLA for AY9) subject 517-C at 0.2yrs. However, it was not observed in the A*30+ mother, 517-M.


Variant ID.  4257
Epitope Seq.  AQNPEIVIY
Variant Seq.  AQNPElVIY
Mutations I/L
Epitope Location I6L
HXB2 Location I333L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note AQNPElVIY (I333L) was observed to arise in A*30+ (which is a restricting HLA for AY9) subject 517-C between 0.2yrs and 2.5yrs. It was sometimes observed as a covariant with A328T.


Variant ID.  4258
Epitope Seq.  AQNPEIVIY
Variant Seq.  tQNPEIVIY
Mutations A/T
Epitope Location A1T
HXB2 Location A328T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note tQNPEIVIY (A328T) was observed to arise in A*30+ (which is a restricting HLA for AY9) subject 517-C between 2.5 and 5yrs. It was always observed as a covariant with I333L.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62245

HXB2 Location  Pol(334-342)   Pol Epitope Map
View variants at this location
Epitope VIYQYMDDL   Epitope Alignment
Variants
iIYQYMDDL   observed variant
VIcQYMDDL   observed variant
Epitope Name Pol-VL9
Species (MHC/HLA human(A*02)

Variant Details

Showing all: 2 variant(s).


Variant ID.  4344
Epitope Seq.  VIYQYMDDL
Variant Seq.  iIYQYMDDL
Mutations V/I
Epitope Location V1I
HXB2 Location V334I
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note iIYQYMDDL (V334I) was observed in A*02+ (which is a restricting HLA for VL9) subject 021-M beginning at 0.1 years before the birth of her A*02+ child, 021-C. However, it did not appear in samples from 021-C.


Variant ID.  4345
Epitope Seq.  VIYQYMDDL
Variant Seq.  VIcQYMDDL
Mutations Y/C
Epitope Location Y3C
HXB2 Location Y336C
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note VIcQYMDDL (Y336C) was observed in A*02+ (which is a restricting HLA for VL9) subject 021-C at 0.1 years.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62216

HXB2 Location  Pol(423-432)   Pol Epitope Map
View variants at this location
Epitope SQIYPGIKVR   Epitope Alignment
Variants
SQIYPGIrVR   observed variant
SQIYPGvKVR   observed variant
SQIYPrIKVR   observed variant
SQIYPGIKiR   observed variant
SQIYPGIKVk   literature escape
Epitope Name Pol-SR10
Species (MHC/HLA human(A*74:01)

Variant Details

Showing all: 5 variant(s).


Variant ID.  4238
Epitope Seq.  SQIYPGIKVR
Variant Seq.  SQIYPGIrVR
Mutations K/R
Epitope Location K8R
HXB2 Location K430R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SQIYPGIrVR was observed at all sampling time points in both the A*74- (which is the restricting HLA for SR10) mother, 133-M, and the A*74+ child, 133-C. As the K430R mutation was at 100% frequency at all sampling time points, it was observed alongside all other mutations listed as variants associated with the CTL Record for Epitope Pol-SR10 (Rec #62216).


Variant ID.  4239
Epitope Seq.  SQIYPGIKVR
Variant Seq.  SQIYPGvKVR
Mutations I/V
Epitope Location I7V
HXB2 Location I429V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SQIYPGvKVR was observed in the A*74- (which is the restricting HLA for SR10) mother, 133-M, but not in the A*74+ child, 133-C. The I429V mutation was always observed as a co-variant with the K430R mutation.


Variant ID.  4240
Epitope Seq.  SQIYPGIKVR
Variant Seq.  SQIYPrIKVR
Mutations G/R
Epitope Location G6R
HXB2 Location G428R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SQIYPrIKVR was observed in the A*74- (which is the restricting HLA for SR10) mother, 133-M, and in the A*74+ child, 133-C. The G428R mutation was always observed as a co-variant with the K430R mutation and sometimes also with the R432K mutation.


Variant ID.  4241
Epitope Seq.  SQIYPGIKVR
Variant Seq.  SQIYPGIKiR
Mutations V/I
Epitope Location V9I
HXB2 Location V431I
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SQIYPGIKiR was observed to arise in the A*74+ (which is the restricting HLA for SR10) child, 133-C, between 0.3 and 2.7yr. The V431I mutation was always observed as a co-variant with both the K430R and R432K mutations.


Variant ID.  4242
Epitope Seq.  SQIYPGIKVR
Variant Seq.  SQIYPGIKVk
Mutations R/K
Epitope Location R10K
HXB2 Location R432K
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SQIYPGIKVk is a known escape variant. It was observed to arise in the A*74+ (which is the restricting HLA for SR10) child, 133-C, between 0.3 and 2.7yr. The R432K mutation was always observed as a co-variant with the K430R mutation and sometimes with the V431I mutation as well.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62244

HXB2 Location  Pol(464-472)   Pol Epitope Map
View variants at this location
Epitope ILKEPVHGV   Epitope Alignment
Variants
ILqEPVHGV   observed variant
ILKEPVHGa   observed variant
Epitope Name Pol-IV9
Species (MHC/HLA human(A*02)

Variant Details

Showing all: 2 variant(s).


Variant ID.  4342
Epitope Seq.  ILKEPVHGV
Variant Seq.  ILqEPVHGV
Mutations K/Q
Epitope Location K3Q
HXB2 Location K466Q
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note ILqEPVHGV (K466Q) was observed in A*02+ (which is a restricting HLA for IV9) subject 021-M beginning at 5 years after the birth of her A*02+ child, 021-C. However, it did not appear in samples from 021-C. K466Q was sometimes observed as a covariant with V472A.


Variant ID.  4343
Epitope Seq.  ILKEPVHGV
Variant Seq.  ILKEPVHGa
Mutations V/A
Epitope Location V9A
HXB2 Location V472A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note ILKEPVHGa (V472A) was observed in A*02+ (which is a restricting HLA for IV9) subject 021-M beginning at 0.1 years before the birth of her A*02+ child, 021-C. However, it did not appear in samples from 021-C until they were 4.9 years old. V472A was sometimes observed as a covariant with K466Q.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62231

HXB2 Location  Pol(743-751)   Pol Epitope Map
View variants at this location
Epitope LPPIVAKEI   Epitope Alignment
Variants
LPPvVAKEI   literature escape
LPPIVArEI   literature escape
Epitope Name Pol-LI9
Species (MHC/HLA human(B*42)

Variant Details

Showing all: 2 variant(s).


Variant ID.  4296
Epitope Seq.  LPPIVAKEI
Variant Seq.  LPPvVAKEI
Mutations I/V
Epitope Location I4V
HXB2 Location I746V
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note LPPvVAKEI (I746V) is a documented escape variant. It was observed at all sampling time points in B*42+ (which is a restricting HLA for LI9) subject 517-M and her B*42+ child, 517-C. It was sometimes observed as a covariant with K749R.


Variant ID.  4297
Epitope Seq.  LPPIVAKEI
Variant Seq.  LPPIVArEI
Mutations K/R
Epitope Location K7R
HXB2 Location K749R
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note LPPIVArEI (K749) is a documented escape variant. It was observed at all sampling time points in B*42+ (which is a restricting HLA for LI9) subject 517-M and her B*42+ child, 517-C. It was sometimes observed as a covariant with I746V.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62232

HXB2 Location  Vif(48-57)   Vif Epitope Map
View variants at this location
Epitope HPKVSSEVHI   Epitope Alignment
Variants
HPKVSSEVHv   observed variant
HPKVSSEiHI   observed variant
HPKVSSEVHt   observed variant
nPKVSSEVHI   observed variant
HPKiSSEVHI   observed variant
HPrVSSEVHI   observed variant
Epitope Name Vif-HI10
Species (MHC/HLA human(B*42)

Variant Details

Showing all: 6 variant(s).


Variant ID.  4298
Epitope Seq.  HPKVSSEVHI
Variant Seq.  HPKVSSEVHv
Mutations I/V
Epitope Location I10V
HXB2 Location I57V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note HPKVSSEVHv (I57V) was observed in B*42+ (which is a restricting HLA for HI10) subject 517-M when her B*42+ child, 517-C, was 0.25 years old. However, it was not observed in 517-C. It was observed as a covariant with V55I.


Variant ID.  4299
Epitope Seq.  HPKVSSEVHI
Variant Seq.  HPKVSSEiHI
Mutations V/I
Epitope Location V8I
HXB2 Location V55I
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note HPKVSSEiHI (V55I) was observed in B*42+ (which is a restricting HLA for HI10) subject 517-M when her B*42+ child, 517-C, was 0.25 years old. However, it was not observed in 517-C. It was sometimes seen as a covariant with I57V.


Variant ID.  4300
Epitope Seq.  HPKVSSEVHI
Variant Seq.  HPKVSSEVHt
Mutations I/T
Epitope Location I10T
HXB2 Location I57T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note HPKVSSEVHt (I57T) was observed in B*42+ (which is a restricting HLA for HI10) subject 517-M when her B*42+ child, 517-C, was 6 years old.


Variant ID.  4301
Epitope Seq.  HPKVSSEVHI
Variant Seq.  nPKVSSEVHI
Mutations H/N
Epitope Location H1N
HXB2 Location H48N
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note nPKVSSEVHI (H48N) arose in B*42+ (which is a restricting HLA for HI10) subject 517-C between 0.2 and 2.5 years. It was sometimes observed as a covariant with V51I.


Variant ID.  4302
Epitope Seq.  HPKVSSEVHI
Variant Seq.  HPKiSSEVHI
Mutations V/I
Epitope Location V4I
HXB2 Location V51I
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note HPKiSSEVHI (V51I) arose in B*42+ (which is a restricting HLA for HI10) subject 517-C between 0.2 and 2.5 years. It was sometimes observed as a covariant with H48N or K50R.


Variant ID.  4303
Epitope Seq.  HPKVSSEVHI
Variant Seq.  HPrVSSEVHI
Mutations K/R
Epitope Location K3R
HXB2 Location K50R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note HPrVSSEVHI (K50R) arose in B*42+ (which is a restricting HLA for HI10) subject 517-C between 2.5 and 5 years. It was sometimes observed as a covariant with V51I.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62234

HXB2 Location  Vif(54-63)   Vif Epitope Map
View variants at this location
Epitope EVHIPLGDAR   Epitope Alignment
Variants
EVHIPLGeAR   observed variant
EVHIPLGDAk   observed variant
EVHIPvGDAR   observed variant
EVHIPLGDgR   observed variant
Epitope Name Vif-ER10
Species (MHC/HLA human(A*68:01)

Variant Details

Showing all: 4 variant(s).


Variant ID.  4311
Epitope Seq.  EVHIPLGDAR
Variant Seq.  EVHIPLGeAR
Mutations D/E
Epitope Location D8E
HXB2 Location D61E
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note EVHIPLGeAR (D61E) was observed at all sampling time points in A*6801+ (which is a restricting HLA for ER10) subject 133-M and her A*6801+ child 133-C. It was sometimes observed as a covariant with L59V, R63K, or A62G.


Variant ID.  4312
Epitope Seq.  EVHIPLGDAR
Variant Seq.  EVHIPLGDAk
Mutations R/K
Epitope Location R10K
HXB2 Location R63K
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note EVHIPLGDAk (R63K) was observed in A*6801+ (which is a restricting HLA for ER10) subject 133-M 7 years after the birth of her child,133-C. It was also observed in 133-C, who is A*6801+ beginning at age 4.9. It always seen as a covariant with D61E and sometimes also observed with A62G.


Variant ID.  4313
Epitope Seq.  EVHIPLGDAR
Variant Seq.  EVHIPvGDAR
Mutations L/V
Epitope Location L6V
HXB2 Location L59V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note EVHIPvGDAR (L59V) was observed in A*6801+ (which is a restricting HLA for ER10) subject 133-M 7 years after the birth of her child,133-C. It was also observed in 133-C, who is A*6801+ at age 4.9. It always seen as a covariant with D61E.


Variant ID.  4314
Epitope Seq.  EVHIPLGDAR
Variant Seq.  EVHIPLGDgR
Mutations A/G
Epitope Location A9G
HXB2 Location A62G
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note EVHIPLGDgR (A62G) arose in A*6801+ (which is a restricting HLA for ER10) subject 133-C between 4.9 and 7.7yr. It was observed as a covariant with both R63K and D61E.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62228

HXB2 Location  Vif(78-87)   Vif Epitope Map
View variants at this location
Epitope DWHLGHGVSI   Epitope Alignment
Variants
DWHLGHGaSI   observed variant
eWHLGHGVSI   observed variant
DWHLGHGiSI   observed variant
DWlLGHGVSI   observed variant
DWqLGHGVSI   observed variant
Epitope Name Vif-WI9
Species (MHC/HLA human(B*15:10)

Variant Details

Showing all: 5 variant(s).


Variant ID.  4284
Epitope Seq.  DWHLGHGVSI
Variant Seq.  DWHLGHGaSI
Mutations V/A
Epitope Location V8A
HXB2 Location V85A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note DWHLGHGaSI (V85A) was observed in B*15+ (which is a restricting HLA for WI9) subject 517-C starting at 0.2 years. However it does not appear to have been transmitted from the B*15- mother, 517-M. It was sometimes observed as a covariant with D78E.


Variant ID.  4285
Epitope Seq.  DWHLGHGVSI
Variant Seq.  eWHLGHGVSI
Mutations D/E
Epitope Location D1E
HXB2 Location D78E
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note eWHLGHGVSI (D78E) was observed in B*15+ (which is a restricting HLA for WI9) subject 517-C starting at 0.2 years. However it does not appear to have been transmitted from the B*15- mother, 517-M. It was sometimes observed as a covariant with V85A.


Variant ID.  4286
Epitope Seq.  DWHLGHGVSI
Variant Seq.  DWHLGHGiSI
Mutations V/I
Epitope Location V8I
HXB2 Location V85I
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note DWHLGHGiSI (V85I) was observed in B*15+ (which is a restricting HLA for WI9) subject 517-C at 0.2 years. However it does not appear to have been transmitted from the B*15- mother, 517-M.


Variant ID.  4287
Epitope Seq.  DWHLGHGVSI
Variant Seq.  DWlLGHGVSI
Mutations H/L
Epitope Location H3L
HXB2 Location H80L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note DWlLGHGVSI (H80L) was observed in B*15+ (which is a restricting HLA for WI9) subject 517-C at 0.2 years. However it does not appear to have been transmitted from the B*15- mother, 517-M.


Variant ID.  4288
Epitope Seq.  DWHLGHGVSI
Variant Seq.  DWqLGHGVSI
Mutations H/Q
Epitope Location H3Q
HXB2 Location H80Q
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note DWqLGHGVSI (H80Q) was observed in B*15+ (which is a restricting HLA for WI9) subject 517-C at 0.2 years. However it does not appear to have been transmitted from the B*15- mother, 517-M.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62235

HXB2 Location  Vif(113-121)   Vif Epitope Map
View variants at this location
Epitope DCFADSAIR   Epitope Alignment
Variants
DCFtDSAIR   observed variant
DCFADSAIg   observed variant
DCFAeSAIR   observed variant
Epitope Name Vif-DR10
Species (MHC/HLA human(A*68:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  4315
Epitope Seq.  DCFADSAIR
Variant Seq.  DCFtDSAIR
Mutations A/T
Epitope Location A4T
HXB2 Location A116T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note DCFtDSAIR (A116T) was observed in A*6801+ (which is a restricting HLA for DR9) subject 133-M 7 years after the birth of her A*6801+ child, 133-C. While it was not observed in 133-C at 0.3yr, it did emerge beginning at 2.7yr.


Variant ID.  4316
Epitope Seq.  DCFADSAIR
Variant Seq.  DCFADSAIg
Mutations R/G
Epitope Location R9G
HXB2 Location R121G
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note DCFADSAIg (A116G) was observed in A*6801+ (which is a restricting HLA for DR9) subject 133-C at 2.7yr.


Variant ID.  4317
Epitope Seq.  DCFADSAIR
Variant Seq.  DCFAeSAIR
Mutations D/E
Epitope Location D5E
HXB2 Location D117E
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note DCFAeSAIR (D117E) arose in A*6801+ (which is a restricting HLA for DR9) subject 133-C between 2.7 and 4.9 years.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62243

HXB2 Location  Vpr(34-42)   Vpr Epitope Map
View variants at this location
Epitope FPRPWLHGL   Epitope Alignment
Variants
FPRvWLHGL   observed variant
FPRmWLHGL   observed variant
FPRPWLHGs   observed variant
FPRtWLHGL   observed variant
FPRaWLHGL   observed variant
FPRPWLHqL   observed variant
Epitope Name Vpr-FL9
Species (MHC/HLA human(B*42)

Variant Details

Showing all: 6 variant(s).


Variant ID.  4336
Epitope Seq.  FPRPWLHGL
Variant Seq.  FPRvWLHGL
Mutations P/V
Epitope Location P4V
HXB2 Location P37V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note FPRvWLHGL (P37V) was observed at various sampling time points in B*42+ (which is a restricting HLA for FL9) subject 021-M and her B*42+ child 021-C. It was sometimes observed as a covariant with L42S or G41Q.


Variant ID.  4337
Epitope Seq.  FPRPWLHGL
Variant Seq.  FPRmWLHGL
Mutations P/M
Epitope Location P4M
HXB2 Location P37M
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note FPRmWLHGL (P37M) was observed at various sampling time points in B*42+ (which is a restricting HLA for FL9) subject 021-M and her B*42+ child 021-C.


Variant ID.  4338
Epitope Seq.  FPRPWLHGL
Variant Seq.  FPRPWLHGs
Mutations L/S
Epitope Location L9S
HXB2 Location L42S
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note FPRPWLHGs (L42S) was observed in B*42+ (which is a restricting HLA for FL9) subject 021-M 0.1 years before the birth of her B*42+ child, 021-C. It was also seen in 021-C at 7.6 years. It was always observed as a covariant with P37V.


Variant ID.  4339
Epitope Seq.  FPRPWLHGL
Variant Seq.  FPRtWLHGL
Mutations P/T
Epitope Location P4T
HXB2 Location P37T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note FPRtWLHGL (P37T) arose in B*42+ (which is a restricting HLA for FL9) subject 021-C between 0.1 and 2.6 years.


Variant ID.  4340
Epitope Seq.  FPRPWLHGL
Variant Seq.  FPRaWLHGL
Mutations P/A
Epitope Location P4A
HXB2 Location P37A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note FPRaWLHGL (P37A) arose in B*42+ (which is a restricting HLA for FL9) subject 021-C between 2.6 and 4.9 years.


Variant ID.  4341
Epitope Seq.  FPRPWLHGL
Variant Seq.  FPRPWLHqL
Mutations G/Q
Epitope Location G8Q
HXB2 Location G41Q
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note FPRPWLHqL (G41Q) observed in B*42+ (which is a restricting HLA for FL9) subject 021-C at 4.9 years. It was observed as a covariant with P37V.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62230

HXB2 Location  Vpr(48-57)   Vpr Epitope Map
View variants at this location
Epitope ETYGDTWTGV   Epitope Alignment
Variants
aTYGDTWTGV   observed variant
ETYGDTWaGV   observed variant
Epitope Name Vpr-EV10
Species (MHC/HLA human(A*68)

Variant Details

Showing all: 2 variant(s).


Variant ID.  4294
Epitope Seq.  ETYGDTWTGV
Variant Seq.  aTYGDTWTGV
Mutations E/A
Epitope Location E1A
HXB2 Location E48A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note aTYGDTWTGV (E48A) was observed to be fixed at 100% frequency at all sampling time points in A*68- (which is a restricting HLA for EV10) subject 517-M and her A*68+ child, 517-C. It was always observed as a covariant with T55A.


Variant ID.  4295
Epitope Seq.  ETYGDTWTGV
Variant Seq.  ETYGDTWaGV
Mutations T/A
Epitope Location T8A
HXB2 Location T55A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note ETYGDTWaGV (T55A) was observed at all sampling time points in A*68- (which is a restricting HLA for EV10) subject 517-M and her A*68+ child, 517-C. It was always observed as a covariant with E48A.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62227

HXB2 Location  Rev(52-60)   Rev Epitope Map
View variants at this location
Epitope IHSISERIL   Epitope Alignment
Variants
IrSISERIL   observed variant
IHaISERIL   observed variant
IHSISERIi   observed variant
InSISERIL   observed variant
lHSISERIL   observed variant
IHSlSERIL   observed variant
vHSISERIL   observed variant
Epitope Name Rev-IL9
Species (MHC/HLA human(B*15:10)

Variant Details

Showing all: 7 variant(s).


Variant ID.  4277
Epitope Seq.  IHSISERIL
Variant Seq.  IrSISERIL
Mutations H/R
Epitope Location H2R
HXB2 Location H53R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IrSISERIL (H53R) was observed in B*15+ (which is a restricting HLA for IL9) subject 517-C at 0.2 years. However, it does not appear to have been transmitted from the B*15- mother, 517-C. This variant was always observed as a covariant with S54A. It was sometimes also observed alongside L60I.


Variant ID.  4278
Epitope Seq.  IHSISERIL
Variant Seq.  IHaISERIL
Mutations S/A
Epitope Location S3A
HXB2 Location S54A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IHaISERIL (S54A) was observed in B*15+ (which is a restricting HLA for IL9) subject 517-C at 0.2 years. However, it does not appear to have been transmitted from the B*15- mother, 517-C. This variant was always observed as a covariant with H53R. It was sometimes also observed alongside L60I.


Variant ID.  4279
Epitope Seq.  IHSISERIL
Variant Seq.  IHSISERIi
Mutations L/I
Epitope Location L9I
HXB2 Location L60I
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IHSISERIi (L60I) was observed in B*15+ (which is a restricting HLA for IL9) subject 517-C at 0.2 years. However, it does not appear to have been transmitted from the B*15- mother, 517-C. This variant was always observed as a covariant with both H53R and S54A.


Variant ID.  4280
Epitope Seq.  IHSISERIL
Variant Seq.  InSISERIL
Mutations H/N
Epitope Location H2N
HXB2 Location H53N
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note InSISERIL (H53N) was observed to arise in B*15+ (which is a restricting HLA for IL9) subject 517-C between 0.2 and 2.5 years. This variant was sometimes observed as a covariant with I52L, I52V, or I55L.


Variant ID.  4281
Epitope Seq.  IHSISERIL
Variant Seq.  lHSISERIL
Mutations I/L
Epitope Location I1L
HXB2 Location I52L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note lHSISERIL (I52L) was observed to arise in B*15+ (which is a restricting HLA for IL9) subject 517-C between 0.2 and 2.5 years. It was always observed as a covariant with H53N.


Variant ID.  4282
Epitope Seq.  IHSISERIL
Variant Seq.  IHSlSERIL
Mutations I/L
Epitope Location I4L
HXB2 Location I55L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IHSlSERIL (I55L) was observed to arise in B*15+ (which is a restricting HLA for IL9) subject 517-C between 2.5 and 5 years. It was always observed as a covariant with H53N.


Variant ID.  4283
Epitope Seq.  IHSISERIL
Variant Seq.  vHSISERIL
Mutations I/V
Epitope Location I1V
HXB2 Location I52V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note vHSISERIL (I52V) was observed to arise in B*15+ (which is a restricting HLA for IL9) subject 517-C between 2.5 and 5 years. It was always observed as a covariant with H53N.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62233

HXB2 Location  Rev(65-75)   Rev Epitope Map
View variants at this location
Epitope GRPAEPVPLQL   Epitope Alignment
Variants
GRPtEPVPLQL   observed variant
GRPAEPVPfQL   observed variant
GRPAEPVhLQL   observed variant
GRPAEPVsLQL   observed variant
GRlAEPVPLQL   observed variant
GRPAEPVaLQL   observed variant
GRPAEPVdLQL   observed variant
Epitope Name Rev-GL11
Species (MHC/HLA human(B*15:10)

Variant Details

Showing all: 7 variant(s).


Variant ID.  4304
Epitope Seq.  GRPAEPVPLQL
Variant Seq.  GRPtEPVPLQL
Mutations A/T
Epitope Location A4T
HXB2 Location A68T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note GRPtEPVPLQL (A68T) was observed at almost all sampling time points (the exception being the sample of 517-C at 0.2yr) in B*1510- (which is a restricting HLA for GL11) subject 517-M and her B*1510+ child, 517-C. It was sometimes observed as a covariant with L73F, P72H, P72S, P67L, P72A, or P72D.


Variant ID.  4305
Epitope Seq.  GRPAEPVPLQL
Variant Seq.  GRPAEPVPfQL
Mutations L/F
Epitope Location L9F
HXB2 Location L73F
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note GRPAEPVPfQL (L73F) was observed at all sampling time points in B*1510- (which is a restricting HLA for GL11) subject 517-M and her B*1510+ child, 517-C. It was always seen as a covariant with A86T, and was sometimes observed also with P72H, P72S, P67L, P72A, or P72D.


Variant ID.  4306
Epitope Seq.  GRPAEPVPLQL
Variant Seq.  GRPAEPVhLQL
Mutations P/H
Epitope Location P8H
HXB2 Location P72H
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note GRPAEPVhLQL (P72H) was observed in B*1510- (which is a restricting HLA for GL11) subject 517-M 0.25 years after the birth of her B*1510+ child, 517-C. However, it was never observed in 517-C. It was always seen as a covariant with A86T and L73H.


Variant ID.  4307
Epitope Seq.  GRPAEPVPLQL
Variant Seq.  GRPAEPVsLQL
Mutations P/S
Epitope Location P8S
HXB2 Location P72S
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note GRPAEPVsLQL (P72S) was observed in B*1510- (which is a restricting HLA for GL11) subject 517-M 6 years after the birth of her B*1510+ child, 517-C. It was also observed in 517-C at age 5. It always appeared alongside A68T and was sometimes also observed as a covariant with L73F.


Variant ID.  4308
Epitope Seq.  GRPAEPVPLQL
Variant Seq.  GRlAEPVPLQL
Mutations P/L
Epitope Location P3L
HXB2 Location P67L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note GRlAEPVPLQL (P67L) was observed in B*1510- (which is a restricting HLA for GL11) subject 517-M 6 years after the birth of her B*1510+ child, 517-C. It was also observed in 517-C at age 2.5. It always appeared alongside both A68T and L73F.


Variant ID.  4309
Epitope Seq.  GRPAEPVPLQL
Variant Seq.  GRPAEPVaLQL
Mutations P/A
Epitope Location P8A
HXB2 Location P72A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note GRPAEPVaLQL (P72A) arose in B*1510+ (which is a restricting HLA for GL11) subject 517-C between 2.5 and 5 years. It appeared alongside both A68T and L73F.


Variant ID.  4310
Epitope Seq.  GRPAEPVPLQL
Variant Seq.  GRPAEPVdLQL
Mutations P/D
Epitope Location P8D
HXB2 Location P72D
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note GRPAEPVdLQL (P72D) arose in B*1510+ (which is a restricting HLA for GL11) subject 517-C between 2.5 and 5 years. It was observed as a covariant with both A68T and L73F.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62240

HXB2 Location  gp160(209-217)   gp160 Epitope Map
View variants at this location
Epitope SFDPIPIHY   Epitope Alignment
Variants
SFnPIPIHY   observed variant
tFDPIPIHY   literature escape
SFDPlPIHY   observed variant
Epitope Name Env-SY9
Species (MHC/HLA human(A*29)

Variant Details

Showing all: 3 variant(s).


Variant ID.  4332
Epitope Seq.  SFDPIPIHY
Variant Seq.  SFnPIPIHY
Mutations D/N
Epitope Location D3N
HXB2 Location D211N
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SFnPIPIHY (D211N) was observed in A*29+ (which is a restricting HLA for SY9) subject 021-C when they were 0.1 years old.


Variant ID.  4333
Epitope Seq.  SFDPIPIHY
Variant Seq.  tFDPIPIHY
Mutations S/T
Epitope Location S1T
HXB2 Location S209T
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note tFDPIPIHY (S206T) is a documented escape variant. It arose in A*29+ (which is a restricting HLA for SY9) subject 021-C between 0.1 and 2.6 years. S206T was fixed to 100% frequency in 021-C before 4.9 years. It was sometimes observed as a covariant with I210L.


Variant ID.  4334
Epitope Seq.  SFDPIPIHY
Variant Seq.  SFDPlPIHY
Mutations I/L
Epitope Location I5L
HXB2 Location I213L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note SFDPlPIHY (I213L) was observed in A*29+ (which is a restricting HLA for SY9) subject 021-C when they were 7.6 years old. It was observed as a covariant with S206T.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62238

HXB2 Location  gp160(272-288)   gp160 Epitope Map
View variants at this location
Epitope IRSENLTNNAKTIIVHL   Epitope Alignment
Variants
IRSENLTdNAKTIIVHL   observed variant
IRSENLTNNvKTIIVHL   observed variant
IRSENLTNNiKTIIVHL   observed variant
IRtENLTNNAKTIIVHL   observed variant
IRSENLTNNtKTIIVHL   observed variant
IRSENLTNNArTIIVHL   observed variant
Epitope Name Env-OLP325
Species (MHC/HLA human(C*06:02)

Variant Details

Showing all: 6 variant(s).


Variant ID.  4326
Epitope Seq.  IRSENLTNNAKTIIVHL
Variant Seq.  IRSENLTdNAKTIIVHL
Mutations N/D
Epitope Location N8D
HXB2 Location N279D
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IRSENLTdNAKTIIVHL(N279D) was observed at all sampling time points in Cw*0602+ (which is a restricting HLA for OLP325) subject 133-M and her Cw*0602+ child, 133-C. It was sometimes observed as a covariant with A281V, A281I, A281T, or K282R.


Variant ID.  4327
Epitope Seq.  IRSENLTNNAKTIIVHL
Variant Seq.  IRSENLTNNvKTIIVHL
Mutations A/V
Epitope Location A10V
HXB2 Location A281V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IRSENLTNNvKTIIVHL(A281V) was observed in Cw*0602+ (which is a restricting HLA for OLP325) subject 133-M 7 years after the birth of her child. It was observed as a covariant with N279D.


Variant ID.  4328
Epitope Seq.  IRSENLTNNAKTIIVHL
Variant Seq.  IRSENLTNNiKTIIVHL
Mutations A/I
Epitope Location A10I
HXB2 Location A281I
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IRSENLTNNiKTIIVHL (A281I) was observed at all sampling time points in Cw*0602+ (which is a restricting HLA for OLP325) subject 133-M and her Cw*0602+ child, 133-C. It was often observed as a covariant with N279D.


Variant ID.  4329
Epitope Seq.  IRSENLTNNAKTIIVHL
Variant Seq.  IRtENLTNNAKTIIVHL
Mutations S/T
Epitope Location S3T
HXB2 Location S274T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IRtENLTNNAKTIIVHL (S274T) was observed in Cw*0602+ (which is a restricting HLA for OLP325) subject 133-M 7 years after the birth of her child, 133-C. It was observed as a covariant with A281I.


Variant ID.  4330
Epitope Seq.  IRSENLTNNAKTIIVHL
Variant Seq.  IRSENLTNNtKTIIVHL
Mutations A/T
Epitope Location A10T
HXB2 Location A281T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IRSENLTNNtKTIIVHL (A281T) was observed in Cw*0602+ (which is a restricting HLA for OLP325) subject 133-C beginning when they were 0.3 years old. It was always observed as a covariant with N279D and sometimes also observed with K282R.


Variant ID.  4331
Epitope Seq.  IRSENLTNNAKTIIVHL
Variant Seq.  IRSENLTNNArTIIVHL
Mutations K/R
Epitope Location K11R
HXB2 Location K282R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IRSENLTNNtKTIIVHL (K282R) was observed in Cw*0602+ (which is a restricting HLA for OLP325) subject 133-C when they were 2.7 years old. It was observed as a covariant with both N279D and A281T.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62225

HXB2 Location  gp160(298-307)   gp160 Epitope Map
View variants at this location
Epitope RPNNNTRKSI   Epitope Alignment
Variants
RPNNNTRrSI   observed variant
RPNNNTRKSt   observed variant
RPNNNTRKSv   observed variant
RPsNNTRKSI   observed variant
RPgNNTRKSI   observed variant
RtNNNTRKSI   observed variant
RPNNNTRKSm   observed variant
Epitope Name Env-RI10
Species (MHC/HLA human(B*42)

Variant Details

Showing all: 7 variant(s).


Variant ID.  4265
Epitope Seq.  RPNNNTRKSI
Variant Seq.  RPNNNTRrSI
Mutations K/R
Epitope Location K8R
HXB2 Location K305R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPNNNTRrSI (K305R) was observed in B*42+ (which is a restricting HLA for RI10) subject 517-M and her B*42+ child, 517-C. In both subjects, this variant was present at the first sampling time point. It was sometimes seen as a covariant with P299T, N300G, I307T, or I307M.


Variant ID.  4266
Epitope Seq.  RPNNNTRKSI
Variant Seq.  RPNNNTRKSt
Mutations I/T
Epitope Location I10T
HXB2 Location I307T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPNNNTRKSt (I307T) was observed to arise in both B*42+ (which is a restricting HLA for RI10) subject 517-M and her B*42+ child, 517-C. In 517-M, it was first observed when her child was 6 years old. In 517-C, it arose between 5 and 8.5yrs and was seen as a covariant with K305R and N300G.


Variant ID.  4267
Epitope Seq.  RPNNNTRKSI
Variant Seq.  RPNNNTRKSv
Mutations I/V
Epitope Location I10V
HXB2 Location I307V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPNNNTRKSv (I307V) was observed to arise in B*42+ (which is a restricting HLA for RI10) subject 517-M between 0.25 and 6 years after the birth of her child. It was sometimes seen as a covariant with N300S.


Variant ID.  4268
Epitope Seq.  RPNNNTRKSI
Variant Seq.  RPsNNTRKSI
Mutations N/S
Epitope Location N3S
HXB2 Location N300S
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPsNNTRKSI (N300S) was observed in B*42+ (which is a restricting HLA for RI10) subject 517-M and her B*42+ child, 517-C. It was first observed in 517-M when her child was aged 6 and in 517-C at age 2.5. It was sometimes seen as a covariant with I307T or K305R.


Variant ID.  4269
Epitope Seq.  RPNNNTRKSI
Variant Seq.  RPgNNTRKSI
Mutations N/G
Epitope Location N3G
HXB2 Location N300G
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPgNNTRKSI (N300G) was observed in B*42+ (which is a restricting HLA for RI10) subject 517-C. While it was observed at the first sampling time point (0.2yr) in subject 517-C, it was never observed in the B*42+ mother, 517-M. It was sometimes seen as a covariant with P299T, I307M, I307T, or K305R.


Variant ID.  4270
Epitope Seq.  RPNNNTRKSI
Variant Seq.  RtNNNTRKSI
Mutations P/T
Epitope Location P2T
HXB2 Location P299T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RtNNNTRKSI (P299T) was observed in B*42+ (which is a restricting HLA for RI10) subject 517-C. While it was observed at the first sampling time point (0.2yr) in subject 517-C, it was never observed in the B*42+ mother, 517-M. It was observed as a covariant with both N300G and K305R.


Variant ID.  4271
Epitope Seq.  RPNNNTRKSI
Variant Seq.  RPNNNTRKSm
Mutations I/M
Epitope Location I10M
HXB2 Location I307M
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPNNNTRKSm (I307M) was observed to arise in B*42+ (which is a restricting HLA for RI10) subject 517-C between 2.5 and 5 years. It was observed as a covariant with both N300G and K305R.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62237

HXB2 Location  gp160(614-631)   gp160 Epitope Map
View variants at this location
Epitope WSNKSQEDIWDNMTWMQW   Epitope Alignment
Variants
WnNKSQEDIWDNMTWMQW   observed variant
WSNKSQtDIWDNMTWMQW   observed variant
WSNKSQEDIWnNMTWMQW   observed variant
WSNKSQEeIWDNMTWMQW   observed variant
WSNKShEDIWDNMTWMQW   observed variant
WSNKSQsDIWDNMTWMQW   observed variant
WSNKSkEDIWDNMTWMQW   observed variant
WSNKSyEDIWDNMTWMQW   observed variant
Epitope Name Env-OLP371
Species (MHC/HLA human(C*04)

Variant Details

Showing all: 8 variant(s).


Variant ID.  4318
Epitope Seq.  WSNKSQEDIWDNMTWMQW
Variant Seq.  WnNKSQEDIWDNMTWMQW
Mutations S/N
Epitope Location S2N
HXB2 Location S615N
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note WnNKSQEDIWDNMTWMQW (S615N) was observed in Cw*04- (which is a restricting HLA for OLP371) subject 133-M 7 years after the birth of her child, 133-C. It was observed as a covariant with E620T and D624N.


Variant ID.  4319
Epitope Seq.  WSNKSQEDIWDNMTWMQW
Variant Seq.  WSNKSQtDIWDNMTWMQW
Mutations E/T
Epitope Location E7T
HXB2 Location E620T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note WSNKSQtDIWDNMTWMQW (E620T) was observed in Cw*04- (which is a restricting HLA for OLP371) subject 133-M 7 years after the birth of her child. It was also seen in her Cw*04+ child, 133-C, at all sampling time points. It was sometimes observed as a covariant with S615N, Q619H, Q619Y, D621E, or D624N.


Variant ID.  4320
Epitope Seq.  WSNKSQEDIWDNMTWMQW
Variant Seq.  WSNKSQEDIWnNMTWMQW
Mutations D/N
Epitope Location D11N
HXB2 Location D624N
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note WSNKSQEDIWnNMTWMQW(D624N) was observed in Cw*04- (which is a restricting HLA for OLP371) subject 133-M 7 years after the birth of her child. It was observed as a covariant with S615N and E620T.


Variant ID.  4321
Epitope Seq.  WSNKSQEDIWDNMTWMQW
Variant Seq.  WSNKSQEeIWDNMTWMQW
Mutations D/E
Epitope Location D8E
HXB2 Location D621E
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note WSNKSQEeIWDNMTWMQW(D621E) arose in Cw*04+ (which is a restricting HLA for OLP371) subject 133-C between 0.3 and 2.7 years. It was observed as a covariant with E620T.


Variant ID.  4322
Epitope Seq.  WSNKSQEDIWDNMTWMQW
Variant Seq.  WSNKShEDIWDNMTWMQW
Mutations Q/H
Epitope Location Q6H
HXB2 Location Q619H
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note WSNKShEDIWDNMTWMQW(Q619H) was observed in Cw*04+ (which is a restricting HLA for OLP371) subject 133-C at 4.9 years. It was observed as a covariant with E620T.


Variant ID.  4323
Epitope Seq.  WSNKSQEDIWDNMTWMQW
Variant Seq.  WSNKSQsDIWDNMTWMQW
Mutations E/S
Epitope Location E7S
HXB2 Location E620S
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note WSNKShEDIWDNMTWMQW(E620S) was observed in Cw*04+ (which is a restricting HLA for OLP371) subject 133-C at 4.9 years. It was observed as a covariant with Q619K.


Variant ID.  4324
Epitope Seq.  WSNKSQEDIWDNMTWMQW
Variant Seq.  WSNKSkEDIWDNMTWMQW
Mutations Q/K
Epitope Location Q6K
HXB2 Location Q619K
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note WSNKSkEDIWDNMTWMQW(Q619K) was observed in Cw*04+ (which is a restricting HLA for OLP371) subject 133-C at 4.9 years. It was observed as a covariant with E620S.


Variant ID.  4325
Epitope Seq.  WSNKSQEDIWDNMTWMQW
Variant Seq.  WSNKSyEDIWDNMTWMQW
Mutations Q/Y
Epitope Location Q6Y
HXB2 Location Q619Y
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note WSNKSyEDIWDNMTWMQW(Q619Y) was observed in Cw*04+ (which is a restricting HLA for OLP371) subject 133-C at 7.7 years. It was observed as a covariant with E620T.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62223

HXB2 Location  gp160(704-712)   gp160 Epitope Map
View variants at this location
Epitope IVNRVRQGY   Epitope Alignment
Variants
vVNRVRQGY   observed variant
IVrRVRQGY   observed variant
IVsRVRQGY   observed variant
IVNkVRQGY   observed variant
Epitope Name Env-IY9
Species (MHC/HLA human(A*30)

Variant Details

Showing all: 4 variant(s).


Variant ID.  4259
Epitope Seq.  IVNRVRQGY
Variant Seq.  vVNRVRQGY
Mutations I/V
Epitope Location I1V
HXB2 Location I704V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note vVNRVRQGY (I704V) was observed in A*30+ (which is a restricting HLA for IY9) subject 517-M 0.24 years after the birth of her A*30+ child, 517-C. While it was not initially observed in 517-C, it was seen in later samples from 2.5 yrs on. It was often observed as a covariant with N706R and sometimes with N706S or R707K.


Variant ID.  4260
Epitope Seq.  IVNRVRQGY
Variant Seq.  IVrRVRQGY
Mutations N/R
Epitope Location N3R
HXB2 Location N706R
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IVrRVRQGY (N706R) was observed in A*30+ (which is a restricting HLA for IY9) subject 517-M 0.24 years after the birth of her A*30+ child, 517-C. While it was not initially observed in 517-C, it was seen in later samples from 2.5 yrs on. It was often observed as a covariant with I704V and sometimes also with R707K.


Variant ID.  4261
Epitope Seq.  IVNRVRQGY
Variant Seq.  IVsRVRQGY
Mutations N/S
Epitope Location N3S
HXB2 Location N706S
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IVsRVRQGY (N706S) was observed in A*30+ (which is a restricting HLA for IY9) subject 517-M 0.25 years after the birth of her A*30+ child, 517-C. It was sometimes observed as a covariant with I704V.


Variant ID.  4262
Epitope Seq.  IVNRVRQGY
Variant Seq.  IVNkVRQGY
Mutations R/K
Epitope Location R4K
HXB2 Location R707K
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IVNkVRQGY (R707K) was observed in A*30+ (which is a restricting HLA for IY9) subject 517-M 6 years after the birth of her A*30+ child, 517-C. Some samples from 517-C also contained this variant. It was observed as a covariant with both I704V and N706R.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62224

HXB2 Location  gp160(794-802)   gp160 Epitope Map
View variants at this location
Epitope KYLGSLVQY   Epitope Alignment
Variants
KYLGnLVQY   observed variant
KYLGSLVlY   observed variant
Epitope Name Env-KY9
Species (MHC/HLA human(A*30)

Variant Details

Showing all: 2 variant(s).


Variant ID.  4263
Epitope Seq.  KYLGSLVQY
Variant Seq.  KYLGnLVQY
Mutations S/N
Epitope Location S5N
HXB2 Location S798N
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note KYLGnLVQY (S798N) was observed in A*30+ (which is a restricting HLA for KY9) subject 517-C beginning at the first sampling time point (age 0.2yrs). However it was not observed in 517-C’s A*30+ mother, 517-M.


Variant ID.  4264
Epitope Seq.  KYLGSLVQY
Variant Seq.  KYLGSLVlY
Mutations Q/L
Epitope Location Q8L
HXB2 Location Q801L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note KYLGSLVlY (Q801L) was observed in A*30+ (which is a restricting HLA for KY9) subject 517-C at the first sampling time point (age 0.2yrs). However it was not observed in 517-C’s A*30+ mother, 517-M.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62226

HXB2 Location  gp160(843-851)   gp160 Epitope Map
View variants at this location
Epitope IPRRIRQGF   Epitope Alignment
Variants
lPRRIRQGF   observed variant
IPRRvRQGF   observed variant
IPRRlRQGF   observed variant
IPRRfRQGF   observed variant
IPtRIRQGF   observed variant
Epitope Name Env-IF9
Species (MHC/HLA human(B*42)

Variant Details

Showing all: 5 variant(s).


Variant ID.  4272
Epitope Seq.  IPRRIRQGF
Variant Seq.  lPRRIRQGF
Mutations I/L
Epitope Location I1L
HXB2 Location I843L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note lPRRIRQGF (I843L) was observed in B*42+ (which is a restricting HLA for IF9) subject 517-M and her B*42+ child, 517-C. It was sometimes observed as a covariant with I847V, I847L, I847F, or R845T.


Variant ID.  4273
Epitope Seq.  IPRRIRQGF
Variant Seq.  IPRRvRQGF
Mutations I/V
Epitope Location I5V
HXB2 Location I847V
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IPRRvRQGF (I847V) was observed in B*42+ (which is a restricting HLA for IF9) subject 517-M and her B*42+ child, 517-C. While it was not observed in 517-C at the first sampling time point, it appeared in later samples. This variant was always observed as a covariant with I843L.


Variant ID.  4274
Epitope Seq.  IPRRIRQGF
Variant Seq.  IPRRlRQGF
Mutations I/L
Epitope Location I5L
HXB2 Location I847L
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IPRRlRQGF (I847L) was observed in B*42+ (which is a restricting HLA for IF9) subject 517-M when her child was 6. While it was not observed in her B*42+ child, 517-C, at the first sampling time point, it appeared in later samples. This variant was always observed as a covariant with I843L.


Variant ID.  4275
Epitope Seq.  IPRRIRQGF
Variant Seq.  IPRRfRQGF
Mutations I/F
Epitope Location I5F
HXB2 Location I847F
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IPRRfRQGF (I847F) was observed in B*42+ (which is a restricting HLA for IF9) subject 517-M when her child was 6. While it was not observed in her B*42+ child, 517-C, at the first sampling time point, it appeared in later samples. This variant was always observed as a covariant with I843L.


Variant ID.  4276
Epitope Seq.  IPRRIRQGF
Variant Seq.  IPtRIRQGF
Mutations R/T
Epitope Location R3T
HXB2 Location R845T
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note IPtRIRQGF (R845T) arose in B*42+ (which is a restricting HLA for IF9) subject 517-C between 5 and 8.5 years. This variant was always observed as a covariant with I843L.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


Displaying record number 62218

HXB2 Location  Nef(71-79)   Nef Epitope Map
View variants at this location
Epitope RPQVPLRPM   Epitope Alignment
Variants
RPQVPvRPM   literature escape
RPQaPLRPM   observed variant
kPQVPLRPM   observed variant
RPQVPiRPM   literature escape
RPQVPtRPM   literature escape
Epitope Name Nef-RM9
Species (MHC/HLA human(B*81:01)

Variant Details

Showing all: 5 variant(s).


Variant ID.  4243
Epitope Seq.  RPQVPLRPM
Variant Seq.  RPQVPvRPM
Mutations L/V
Epitope Location L6V
HXB2 Location L76V
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPQVPvRPM (L76X) is a known escape variant. It was observed in the B*81+ (which is the restricting HLA for RM9) child, 133-C, at 0.3yr. The only available data from the B*81- mother, 133-M, shows no L76X variant present in 133-M when her child was of age 7yr. In 133-C, the L76V mutation was sometimes observed as a co-variant with the R71K mutation.


Variant ID.  4244
Epitope Seq.  RPQVPLRPM
Variant Seq.  RPQaPLRPM
Mutations V/A
Epitope Location V4A
HXB2 Location V74A
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPQaPLRPM was observed in the B*81+ (which is the restricting HLA for RM9) child, 133-C, at 0.3yr.


Variant ID.  4245
Epitope Seq.  RPQVPLRPM
Variant Seq.  kPQVPLRPM
Mutations R/K
Epitope Location R1K
HXB2 Location R71K
Mutation Type OV: observed variant
Epitope Subtype C
Variant Subtype C
Method Sequence
Note kPQVPLRPM was observed in the B*81+ (which is the restricting HLA for RM9) child, 133-C, at 0.3yr. The R71K mutation was sometimes observed as a co-variant with the L76V mutation.


Variant ID.  4246
Epitope Seq.  RPQVPLRPM
Variant Seq.  RPQVPiRPM
Mutations L/I
Epitope Location L6I
HXB2 Location L76I
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPQVPiRPM (L76X) is a known escape variant. It arose in the B*81+ (which is the restricting HLA for RM9) child, 133-C, between 0.3 and 2.7yr.


Variant ID.  4247
Epitope Seq.  RPQVPLRPM
Variant Seq.  RPQVPtRPM
Mutations L/T
Epitope Location L6T
HXB2 Location L76T
Mutation Type LE: literature escape
Epitope Subtype C
Variant Subtype C
Method Sequence
Note RPQVPtRPM (L76X) is a known escape variant. It arose in the B*81+ (which is the restricting HLA for RM9) child, 133-C, between 2.7 and 4.9yr.

References

Leitman2017 Ellen M. Leitman, Christina F. Thobakgale, Emily Adland, M. Azim Ansari, Jayna Raghwani, Andrew J. Prendergast, Gareth Tudor-Williams, Photini Kiepiela, Joris Hemelaar, Jacqui Brener, Ming-Han Tsai, Masahiko Mori, Lynn Riddell, Graz Luzzi, Pieter Jooste, Thumbi Ndung'u, Bruce D. Walker, Oliver G. Pybus, Paul Kellam, Vivek Naranbhai, Philippa C. Matthews, Astrid Gall, and Philip J. R. Goulder. Role of HIV-Specific CD8+ T Cells in Pediatric HIV Cure Strategies after Widespread Early Viral Escape. J. Exp. Med., 214(11):3239-3261, 6 Nov 2017. PubMed ID: 28983013. Show all entries for this paper.


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