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Found 20 matching records:

Displaying record number 54627

HXB2 Location  Gag(24-31)   Gag Epitope Map
View variants at this location
Epitope GGKKKYKL   Epitope Alignment
Variants
GGKKKYKf   escape documented in this paper
Epitope Name GL8
Species (MHC/HLA human(B8)

Variant Details

Showing all: 1 variant(s).


Variant ID.  954
Epitope Seq.  GGKKKYKL
Variant Seq.  GGKKKYKf
Mutations L/F
Epitope Location L8F
HXB2 Location L31F
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Presumed escape variant was transmitted from a B8 positive donor to a B8 negative recipient. The variant was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54145

HXB2 Location  Gag(145-155)   Gag Epitope Map
View variants at this location
Epitope QAISPRTLNAW   Epitope Alignment
Variants
QAlSPRTLNAW   diminished response
Epitope Name QW11
Species (MHC/HLA human(A*25:01)

Variant Details

Showing all: 1 variant(s).


Variant ID.  955
Epitope Seq.  QAISPRTLNAW
Variant Seq.  QAlSPRTLNAW
Mutations I/L
Epitope Location I3L
HXB2 Location I147L
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Amino acid site in the third position potentially experienced positive selection. Wt form of the epitope was 2.4 times better recognized than the variant.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54147

HXB2 Location  Gag(203-212)   Gag Epitope Map
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Epitope ETINEEAAEW   Epitope Alignment
Variants
ETINdEAAEW   diminished response
Epitope Name EW10
Species (MHC/HLA human(A*25:01)

Variant Details

Showing all: 1 variant(s).


Variant ID.  956
Epitope Seq.  ETINEEAAEW
Variant Seq.  ETINdEAAEW
Mutations E/D
Epitope Location E5D
HXB2 Location E207D
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Amino acid site in the 5th position potentially experienced positive selection. Wt form of the epitope was 27 times better recognized than the variant, making the variant a partial escape.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54149

HXB2 Location  Pol(24-31)   Pol Epitope Map
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Epitope NSPTRREL   Epitope Alignment
Variants
tSPTRREL   escape documented in this paper
Epitope Name NL8
Species (MHC/HLA human(C*01:02)

Variant Details

Showing all: 1 variant(s).


Variant ID.  957
Epitope Seq.  NSPTRREL
Variant Seq.  tSPTRREL
Mutations N/T
Epitope Location N1T
HXB2 Location N24T
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Position 4 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54151

HXB2 Location  Pol(283-290)   Pol Epitope Map
View variants at this location
Epitope TAFTIPSI   Epitope Alignment
Variants
TAFTIPSt   diminished response
TAFTIPSr   diminished response
TAFTIPSv   diminished response
Epitope Name TI8
Species (MHC/HLA human(B*51:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  958
Epitope Seq.  TAFTIPSI
Variant Seq.  TAFTIPSt
Mutations I/T
Epitope Location I8T
HXB2 Location I290T
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Last position (8) of the epitope had potentially experienced positive selection. Wt form of the epitope was >100 times better recognized than the variant, making the variant a partial escape.


Variant ID.  959
Epitope Seq.  TAFTIPSI
Variant Seq.  TAFTIPSr
Mutations I/R
Epitope Location I8R
HXB2 Location I290R
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Last position (8) of the epitope had potentially experienced positive selection. Wt form of the epitope was >100 times better recognized than the variant, making the variant a partial escape.


Variant ID.  960
Epitope Seq.  TAFTIPSI
Variant Seq.  TAFTIPSv
Mutations I/V
Epitope Location I8V
HXB2 Location I290V
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Last position (8) of the epitope had potentially experienced positive selection. Wt form of the epitope was >100 times better recognized than the variant, making the variant a partial escape.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54152

HXB2 Location  Pol(291-299)   Pol Epitope Map
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Epitope NNETPGVRY   Epitope Alignment
Variants
NNETPGiRY   susceptible form
NsETPGVRY   susceptible form
NNEiPGVRY   susceptible form
NNEiPGiRY   susceptible form
NNgTPGVRY   diminished response
NNEvPGiRY   susceptible form
Epitope Name NY9
Species (MHC/HLA human(B*18:01)

Variant Details

Showing all: 6 variant(s).


Variant ID.  961
Epitope Seq.  NNETPGVRY
Variant Seq.  NNETPGiRY
Mutations V/I
Epitope Location V7I
HXB2 Location V297I
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note The variant was recognized by CTLs to a similar extent as the wt form of the epitope.


Variant ID.  962
Epitope Seq.  NNETPGVRY
Variant Seq.  NsETPGVRY
Mutations N/S
Epitope Location N2S
HXB2 Location N292S
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note The variant was recognized by CTLs to a similar extent as the wt form of the epitope.


Variant ID.  963
Epitope Seq.  NNETPGVRY
Variant Seq.  NNEiPGVRY
Mutations T/I
Epitope Location T4I
HXB2 Location T294I
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note The variant was recognized by CTLs to a similar extent as the wt form of the epitope.


Variant ID.  964
Epitope Seq.  NNETPGVRY
Variant Seq.  NNEiPGiRY
Mutations T/I V/I
Epitope Location T4I V7I
HXB2 Location T294I V297I
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note The variant was recognized by CTLs to a similar extent as the wt form of the epitope.


Variant ID.  965
Epitope Seq.  NNETPGVRY
Variant Seq.  NNgTPGVRY
Mutations E/G
Epitope Location E3G
HXB2 Location E293G
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Wt form of the epitope was 22 times better recognized than the variant, making the variant a partial escape.


Variant ID.  966
Epitope Seq.  NNETPGVRY
Variant Seq.  NNEvPGiRY
Mutations T/V V/I
Epitope Location T4V V7I
HXB2 Location T294V V297I
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note The variant was recognized by CTLs to a similar extent as the wt form of the epitope.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54153

HXB2 Location  Pol(359-367)   Pol Epitope Map
View variants at this location
Epitope ELRQHLLRW   Epitope Alignment
Variants
ELRQHLLkW   escape documented in this paper
Epitope Name EW9
Species (MHC/HLA human(A*25:01)

Variant Details

Showing all: 1 variant(s).


Variant ID.  967
Epitope Seq.  ELRQHLLRW
Variant Seq.  ELRQHLLkW
Mutations R/K
Epitope Location R8K
HXB2 Location R366K
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note This is a newly defined epitope. Position 8 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54155

HXB2 Location  Vpr(29-37)   Vpr Epitope Map
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Epitope EAVRHFPRI   Epitope Alignment
Variants
EAVRHFPRt   diminished response
EAVRHFPRl   diminished response
Epitope Name EI9
Species (MHC/HLA human(B*51:01)

Variant Details

Showing all: 2 variant(s).


Variant ID.  968
Epitope Seq.  EAVRHFPRI
Variant Seq.  EAVRHFPRt
Mutations I/T
Epitope Location I9T
HXB2 Location I37T
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Last position (9)in the epitope had potentially experienced positive selection. Wt form of the epitope was 43 times better recognized than the variant, making the variant a partial escape.


Variant ID.  969
Epitope Seq.  EAVRHFPRI
Variant Seq.  EAVRHFPRl
Mutations I/L
Epitope Location I9L
HXB2 Location I37L
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Last position (9)in the epitope had potentially experienced positive selection. Wt form of the epitope was 18 times better recognized than the variant, making the variant a partial escape.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54158

HXB2 Location  Tat(3-11)   Tat Epitope Map
View variants at this location
Epitope PVDPRLEPW   Epitope Alignment
Variants
PVDPRLdPW   escape documented in this paper
PVDPsLEPW   escape documented in this paper
PVDPkLEPW   escape documented in this paper
Epitope Name PW9
Species (MHC/HLA human(A*25:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  970
Epitope Seq.  PVDPRLEPW
Variant Seq.  PVDPRLdPW
Mutations E/D
Epitope Location E7D
HXB2 Location E9D
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 5 and 7 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.


Variant ID.  971
Epitope Seq.  PVDPRLEPW
Variant Seq.  PVDPsLEPW
Mutations R/S
Epitope Location R5S
HXB2 Location R7S
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 5 and 7 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.


Variant ID.  972
Epitope Seq.  PVDPRLEPW
Variant Seq.  PVDPkLEPW
Mutations R/K
Epitope Location R5K
HXB2 Location R7K
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 5 and 7 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54159

HXB2 Location  Tat(30-37)   Tat Epitope Map
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Epitope CCFHCQVC   Epitope Alignment
Variants
CClHCQVC   escape documented in this paper
CCFHCQsC   escape documented in this paper
Epitope Name CC8
Species (MHC/HLA human(C*12:03)

Variant Details

Showing all: 2 variant(s).


Variant ID.  973
Epitope Seq.  CCFHCQVC
Variant Seq.  CClHCQVC
Mutations F/L
Epitope Location F3L
HXB2 Location F32L
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Position 3 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.


Variant ID.  974
Epitope Seq.  CCFHCQVC
Variant Seq.  CCFHCQsC
Mutations V/S
Epitope Location V7S
HXB2 Location V36S
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Position 3 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54157

HXB2 Location  Vpu(74-82)   Vpu Epitope Map
View variants at this location
Epitope HAPWDVNDL   Epitope Alignment
Variants
HAPWDVNDm   susceptible form
Epitope Name HL9
Species (MHC/HLA human(C*01:02)

Variant Details

Showing all: 1 variant(s).


Variant ID.  975
Epitope Seq.  HAPWDVNDL
Variant Seq.  HAPWDVNDm
Mutations L/M
Epitope Location L9M
HXB2 Location L82M
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note Last position (9) in the epitope had potentially experienced positive selection. The variant was recognized by CTLs to at a better extent than the wt form of the epitope.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54160

HXB2 Location  gp160(31-39)   gp160 Epitope Map
View variants at this location
Epitope AENLWVTVY   Epitope Alignment
Variants
AdNLWVTVY   susceptible form
tdNLWVTVY   susceptible form
tEdLWVTVY   escape documented in this paper
eEdLWVTVY   escape documented in this paper
AEdsWVTVY   escape documented in this paper
Epitope Name AY9
Species (MHC/HLA human(B*18:01)

Variant Details

Showing all: 5 variant(s).


Variant ID.  976
Epitope Seq.  AENLWVTVY
Variant Seq.  AdNLWVTVY
Mutations E/D
Epitope Location E2D
HXB2 Location E32D
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note Position 1 in the epitope had potentially experienced positive selection. The variant was recognized by CTLs to a similar extent as the wt form of the epitope.


Variant ID.  977
Epitope Seq.  AENLWVTVY
Variant Seq.  tdNLWVTVY
Mutations A/T E/D
Epitope Location A1T E2D
HXB2 Location A31T E32D
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note Position 1 in the epitope had potentially experienced positive selection. The variant was recognized by CTLs to a similar extent as the wt form of the epitope.


Variant ID.  978
Epitope Seq.  AENLWVTVY
Variant Seq.  tEdLWVTVY
Mutations A/T N/D
Epitope Location A1T N3D
HXB2 Location A31T N33D
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Position 1 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.


Variant ID.  979
Epitope Seq.  AENLWVTVY
Variant Seq.  eEdLWVTVY
Mutations A/E N/D
Epitope Location A1E N3D
HXB2 Location A31E N33D
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Position 1 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.


Variant ID.  980
Epitope Seq.  AENLWVTVY
Variant Seq.  AEdsWVTVY
Mutations N/D L/S
Epitope Location N3D L4S
HXB2 Location N33D L34S
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Position 1 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54161

HXB2 Location  gp160(61-69)   gp160 Epitope Map
View variants at this location
Epitope YETEVHNVW   Epitope Alignment
Variants
YgTEVHNVW   diminished response
YdTEVHNVW   diminished response
YETEaHNVW   susceptible form
YdTEaHNVW   diminished response
Epitope Name YW9
Species (MHC/HLA human(B*18:01)

Variant Details

Showing all: 4 variant(s).


Variant ID.  981
Epitope Seq.  YETEVHNVW
Variant Seq.  YgTEVHNVW
Mutations E/G
Epitope Location E2G
HXB2 Location E62G
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Positions 2 and 5 in the epitope had potentially experienced positive selection. Wt form of the epitope was 22 times better recognized than the variant, making the variant a partial escape.


Variant ID.  982
Epitope Seq.  YETEVHNVW
Variant Seq.  YdTEVHNVW
Mutations E/D
Epitope Location E2D
HXB2 Location E62D
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Positions 2 and 5 in the epitope had potentially experienced positive selection. Wt form of the epitope was 13 times better recognized than the variant, making the variant a partial escape.


Variant ID.  983
Epitope Seq.  YETEVHNVW
Variant Seq.  YETEaHNVW
Mutations V/A
Epitope Location V5A
HXB2 Location V65A
Mutation Type SF: susceptible form
Method CD8 T-cell Elispot - IFNy
Note Positions 2 and 5 in the epitope had potentially experienced positive selection. The variant was recognized by CTLs to a similar extent as the wt form of the epitope.


Variant ID.  984
Epitope Seq.  YETEVHNVW
Variant Seq.  YdTEaHNVW
Mutations E/D V/A
Epitope Location E2D V5A
HXB2 Location E62D V65A
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Positions 2 and 5 in the epitope had potentially experienced positive selection. Wt form of the epitope was >83 times better recognized than the variant, making the variant a partial escape.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54162

HXB2 Location  gp160(88-96)   gp160 Epitope Map
View variants at this location
Epitope NVTENFNMW   Epitope Alignment
Variants
NVTEdFdMW   escape documented in this paper
NVTEeFdMW   escape documented in this paper
NVTEsFdMW   escape documented in this paper
Epitope Name NW9
Species (MHC/HLA human(A*25:01)

Variant Details

Showing all: 3 variant(s).


Variant ID.  985
Epitope Seq.  NVTENFNMW
Variant Seq.  NVTEdFdMW
Mutations N/D N/D
Epitope Location N5D N7D
HXB2 Location N92D N94D
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 5 and 7 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.


Variant ID.  986
Epitope Seq.  NVTENFNMW
Variant Seq.  NVTEeFdMW
Mutations N/E N/D
Epitope Location N5E N7D
HXB2 Location N92E N94D
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 5 and 7 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.


Variant ID.  987
Epitope Seq.  NVTENFNMW
Variant Seq.  NVTEsFdMW
Mutations N/S N/D
Epitope Location N5S N7D
HXB2 Location N92S N94D
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 5 and 7 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54163

HXB2 Location  gp160(217-226)   gp160 Epitope Map
View variants at this location
Epitope YCAPAGFAIL   Epitope Alignment
Variants
YCAPAGFAIi   escape documented in this paper
Epitope Name YL10
Species (MHC/HLA human(C*01:02)

Variant Details

Showing all: 1 variant(s).


Variant ID.  988
Epitope Seq.  YCAPAGFAIL
Variant Seq.  YCAPAGFAIi
Mutations L/I
Epitope Location L10I
HXB2 Location L226I
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Last position (10)in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54164

HXB2 Location  gp160(321-330)   gp160 Epitope Map
View variants at this location
Epitope EIIGDIRQAY   Epitope Alignment
Variants
qIIGDIRQAY   diminished response
dIIGDIRQAh   diminished response
EIIGnIRQAh   diminished response
EIIGDIRQAh   escape documented in this paper
Epitope Name EY10
Species (MHC/HLA human(A*25:01)

Variant Details

Showing all: 4 variant(s).


Variant ID.  989
Epitope Seq.  EIIGDIRQAY
Variant Seq.  qIIGDIRQAY
Mutations E/Q
Epitope Location E1Q
HXB2 Location E321Q
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Positions 1, 5 and 10 (last)in the epitope had potentially experienced positive selection. Wt form of the epitope was >200 times better recognized than the variant, making the variant a partial escape.


Variant ID.  990
Epitope Seq.  EIIGDIRQAY
Variant Seq.  dIIGDIRQAh
Mutations E/D Y/H
Epitope Location E1D Y10H
HXB2 Location E321D Y330H
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Positions 1, 5 and 10 (last)in the epitope had potentially experienced positive selection. Wt form of the epitope was 34 times better recognized than the variant, making the variant a partial escape.


Variant ID.  991
Epitope Seq.  EIIGDIRQAY
Variant Seq.  EIIGnIRQAh
Mutations Y/H D/N
Epitope Location Y10H D5N
HXB2 Location Y330H D325N
Mutation Type DR: diminished response
Method CD8 T-cell Elispot - IFNy
Note Positions 1, 5 and 10 (last)in the epitope had potentially experienced positive selection. Wt form of the epitope was 15.9 times better recognized than the variant, making the variant a partial escape.


Variant ID.  992
Epitope Seq.  EIIGDIRQAY
Variant Seq.  EIIGDIRQAh
Mutations Y/H
Epitope Location Y10H
HXB2 Location Y330H
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 1, 5 and 10 (last)in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54165

HXB2 Location  gp160(341-349)   gp160 Epitope Map
View variants at this location
Epitope TLSQIVTKL   Epitope Alignment
Variants
TLSkIVTKL   escape documented in this paper
Epitope Name TL9
Species (MHC/HLA human(A*02:01)

Variant Details

Showing all: 1 variant(s).


Variant ID.  993
Epitope Seq.  TLSQIVTKL
Variant Seq.  TLSkIVTKL
Mutations Q/K
Epitope Location Q4K
HXB2 Location Q344K
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Position 4 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54167

HXB2 Location  gp160(712-720)   gp160 Epitope Map
View variants at this location
Epitope YSPLSLQTL   Epitope Alignment
Variants
YSPLSLQTr   escape documented in this paper
Epitope Name YL9
Species (MHC/HLA human(C*01:02)

Variant Details

Showing all: 1 variant(s).


Variant ID.  994
Epitope Seq.  YSPLSLQTL
Variant Seq.  YSPLSLQTr
Mutations L/R
Epitope Location L9R
HXB2 Location L720R
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Last position (9)in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54168

HXB2 Location  Nef(5-13)   Nef Epitope Map
View variants at this location
Epitope WSKSSIIGW   Epitope Alignment
Variants
WSKtSIIGW   escape documented in this paper
WSKSSmIGW   escape documented in this paper
Epitope Name WW9
Species (MHC/HLA human(A*25:01)

Variant Details

Showing all: 2 variant(s).


Variant ID.  995
Epitope Seq.  WSKSSIIGW
Variant Seq.  WSKtSIIGW
Mutations S/T
Epitope Location S4T
HXB2 Location S8T
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 4 and 6 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.


Variant ID.  996
Epitope Seq.  WSKSSIIGW
Variant Seq.  WSKSSmIGW
Mutations I/M
Epitope Location I6M
HXB2 Location I10M
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Positions 4 and 6 in the epitope had potentially experienced positive selection. The variant was full escape, as it was not recognized by CTLs.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


Displaying record number 54172

HXB2 Location  Nef(90-97)   Nef Epitope Map
View variants at this location
Epitope FLKEKGGL   Epitope Alignment
Variants
FLKEeGGL   escape documented in this paper
FLKEgGGL   observed variant
FLKgeGGL   observed variant
FLKveGGL   observed variant
cLKEKGGL   observed variant
sLKEKGGL   observed variant
FLKEeGGL{p}   observed variant
Epitope Name FL8
Species (MHC/HLA human(B8)

Variant Details

Showing all: 7 variant(s).


Variant ID.  997
Epitope Seq.  FLKEKGGL
Variant Seq.  FLKEeGGL
Mutations K/E
Epitope Location K5E
HXB2 Location K94E
Mutation Type E: escape documented in this paper
Method CD8 T-cell Elispot - IFNy
Note Presumed escape variant was transmitted from a B8 positive donor to a B8 negative recipient. The variant was not recognized by CTLs.


Variant ID.  998
Epitope Seq.  FLKEKGGL
Variant Seq.  FLKEgGGL
Mutations K/G
Epitope Location K5G
HXB2 Location K94G
Mutation Type OV: observed variant
Note Variant was found in 2/26 clones in the patient at sampling times 76 and 113.


Variant ID.  999
Epitope Seq.  FLKEKGGL
Variant Seq.  FLKgeGGL
Mutations E/G K/E
Epitope Location E4G K5E
HXB2 Location E93G K94E
Mutation Type OV: observed variant
Note Variant was found in 1/39 clones in the patient at sampling times 8, 22 and 50.


Variant ID.  1001
Epitope Seq.  FLKEKGGL
Variant Seq.  FLKveGGL
Mutations E/V K/E
Epitope Location E4V K5E
HXB2 Location E93V K94E
Mutation Type OV: observed variant
Note Variant was found in 2/10 clones in the patient at sampling time 23.


Variant ID.  2259
Epitope Seq.  FLKEKGGL
Variant Seq.  cLKEKGGL
Mutations F/C
Epitope Location F1C
HXB2 Location F90C
Mutation Type OV: observed variant
Note Variant was found in 1/68 clones in the patient at several latter sampling times.


Variant ID.  2260
Epitope Seq.  FLKEKGGL
Variant Seq.  sLKEKGGL
Mutations F/S
Epitope Location F1S
HXB2 Location F90S
Mutation Type OV: observed variant
Note Variant was found in 1/68 clones in the patient at several latter sampling times.


Variant ID.  2275
Epitope Seq.  FLKEKGGL{E}
Variant Seq.  FLKEeGGL{p}
Mutations E/P K/E
Epitope Location E+1P K5E
HXB2 Location E98P K94E
Mutation Type OV: observed variant
Note Reversion variant was observed in the patient at several different sampling times.

References

Liu2006 Yi Liu, John McNevin, Jianhong Cao, Hong Zhao, Indira Genowati, Kim Wong, Sherry McLaughlin, Matthew D. McSweyn, Kurt Diem, Claire E. Stevens, Janine Maenza, Hongxia He, David C. Nickle, Daniel Shriner, Sarah E. Holte, Ann C. Collier, Lawrence Corey, M. Juliana McElrath, and James I. Mullins. Selection on the Human Immunodeficiency Virus Type 1 Proteome following Primary Infection. J. Virol., 80(19):9519-9529, Oct 2006. PubMed ID: 16973556. Show all entries for this paper.


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