Search CTL/CD8+ T-Cell Epitope Database

Found 33 matching records:

Displaying record number 56676

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HXB2 Location	Gag(25-42) p17(25-42) DNA(862..915)	Gag Epitope Map
Author Location	Gag(25-42)
Epitope	GKKQYKLKHIVWASRELE	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This invariant peptide sequence, GKKQYKLKHIVWASRELE, studied as part of transmitted sequence GKKQYKLKHIVWASRELERFAVNPSLLETSEGCR, was recognized in patient CH77. No mutants were seen and there is no statistical evidence for selection towards change in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56678

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HXB2 Location	Gag(33-50) p17(33-50) DNA(886..939)	Gag Epitope Map
Author Location	Gag(33-50)
Epitope	HIVWASRELERFAVNPSL	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This invariant peptide sequence, HIVWASRELERFAVNPSL, studied as part of transmitted sequence GKKQYKLKHIVWASRELERFAVNPSLLETSEGCR, was recognized in patient CH77. No mutants were seen and there is no statistical evidence for selection towards change in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56677

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HXB2 Location	Gag(41-58) p17(41-58) DNA(910..963)	Gag Epitope Map
Author Location	Gag(41-58)
Epitope	LERFAVNPSLLETSEGCR	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This invariant peptide sequence, LERFAVNPSLLETSEGCR, studied as part of transmitted sequence GKKQYKLKHIVWASRELERFAVNPSLLETSEGCR, was recognized in patient CH77. No mutants were seen and there is no statistical evidence for selection towards change in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56630

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HXB2 Location	Gag(147-155) p24(15-23) DNA(1228..1254)	Gag Epitope Map
Author Location	Gag(140-157)
Epitope	ISPRTLNAW	Epitope Alignment
		Show epitope variants
Epitope Name	IW9
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This epitope, ISPRTLNAW, was studied as part of peptide GQMVHQAISPRTLNAWVK and showed a rare pattern of escape in patient CH77, where the transmitted form was replaced completely by the single variant, lSPRTLNAW.
• In patient CH58, responses to this epitope were strong even at 6 months and persisted to at least a year when signs of variation were seen to lSPRTLNAW and x(i.e.l/i)SPRTLNAW. There was no statistical evidence for selection towards change for epitope IW9 in this patient.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56633

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HXB2 Location	Gag(240-249) p24(108-117) DNA(1507..1536)	Gag Epitope Map
Author Location	Gag(236-253)
Epitope	TSTLQEQVGW	Epitope Alignment
		Show epitope variants
Epitope Name	TW10
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This epitope, TSTLQEQVGW, was studied as part of peptide IAGSTSTLQEQVGWMTSN. In patient CH77 it showed early development of immunodominant response followed by a complex pattern of escape.
• In patient 77 at day 159, the transmitted epitope disappeared and was substituted by two variants, TSTLQEQiGW (89%) and TSTLQEQVeW (11%). At the same time, response was strong. By day 592, inferred escape occurred and variant IAGSTSnLQEQiaWMTSN dominated.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56673

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HXB2 Location	Gag(240-249) p24(108-117) DNA(1507..1536)	Gag Epitope Map
Author Location	Gag(240-249)
Epitope	TSTLQEQIGW	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*01:01, A*23:01, B*14:02, B*57:01, C*07:01, C*08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted epitope, TSTLQEQIGW, studied as part of peptide IAGSTSTLQEQIGWMTSN, was recognized in patient CH58. By day 85, two mutants, TnTLQEQIGW (22%) and TSTLQEQIeW (67%) dominated; pooled mutants were reactive to the same extent as the transmitted form. HLA-B*5701 restriction was validated.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56679

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HXB2 Location	Gag(268-285) p24(136-153) DNA(1591..1644)	Gag Epitope Map
Author Location	Gag(268-285)
Epitope	LGLNKIVRMYSPTSILDI	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This invariant peptide sequence, LGLNKIVRMYSPTSILDI, was recognized in patient CH77. No mutants were seen and there is no statistical evidence for selection towards change in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56680

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HXB2 Location	Gag(300-308) p24(168-176) DNA(1687..1713)	Gag Epitope Map
Author Location	Gag(292-309)
Epitope	FYKTLRAEQ	Epitope Alignment
Species (MHC/HLA)	human(C*04:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• FYKTLRAEQ is the overlap of two reactive peptides, pfrdyvdrFYKTLRAEQ and FYKTLRAEQsqevknwm. In addition, Cw*0401 restriction is predicted based on the 2Y anchor motif and the presence of the HLA in the patient.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56638

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HXB2 Location	Gag(395-403) p2p7p1p6(32-40) DNA(1972..1998)	Gag Epitope Map
Author Location	Gag(395-404)
Epitope	CGKEGHIAR	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A*31:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted, newly predicted epitope, CGKEGHIAR, was studied in patient CH40 as part of peptide Gag(389-406) IVKCFNCGKEGHIARNCR. A rapid change, R403K, toward the B clade sequence was seen. A gradual change I401L away from the consensus was also seen. Both substitutions persisted at least for a year.
• Escape mutations of CGKEGHIAR seen in Patient CH40 were CGKEGHIAk and CGKEGIAR, and both were not recognized by CTL.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56654

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HXB2 Location	Gag(481-498) p2p7p1p6(118-135) DNA(2230..2283)	Gag Epitope Map
Author Location	Gag(481-498)
Epitope	KELYPLASLRSLFGNDPS	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted peptide sequence, KELYPLASLRSLFGNDPS, was recognized in patient CH40. One variant, qELYPLASLRSLFGNDPS was seen at day 181. There is no statistical evidence for positive selection in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56639

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HXB2 Location	Pol(81-98) Protease(25-42) DNA(2325..2378)	Pol Epitope Map
Author Location	Pol(80-97)
Epitope	DTGADDTVLEEMNLPGRW	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted, epitope-containing peptide sequence, gqlkeallDTGADDTVLEEMNLPGRW, was studied in patient CH40 and contained epitope Pol(80-97), DTGADDTVLEEMNLPGRW. A single change K76R was seen with almost complete loss of the transmitted form.
• The mutation seen proximal to DTGADDTVLEEMNLPGRW was gqlReallDTGADDTVLEEMNLPGRW and it was predicted to be a processing escape.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56682

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HXB2 Location	Pol(529-538) RT(374-383) DNA(3669..3698)	Pol Epitope Map
Author Location	Pol(528-545)
Epitope	KITTESIVIW	Epitope Alignment
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This invariant epitope, KITTESIVIW, was studied as part of peptides kqlteavqKITTESIVIW and KITTESIVIWgrtpkfrl. Transmitted sequence KQLTEAVQKISTESIVIWGRTPKFRL was recognized in patient CH77. No mutants were seen and there is no statistical evidence for selection towards change in this region. Predicted HLA-B*5701 restriction was based on database.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56655

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HXB2 Location	Pol(825-842) Integrase(110-127) DNA(4557..4610)	Pol Epitope Map
Author Location	Pol(824-841)
Epitope	VKTIHTDNGSNFTSTTVK	Epitope Alignment
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted peptide sequence, VKTIHTDNGSNFTSTTVK, was recognized in patient CH40 from day 13 onwards. No variants were seen. There is no statistical evidence for positive selection in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56658

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HXB2 Location	Vif(119-127) DNA(5395..5421)	Vif Epitope Map
Author Location	Vif(119-127)
Epitope	AIRKAILGR	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted epitope, AIRKAILGR, studied as part of peptide dcfsesAIRKAILGRiv, was recognized in patient CH40. Unrecognized mutants, AIRKAlLGR, AIRKAIvGR, AIRtAILGR, AIReAILGR and dcfsDsAIReAILGRiv were seen from day 111 on. There is statistical evidence for variation and escape in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56636

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HXB2 Location	Vpr(73-90) DNA(5775..5828)	Vpr Epitope Map
Author Location	Vpr(74-91)
Epitope	RIGCQHSRIGISQRRRAR	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted, epitope-containing peptide sequence, RIGCQHSRIGISQRRRAR, which corresponds to an HLA-matched T cell motif, had an S84R change to consensus B that persisted at least for a year. The S84R mutation was thus a candidate for early reversion.
• Mutations in RIGCQHSRIGISQRRRAR seen in Patient CH40 were RIGCQHSRIGIrQRRRAR, RIGCQrSRIGIrQRRRAR, RIGCQHSRIGIrhRRRAR, RIGCQHSRIGIgQRRRAR and RIGCQHSRIGlgQRRRAR.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 57343

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HXB2 Location	Rev(9-26) DNA(5994..6045,8379..8380)	Rev Epitope Map
Author Location	Rev(9-26)
Epitope	DEDLLKTVRLIKRLYQSS	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• The transmitted peptide sequence DEDLLKTVRLIKRLYQSS, elicited an EliSpot response in patient CH77. A validated embedded epitope, KTVRLIKRLY, exists in this peptide.
• Mutations seen at various time points were DEnLLKTVRLIKRLYQSS, DEDLLKaVRLIKRLYQSS, DEDLLKiVRLIKRLYQSS, DEDLLKTVgiIKRLYQSS, DEDLLKTVRvIKRLYQSS, DEDLLKTVRiIKRLYQSS and DEDLLrTVRLIKRLYQSS.
• In another reading frame, the corresponding peptide RRPAQDSKINQAPLPKQ (Tat 9-26) did not elicit an EliSpot response, but multiple variants were seen at various time points, which could be explained by an early reversion coupled with selection in the Rev reading frame.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56644

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HXB2 Location	Rev(14-23) DNA(6009..6038)	Rev Epitope Map
Author Location	Rev(9-18)
Epitope	KTVRLIKRLY	Epitope Alignment
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• The transmitted peptide sequence DEDLLKTVRLIKRLYQSS elicited a positive response in patient CH77 at only one time point. A validated embedded epitope, KTVRLIKRLY, exists in this peptide.
• Variants observed were DEnLLKTVRLIKRLYQSS, DEDLLKaVRLIKRLYQSS, DEDLLKiVRLIKRLYQSS, DEDLLKTVgiIKRLYQSS, DEDLLKTVRvIKRLYQSS, DEDLLKTVRiIKRLYQSS and DEDLLrTVRLIKRLYQSS; none were validated as escape mutants.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56634

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HXB2 Location	Rev(47-55) DNA(8441..8467)	Rev Epitope Map
Author Location	Rev(47-56)
Epitope	QRQRQIQSL	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This epitope, QRQRQIQSL, was studied in patient SUMA0874. 20 days following seroconversion only 1 variant was detected, but by D34SFOx 22/28 sequences contained such nonsynonymous substitutions.
• Variants of QRQRQIQSL seen in Patient SUMA0874 were QkQRQIQSL, QRQRhIQSL, QRQRQIrSL, QRQRQIQlL and QRQRQIQSi.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56659

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HXB2 Location	Rev(49-66) DNA(8447..8500)	Rev Epitope Map
Author Location	Rev(49-66)
Epitope	QRQIRSISERILSTYLER	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted peptide sequence, QRQIRSISERILSTYLER, was recognized in patient CH40 from day 14 onwards. Unrecognized mutants, QRQIRSISERIfSTYLER, QRQIRSISERILnTYLER and QkQIRSISERILSTYLER were seen. There is statistical evidence for variation and escape in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56647

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HXB2 Location	gp160(334-351) gp120(334-351) DNA(7224..7277)	gp160 Epitope Map
Author Location	Env(334-351)
Epitope	SGEDWNKTLSHVVDKLRE	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted peptide sequence SGEDWNKTLSHVVDKLRE elicited strong responses in patient CH77.
• Variants observed were: SGEDWNKTLSyVVDKLRE, SGEDWNKTLSHVVnKLRE, SGEDWNKTLgHVVDKLRE, SGEDWNKTLnHVVDKLRE and SGEDWNKTLSHVVaKLRE.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56642

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HXB2 Location	gp160(352-361) gp120(352-361) DNA(7278..7307)	gp160 Epitope Map
Author Location	Env(352-360)
Epitope	QFRNKTIVF	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted, newly described epitope, QFRNKTIVF, was studied in patient CH77. A rapid change R355K was seen before day 14, with complete loss of the transmitted form.
• Escape mutations seen were QFkNKTIVF, QFkNKaIVF and QFkdKTIVF. Other variants seen were QFnNKTIVF, QFsNKTIVF and QFRNKaIVF.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56649

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HXB2 Location	gp160(584-592) gp41(73-81) DNA(7974..8000)	gp160 Epitope Map
Author Location	Env(584-592)
Epitope	ERYLRDQQL	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B*14:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*01:01, A*23:01, B*14:02, B*57:01, C*07:01, C*08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted epitope, ERYLRDQQL which is part of tested peptide sequence LALERYLRDQQLLGIW, elicited an EliSpot response in patient CH58. HLA-restriction was as found in database.
• Escape mutations were ERYLgDQQL, ERhLRDQQL, ERYLkDQQL and ERYLsDQQL. Response to mutant peptides was not detected. Escape from this epitope precedes escape from B*5701-restricted TW10, which goes from a subdominant to immunodominant response.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 57344

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HXB2 Location	gp160(597-622) gp41(86-111) DNA(8013..8090)	gp160 Epitope Map
Author Location	Env(597-622)
Epitope	GCSGRVICTTTVPWNVSWSNKSLNEI	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted epitope transmitted sequnence (containing epitope TTVPWNVSW), GCSGRVICTTTVPWNVSWSNKSLNEI, made up of two overlapping peptides, gcsgrvicTTVPWNVSW and TTVPWNVSWsnkslnei, was studied in patient CH77. Strong responses were seen to this epitope. HLA-B*5701 restriction was predicted by anchor residues at 2T and 9W.
• Escape mutations were seen outside the epitope at dCSGRVICTTTVPWNVSWSNKSLNEI; and within the epitope at GCSGRVICTTTVPWNsSWSNKSLNEI, GCSGRVICTTTVPWNtSWSNKSLsEI and GCSGRVICTTTVPWNtSWSNKSLNEI.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56646

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HXB2 Location	gp160(606-614) gp41(95-103) DNA(8040..8066)	gp160 Epitope Map
Author Location	Env(606-614)
Epitope	TTVPWNVSW	Epitope Alignment
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted epitope TTVPWNVSW which is part of a larger transmitted sequence, GCSGRVICTTTVPWNVSWSNKSLNEI, and two overlapping peptides, gcsgrvicTTVPWNVSW and TTVPWNVSWsnkslnei, was studied in patient CH77. Strong responses were seen both overlapping 18mers. HLA-B*5701 restriction was predicted by anchor residues at 2T and 9W.
• Mutations were seen outside the epitope at dCSGRVICTTTVPWNVSWSNKSLNEI; and within the epitope at GCSGRVICTTTVPWNsSWSNKSLNEI, GCSGRVICTTTVPWNtSWSNKSLsEI and GCSGRVICTTTVPWNtSWSNKSLNEI. There was evidence of positive selection in the epitope, but the mutations were not documented as escapes.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56657

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HXB2 Location	gp160(765-782) gp41(254-271) DNA(8517..8570)	gp160 Epitope Map
Author Location	Env(765-782)
Epitope	LFSYHRLRDLLLIVTRIV	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted peptide sequence, LFSYHRLRDLLLIVTRIV, was recognized in patient CH40. One variant, LFrYHRLRDLLLIVTRIV was seen at day 412. There is no statistical evidence for positive selection in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56684

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HXB2 Location	gp160(822-836) gp41(311-325) DNA(8688..8732)	gp160 Epitope Map
Author Location	Env(822-839)
Epitope	VAEGTDRVIEELQRA	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted peptide sequence VAEGTDRVIEELQRA which is part of a larger transmitted sequence, llntiaiaVAEGTDRVIEELQRA elicited a positive response in patient CH77 at week 24, but not at week 1.
• At the positive timepoint (week 24) none of the transmitted sequence was present; the variants were VAEGTgRVIEgLQRA, VAEGTDRVIEgLQRA, VAEGTDRVIEEsQRA, VAEGTDRiIEEsQRA and VAEGTDRVIEaLQRA. Proximal variations that may impact processing or be compensatory mutations were also seen at other timepoints - llntiTiaVAEGTDRVIEELQRA, llntiaiT|VAEGTDRVIEELQRA, llntiaiT|VAEGTDRVIEgLQRA, llntiaiT|VAEGTDRiIEgLQRA, llntiaiV|VAEGTDRiIEgLQRv and llntiaiV|VAEGTDRiIEgLQRA.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56661

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HXB2 Location	gp160(830-847) gp41(319-336) DNA(8712..8765)	gp160 Epitope Map
Author Location	Env(830-847)
Epitope	IEVVQRACRAILHIPRRI	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted peptide sequence, IEVVQRACRAILHIPRRI, was recognized in patient CH40 from enrollment in the study. Mutants IEVVQRACRAILHIPRkI, IEVVQRACRAIfHIPRRI, IEiVQRACRAILHIPRRI, IEVVQRACRAIcHIPRRI and IEVVQRACRAIrHIPRRI were seen. There is statistical evidence for variation and escape in this region.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56686

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HXB2 Location	gp160(838-855) gp41(327-344) DNA(8736..8789)	gp160 Epitope Map
Author Location	Env(838-855)
Epitope	RAVLNIPTRIRQGLERAL	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted peptide sequence RAVLNIPTRIRQGLERAL was recognized in patient CH77 by week 24. A mutation was seen at RAVLNvPTRIRQGLERAL.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56640

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HXB2 Location	Nef(17-34) DNA(8845..8898)	Nef Epitope Map
Author Location	Nef(17-35)
Epitope	RERRRRDEPAAVGVGPAS	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted, newly described epitope-containing peptide sequence, RERRRRDEPAAVGVGPAS, was studied in patient CH77. CTL response to the founder sequence was lost with its loss.
• The authors used SGA sequencing to document variants in this peptide region. The following had evidence of being escape variants: kERRRReEPAAVGVGPAS, RERRgRDEPAAVGVGPAS, RERRgRDEPAAVGVGPAS|r, RERRkRDEPAAVGVGPAS, RERRRgDEPA.......S, RERRRgDEPAAVGVGPAS, RERRRgDEPAAVGVGtAS, RERRRkDEPAAVGVGPAS, RERRRkDEPAAVGVGPvS, RERRRReEPAAVGVGPAS, RERRRReEPAAVGVGPvS, RERRRRnEPAAVGVGPASQ, RERRRRnEPAAVGVGsAS, RERRRtDEPAAVGVGPAS, RERRRtDEPAAVGVGPAS|r

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56632

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HXB2 Location	Nef(82-90) DNA(9040..9066)	Nef Epitope Map
Author Location	Nef(82-90)
Epitope	KAALDLSHF	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:05, B*53:01, B*57:01, C*04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This epitope, KAALDLSHF, was studied as part of peptide qvpvrpmtyKAALDLSHF and showed a pattern typical of rapid escape in patient CH77, where the transmitted form was replaced quickly by many variants. The dominant form (A83G) at the last assayed point was not among the earliest escapes.
• Variants of KAALDLSHF seen in patient CH77 were qAALDLSHF, tAALDLSHF, pAALDLSHF, KAAhDLSHF, KAALDiSHF and KgALDLSHF. While pooled mutants elicited a reduced magnitude of response from CTL, proximal substitutions (V76L, M79I) may impact processing or be compensatory mutations.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56652

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HXB2 Location	Nef(105-115) DNA(9109..9141)	Nef Epitope Map
Author Location	Nef(105-115)
Epitope	KRQDILDLWVY	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(C*07:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*01:01, A*23:01, B*14:02, B*57:01, C*07:01, C*08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted epitope, KRQDILDLWVY which is part of tested peptide sequence KRQDILDLWVYHTQGYFP, was studied in patient CH58. HLA-Cw*0701 restriction was as found from database.
• Escape mutations in KRQDILDLWVY were seen at nonsynonymous changes, K110R and D113E - rRQDILDLWVY and KRQeILDLWVY. Response to pooled mutant peptides was detected, but at 50% of the response to wild type sequence. These mutations might also impact processing (antigen presentation) of downstream epitope, HTQGYFPDWQ.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56675

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HXB2 Location	Nef(116-124) DNA(9142..9168)	Nef Epitope Map
Author Location	Nef(116-124)
Epitope	HTQGYFPDW	Epitope Alignment
Species (MHC/HLA)	human(B*57:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*01:01, A*23:01, B*14:02, B*57:01, C*07:01, C*08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	acute/early infection

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted, invariant epitope, HTQGYFPDW, studied as part of peptide WVYHTQGYFPDWWNYTPG, was recognized in patient CH58. No mutants were seen and there is no statistical evidence for selection towards change in this region. HLA-B*5701 restriction was concluded from database.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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Displaying record number 56635

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HXB2 Location	Nef(188-196) DNA(9358..9384)	Nef Epitope Map
Author Location	Nef(187-196)
Epitope	SLAFRHVAR	Epitope Alignment
		Show epitope variants
Species (MHC/HLA)	human(A*31:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	A*02:01, A*31:01, B*40:01, B*44:02, C*03:02, C*05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Intracellular cytokine staining, Other
Keywords	escape, acute/early infection, novel epitope

Notes

• Using overlapping 15-mer peptides, CTL responses to early, acute HIV infection were determined. Early virus escape attributed to CTL response was charted and subsequent clusters of mutations due to NAb targeting were also found.
• Five findings made: (i) exact numbers of transmitted HIV-1 actual and potential T cell epitopes were determined (ii) CTL-mediated virus escape occurring as viremia peaks, drops and reaches set point earlier and faster than previously known (iii) CTL responses to some transmitted virus epitopes were lost after early escapes were selected (iv) a few unexplained escapes were probably due to bystander mutations (v) earliest CTL responses cause the decline of VL in acute infection.
• This transmitted, newly predicted epitope, SLAFRHVAR, was studied in patient CH40 as part of peptide Nef(185-202) FDSSLAFRHVARELHPEY. Within 14 days the majority of sequences contained an R192H substitution to the clade B consensus. Founder, SLAFRHVAR, was completely lost by 29d; instead R196Q and S188R/N forms predominated.
• Escape mutations of SLAFRHVAR seen in Patient CH40 were SSLAFhHVAR, SLAFRHVAq, SrLAFRHVAR and SnLAFRHVAR, and all were not recognized by CTL.

References

Goonetilleke2009 Nilu Goonetilleke, Michael K. P. Liu, Jesus F. Salazar-Gonzalez, Guido Ferrari, Elena Giorgi, Vitaly V. Ganusov, Brandon F. Keele, Gerald H. Learn, Emma L. Turnbull, Maria G Salazar, Kent J Weinhold, Stephen Moore, CHAVI Clinical Core B, Norman Letvin, Barton F. Haynes, Myron S. Cohen, Peter Hraber, Tanmoy Bhattacharya, Persephone Borrow, Alan S. Perelson, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, and Andrew J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med., 206(6):1253-1272, 8 Jun 2009. PubMed ID: 19487423. Show all entries for this paper.

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