Search CTL/CD8+ T-Cell Epitope Database

Found 71 matching records:

Displaying record number 61101

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HXB2 Location	Gag(24-32) p17(24-32) DNA(859..885)	Gag Epitope Map
Author Location	p17(24-32)
Epitope	`GGKKKYQLK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH470: A01:01, A03:01, B08:01, B49:01, C*07:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope GGKKKYQLK had a fitness cost ΔE of -0.566 and T cell response was first detected to it at 13d, escape time was 187.75 days.

References

Barton2016 John P. Barton, Nilu Goonetilleke, Thomas C. Butler, Bruce D. Walker, Andrew J. McMichael, and Arup K. Chakraborty. Relative Rate and Location of Intra-Host HIV Evolution to Evade Cellular Immunity Are Predictable. Nat. Commun., 7:11660, 23 May 2016. PubMed ID: 27212475. Show all entries for this paper.

Displaying record number 61064

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HXB2 Location	Gag(37-44) p17(37-44) DNA(898..921)	Gag Epitope Map
Author Location	p17(37-44)
Epitope	`ASRELERF`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH077: A02:05, B53:01, B57:01, C04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope ASRELERF had a fitness cost ΔE of 6.606 and T cell response was first detected to it at 21d, escape time was 571 days.

References

Displaying record number 61089

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HXB2 Location	Gag(71-79) p17(71-79) DNA(1000..1026)	Gag Epitope Map
Author Location	p17(71-79)
Epitope	`GTEELRSLY`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH185: A01:01, A74:01, B15:03, B81:01, C02:02, C18:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope GTEELRSLY had a fitness cost ΔE of 0.435 and T cell response was first detected to it at 11d, escape time was 34.04 days.

References

Displaying record number 61071

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HXB2 Location	Gag(71-79) p17(71-79) DNA(1000..1026)	Gag Epitope Map
Author Location	p17(71-79)
Epitope	`GTEELKSLY`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH067: A01:01, A33:01, B53:01, B81:01, C04:01, C18:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope GTEELKSLY had a fitness cost ΔE of 1.534 and T cell response was first detected to it at 42d, escape time was 12.89 days.

References

Displaying record number 61093

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HXB2 Location	Gag(140-157) p24(8-25) DNA(1207..1260)	Gag Epitope Map
Author Location	p24(8-25)
Epitope	`GQMVHQPLSPRTLNAWVK`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH256: A33:01, A68:01, B14:01, B53:01, C04:01, C08:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope GQMVHQPLSPRTLNAWVK had a fitness cost ΔE of 1.332 and T cell response was first detected to it at 28d, escape time was 656 days.

References

Displaying record number 61073

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HXB2 Location	Gag(141-149) p24(9-17) DNA(1210..1236)	Gag Epitope Map
Author Location	p24(9-17)
Epitope	`QMVHQALSP`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH042: A23:01, A30:02, B15:03, B18:01, C02:02, C07:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope QMVHQALSP had a fitness cost ΔE of 1.601 and T cell response was first detected to it at 21d, escape time was 1 days.

References

Displaying record number 61032

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HXB2 Location	Gag(143-152) p24(11-20) DNA(1216..1245)	Gag Epitope Map
Author Location	p24(11-20)
Epitope	`VHQPMSPRTL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP045: A23:01, A29:02, B15:10, B45:01, C16:01, C16:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope VHQPMSPRTL had a fitness cost ΔE of 0.532 and T cell response was first detected to it at 49d, escape time was 381.31 days.

References

Displaying record number 61043

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HXB2 Location	Gag(143-152) p24(11-20) DNA(1216..1245)	Gag Epitope Map
Author Location	p24(11-20)
Epitope	`VHQAISPRTL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP210: A68:02, B15:10, C*03:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope VHQAISPRTL had a fitness cost ΔE of 2.408 and T cell response was first detected to it at 22d, escape time was 144.01 days.

References

Displaying record number 61060

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HXB2 Location	Gag(147-155) p24(15-23) DNA(1228..1254)	Gag Epitope Map
Author Location	p24(15-23)
Epitope	`ISPRTLNAW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH058: A01:01, A23:01, B14:02, B57, C07:01, C08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope ISPRTLNAW had a fitness cost ΔE of 4.142 and T cell response was first detected to it at 21d, escape time was 346.77 days.

References

Displaying record number 61090

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HXB2 Location	Gag(180-188) p24(48-56) DNA(1327..1353)	Gag Epitope Map
Author Location	p24(48-56)
Epitope	`TPQDLNTML`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH185: A01:01, A74:01, B15:03, B81:01, C02:02, C18:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope TPQDLNTML had a fitness cost ΔE of 4.333 and T cell response was first detected to it at 11d, escape time was 122.22 days.

References

Displaying record number 61080

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HXB2 Location	Gag(180-188) p24(48-56) DNA(1327..1353)	Gag Epitope Map
Author Location	p24(48-56)
Epitope	`TPQDLNTML`	Epitope Alignment
Epitope Name	TL9
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH159: A23:01, A68:02, B18:01, B81:01, C07:04, C18:01; CH185: A01:01, A74:01, B15:03, B81:01, C02:02, C18:01
Country	Malawi
Experimental methods	CD8 T-cell RecycleSpot - IFNγ
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope TPQDLNTML (TL9) had a fitness cost ΔE of 6.11 and T cell response was first detected to it at 29d, escape time was 1103 days.
TL9 escaped after 122d in patient CH185, but 1,103 days in patient CH159 due to sequence background in TF virus.

References

Displaying record number 61048

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HXB2 Location	Gag(240-249) p24(108-117) DNA(1507..1536)	Gag Epitope Map
Author Location	p24(108-117)
Epitope	`TSTLQEQVAW`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(B*58:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP239: A01:01, A29:02, B42:01, B58:01, C06:02, C07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope TSTLQEQVAW had a fitness cost ΔE of -1.439 and T cell response was first detected to it at 22d, escape time was 1 days.

References

Displaying record number 61065

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HXB2 Location	Gag(240-249) p24(108-117) DNA(1507..1536)	Gag Epitope Map
Author Location	p24(108-117)
Epitope	`TSTLQEQVGW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH077: A02:05, B53:01, B57:01, C04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope TSTLQEQVGW had a fitness cost ΔE of -0.905 and T cell response was first detected to it at 21d, escape time was 104.16 days.

References

Displaying record number 61091

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HXB2 Location	Gag(240-249) p24(108-117) DNA(1507..1536)	Gag Epitope Map
Author Location	p24(108-117)
Epitope	`TSTLQEQVAW`	Epitope Alignment
Epitope Name	TW10
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH198: A03:01, A74:01, B08:01, B57, C07:01, C07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope TSTLQEQVAW (TW10) had a fitness cost ΔE of 0.053 and T cell response was first detected to it at 32d, escape time was 220.21 days.
TW10 escaped within days in patient CAP239 even though it is a protective epitope, but took 220 days in patient CH198 due to sequence background in TF virus.

References

Displaying record number 61061

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HXB2 Location	Gag(240-249) p24(108-117) DNA(1507..1536)	Gag Epitope Map
Author Location	p24(108-117)
Epitope	`TSTLQEQIGW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH058: A01:01, A23:01, B14:02, B57, C07:01, C08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope TSTLQEQIGW had a fitness cost ΔE of 3.284 and T cell response was first detected to it at 21d, escape time was 39.75 days.

References

Displaying record number 61066

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HXB2 Location	Gag(275-283) p24(143-151) DNA(1612..1638)	Gag Epitope Map
Author Location	p24(143-151)
Epitope	`RMYSPTSIL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH077: A02:05, B53:01, B57:01, C04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope RMYSPTSIL had a fitness cost ΔE of 4.811 and T cell response was first detected to it at 21d, escape time was 571 days.

References

Displaying record number 61086

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HXB2 Location	Gag(292-300) p24(160-168) DNA(1663..1689)	Gag Epitope Map
Author Location	p24(160-168)
Epitope	`PFRDYVDRF`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH164: A02:01, A29:01, B44:03, B45:01, C07:01, C16:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope PFRDYVDRF had a fitness cost ΔE of 3.993 and T cell response was first detected to it at 21d, escape time was 200.07 days.

References

Displaying record number 61044

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HXB2 Location	Gag(296-304) p24(164-172) DNA(1675..1701)	Gag Epitope Map
Author Location	p24(164-172)
Epitope	`YVDRFFKTL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP210: A68:02, B15:10, C*03:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope YVDRFFKTL had a fitness cost ΔE of 3.175 and T cell response was first detected to it at 22d, escape time was 289 days.

References

Displaying record number 61094

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HXB2 Location	Gag(298-306) p24(166-174) DNA(1681..1707)	Gag Epitope Map
Author Location	p24(166-174)
Epitope	`DRFFKTLRA`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH256: A33:01, A68:01, B14:01, B53:01, C04:01, C08:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope DRFFKTLRA had a fitness cost ΔE of 5.091 and T cell response was first detected to it at 28d, escape time was 656 days.

References

Displaying record number 61067

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HXB2 Location	Gag(300-308) p24(168-176) DNA(1687..1713)	Gag Epitope Map
Author Location	p24(168-176)
Epitope	`FYKTLRAEQ`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH077: A02:05, B53:01, B57:01, C04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope FYKTLRAEQ had a fitness cost ΔE of 3.886 and T cell response was first detected to it at 21d, escape time was 571 days.

References

Displaying record number 61053

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HXB2 Location	Gag(395-403) p2p7p1p6(32-40) DNA(1972..1998)	Gag Epitope Map
Author Location	p7(18-26)
Epitope	`CGKEGHIAR`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH040: A02:01, A31:01, B40:01, B44:02, C03:02, C05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope CGKEGHIAR had a fitness cost ΔE of 0.07 and T cell response was first detected to it at 16d, escape time was 4.31 days.

References

Displaying record number 61083

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HXB2 Location	Gag(396-404) p2p7p1p6(33-41) DNA(1975..2001)	Gag Epitope Map
Author Location	p7(19-27)
Epitope	`GKEGHIAKN`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH162: A30:01, A34:02, B42:02, B44:03, C04:01, C17:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope GKEGHIAKN had a fitness cost ΔE of 0.398 and T cell response was first detected to it at 40d, escape time was 26.86 days.

References

Displaying record number 61087

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HXB2 Location	Gag(397-407) p2p7p1p6(34-44) DNA(1978..2010)	Gag Epitope Map
Author Location	p7(20-30)
Epitope	`KEGHIARNCKA`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH164: A02:01, A29:01, B44:03, B45:01, C07:01, C16:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope KEGHIARNCKA had a fitness cost ΔE of -2.918 and T cell response was first detected to it at 21d, escape time was 413 days.

References

Displaying record number 61054

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HXB2 Location	Gag(481-489) p2p7p1p6(118-126) DNA(2230..2256)	Gag Epitope Map
Author Location	p6(33-41)
Epitope	`KELYPLASL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH040: A02:01, A31:01, B40:01, B44:02, C03:02, C05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope KELYPLASL had a fitness cost ΔE of 2.388 and T cell response was first detected to it at 16d, escape time was 464.69 days.

References

Displaying record number 61084

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HXB2 Location	Pol(90-98) Protease(34-42) DNA(2352..2378)	Pol Epitope Map
Author Location	Protease(34-42)
Epitope	`EEMNLTGKW`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH162: A30:01, A34:02, B42:02, B44:03, C04:01, C17:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope EEMNLTGKW had a fitness cost ΔE of -4.783 and T cell response was first detected to it at 40d, escape time was 86.58 days.

References

Displaying record number 61095

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HXB2 Location	Pol(398-406) RT(243-251) DNA(3276..3302)	Pol Epitope Map
Author Location	RT(243-251)
Epitope	`PIQLPEKDS`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH256: A33:01, A68:01, B14:01, B53:01, C04:01, C08:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope PIQLPEKDS had a fitness cost ΔE of 2.963 and T cell response was first detected to it at 35d, escape time was 196.16 days.

References

Displaying record number 61049

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HXB2 Location	Pol(399-407) RT(244-252) DNA(3279..3305)	Pol Epitope Map
Author Location	RT(244-252)
Epitope	`IVLPEKESW`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP239: A01:01, A29:02, B42:01, B58:01, C06:02, C07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope IVLPEKESW had a fitness cost ΔE of 0.178 and T cell response was first detected to it at 29d, escape time was 38.45 days.

References

Displaying record number 61102

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HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	RT(269-277)
Epitope	`QIYPGIKVK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH470: A01:01, A03:01, B08:01, B49:01, C*07:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope QIYPGIKVK had a fitness cost ΔE of 0.507 and T cell response was first detected to it at 13d, escape time was 50.54 days.

References

Displaying record number 61037

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HXB2 Location	Pol(781-789) Integrase(66-74) DNA(4425..4451)	Pol Epitope Map
Author Location	Integrase(66-74)
Epitope	`THLEGKIIL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP045: A23:01, A29:02, B15:10, B45:01, C16:01, C16:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope THLEGKIIL had a fitness cost ΔE of 0.345 and T cell response was first detected to it at 48d, escape time was 382.23 days.

References

Displaying record number 61103

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HXB2 Location	Vif(17-26) DNA(5089..5118)	Vif Epitope Map
Author Location	Vif(17-26)
Epitope	`RIKTWKSLVK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH470: A01:01, A03:01, B08:01, B49:01, C*07:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope RIKTWKSLVK had a fitness cost ΔE of -0.931 and T cell response was first detected to it at 13d, escape time was 42.18 days.

References

Displaying record number 61045

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HXB2 Location	Vif(79-87) DNA(5275..5301)	Vif Epitope Map
Author Location	Vif(79-87)
Epitope	`WHLGHGVSI`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(B*15:10)
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP210: A68:02, B15:10, C*03:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope WHLGHGVSI had a fitness cost ΔE of 2.828 and T cell response was first detected to it at 22d, escape time was 127.37 days.

References

Displaying record number 61038

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HXB2 Location	Vif(79-87) DNA(5275..5301)	Vif Epitope Map
Author Location	Vif(79-87)
Epitope	`WHLGHGVSI`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(B*15:10)
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP045: A23:01, A29:02, B15:10, B45:01, C16:01, C16:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope WHLGHGVSI had a fitness cost ΔE of 4.672 and T cell response was first detected to it at 21d, escape time was 408.47 days.

References

Displaying record number 61055

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HXB2 Location	Vif(119-127) DNA(5395..5421)	Vif Epitope Map
Author Location	Vif(119-127)
Epitope	`AIRKAILGR`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH040: A02:01, A31:01, B40:01, B44:02, C03:02, C05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope AIRKAILGR had a fitness cost ΔE of -0.572 and T cell response was first detected to it at 16d, escape time was 171.97 days.

References

Displaying record number 61050

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HXB2 Location	Vpr(33-41) DNA(5655..5681)	Vpr Epitope Map
Author Location	Vpr(33-41)
Epitope	`HFPRPWLHN`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP239: A01:01, A29:02, B42:01, B58:01, C06:02, C07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope HFPRPWLHN had a fitness cost ΔE of 1.608 and T cell response was first detected to it at 22d, escape time was 546.25 days.

References

Displaying record number 61096

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HXB2 Location	Tat(2-11) DNA(5834..5863)	Tat Epitope Map
Author Location	Tat(2-11)
Epitope	`EPIDPNLEPW`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH256: A33:01, A68:01, B14:01, B53:01, C04:01, C08:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope EPIDPNLEPW had a fitness cost ΔE of 0.342 and T cell response was first detected to it at 28d, escape time was 199.78 days.

References

Displaying record number 61040

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HXB2 Location	Tat(24-32) DNA(5900..5926)	Tat Epitope Map
Author Location	Tat(24-32)
Epitope	`NCYCKHCSY`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP045: A23:01, A29:02, B15:10, B45:01, C16:01, C16:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope NCYCKHCSY had a fitness cost ΔE of -0.406 and T cell response was first detected to it at 48d, escape time was 22 days.

References

Displaying record number 61077

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HXB2 Location	Tat(38-47) DNA(5942..5971)	Tat Epitope Map
Author Location	Tat(38-47)
Epitope	`FQKKGLGISY`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH131: A23:01, A29:01, B15:03, B45:01, C02:02, C06:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope FQKKGLGISY had a fitness cost ΔE of 2.006 and T cell response was first detected to it at 7d, escape time was 100.25 days.

References

Displaying record number 61074

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HXB2 Location	Rev(9-17) DNA(5994..6020)	Rev Epitope Map
Author Location	Rev(9-17)
Epitope	`DETLLQAVR`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH042: A23:01, A30:02, B15:03, B18:01, C02:02, C07:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope DETLLQAVR had a fitness cost ΔE of -3.623 and T cell response was first detected to it at 4d, escape time was 1 days.

References

Displaying record number 61039

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HXB2 Location	Rev(52-60) DNA(8456..8482)	Rev Epitope Map
Author Location	Rev(52-60)
Epitope	`IHSISERIL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP045: A23:01, A29:02, B15:10, B45:01, C16:01, C16:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope IHSISERIL had a fitness cost ΔE of 3.195 and T cell response was first detected to it at 21d, escape time was 191.09 days.

References

Displaying record number 61056

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HXB2 Location	Rev(57-65) DNA(8471..8497)	Rev Epitope Map
Author Location	Rev(57-65)
Epitope	`ERILSTYLE`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH040: A02:01, A31:01, B40:01, B44:02, C03:02, C05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope ERILSTYLE had a fitness cost ΔE of -3.805 and T cell response was first detected to it at 45d, escape time was 157.19 days.

References

Displaying record number 61081

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HXB2 Location	Rev(67-75) DNA(8501..8527)	Rev Epitope Map
Author Location	Rev(67-75)
Epitope	`PTEPVPFQL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH159: A23:01, A68:02, B18:01, B81:01, C07:04, C18:01
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope PTEPVPFQL had a fitness cost ΔE of 0.408 and T cell response was first detected to it at 29d, escape time was 1 days.

References

Displaying record number 61062

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HXB2 Location	gp160(584-592) gp41(73-81) DNA(7974..8000)	gp160 Epitope Map
Author Location	gp41(73-81)
Epitope	`ERYLRDQQL`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH058: A01:01, A23:01, B14:02, B57, C07:01, C08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope ERYLRDQQL had a fitness cost ΔE of -0.73 and T cell response was first detected to it at 21d, escape time was 1 days.

References

Displaying record number 61097

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HXB2 Location	gp160(606-614) gp41(95-103) DNA(8040..8066)	gp160 Epitope Map
Author Location	gp41(95-103)
Epitope	`TAVPWDSSW`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH256: A33:01, A68:01, B14:01, B53:01, C04:01, C08:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope TAVPWDSSW had a fitness cost ΔE of -4.842 and T cell response was first detected to it at 7d, escape time was 85.62 days.

References

Displaying record number 61075

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HXB2 Location	gp160(637-645) gp41(126-134) DNA(8133..8159)	gp160 Epitope Map
Author Location	gp41(126-134)
Epitope	`NYTDIIYRL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH042: A23:01, A30:02, B15:03, B18:01, C02:02, C07:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope NYTDIIYRL had a fitness cost ΔE of -1.585 and T cell response was first detected to it at 4d, escape time was 131.1 days.

References

Displaying record number 61078

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HXB2 Location	gp160(713-721) gp41(202-210) DNA(8361..8387)	gp160 Epitope Map
Author Location	gp41(202-210)
Epitope	`SPLSFQTLI`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH131: A23:01, A29:01, B15:03, B45:01, C02:02, C06:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope SPLSFQTLI had a fitness cost ΔE of 0.715 and T cell response was first detected to it at 7d, escape time was 315.08 days.

References

Displaying record number 61098

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HXB2 Location	gp160(742-750) gp41(231-239) DNA(8448..8474)	gp160 Epitope Map
Author Location	gp41(231-239)
Epitope	`RNRSIRLVN`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH256: A33:01, A68:01, B14:01, B53:01, C04:01, C08:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope RNRSIRLVN had a fitness cost ΔE of -1.163 and T cell response was first detected to it at 7d, escape time was 17.43 days.

References

Displaying record number 61057

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HXB2 Location	gp160(770-778) gp41(259-267) DNA(8532..8558)	gp160 Epitope Map
Author Location	gp41(259-267)
Epitope	`RLRDLLLIV`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH040: A02:01, A31:01, B40:01, B44:02, C03:02, C05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope RLRDLLLIV had a fitness cost ΔE of 4.374 and T cell response was first detected to it at 16d, escape time was 1072.47 days.

References

Displaying record number 61099

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HXB2 Location	gp160(799-807) gp41(288-296) DNA(8619..8645)	gp160 Epitope Map
Author Location	gp41(288-296)
Epitope	`LVQDWGLEL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH256: A33:01, A68:01, B14:01, B53:01, C04:01, C08:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope LVQDWGLEL had a fitness cost ΔE of -3.532 and T cell response was first detected to it at 28d, escape time was 75.17 days.

References

Displaying record number 61046

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HXB2 Location	gp160(824-832) gp41(313-321) DNA(8694..8720)	gp160 Epitope Map
Author Location	gp41(313-321)
Epitope	`EATDRILEL`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP210: A68:02, B15:10, C*03:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope EATDRILEL had a fitness cost ΔE of -0.304 and T cell response was first detected to it at 34d, escape time was 1 days.

References

Displaying record number 61068

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HXB2 Location	gp160(827-835) gp41(316-324) DNA(8703..8729)	gp160 Epitope Map
Author Location	gp41(316-324)
Epitope	`DRVIEELQR`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH077: A02:05, B53:01, B57:01, C04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope DRVIEELQR had a fitness cost ΔE of 0.339 and T cell response was first detected to it at 21d, escape time was 49.92 days.

References

Displaying record number 61058

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HXB2 Location	gp160(835-843) gp41(324-332) DNA(8727..8753)	gp160 Epitope Map
Author Location	gp41(324-332)
Epitope	`RACRAILHI`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH040: A02:01, A31:01, B40:01, B44:02, C03:02, C05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope RACRAILHI had a fitness cost ΔE of 1.634 and T cell response was first detected to it at 16d, escape time was 741.44 days.

References

Displaying record number 61051

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HXB2 Location	gp160(838-846) gp41(327-335) DNA(8736..8762)	gp160 Epitope Map
Author Location	gp41(327-335)
Epitope	`RAIYSIPRR`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP239: A01:01, A29:02, B42:01, B58:01, C06:02, C07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope RAIYSIPRR had a fitness cost ΔE of 0.832 and T cell response was first detected to it at 36d, escape time was 607.59 days.

References

Displaying record number 61072

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HXB2 Location	gp160(841-849) gp41(330-338) DNA(8745..8771)	gp160 Epitope Map
Author Location	gp41(330-338)
Epitope	`RNIPIRIRQ`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH067: A01:01, A33:01, B53:01, B81:01, C04:01, C18:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope RNIPIRIRQ had a fitness cost ΔE of 0.295 and T cell response was first detected to it at 42d, escape time was 13.2 days.

References

Displaying record number 61041

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HXB2 Location	Nef(64-74) DNA(8986..9018)	Nef Epitope Map
Author Location	Nef(64-74)
Epitope	`EEVGFPVRPQV`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human(B*45:01)
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP045: A23:01, A29:02, B15:10, B45:01, C16:01, C16:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope EEVGFPVRPQV had a fitness cost ΔE of 4.039 and T cell response was first detected to it at 21d, escape time was 43.26 days.

References

Displaying record number 61088

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HXB2 Location	Nef(64-74) DNA(8986..9018)	Nef Epitope Map
Author Location	Nef(64-74)
Epitope	`EEVGFPVRPQV`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH164: A02:01, A29:01, B44:03, B45:01, C07:01, C16:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope EEVGFPVRPQV had a fitness cost ΔE of 2.637 and T cell response was first detected to it at 21d, escape time was 31.43 days.

References

Displaying record number 61079

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HXB2 Location	Nef(64-74) DNA(8986..9018)	Nef Epitope Map
Author Location	Nef(64-74)
Epitope	`EEVGFPVKPQV`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH131: A23:01, A29:01, B15:03, B45:01, C02:02, C06:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope EEVGFPVKPQV had a fitness cost ΔE of -0.619 and T cell response was first detected to it at 7d, escape time was 18.9 days.

References

Displaying record number 61047

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HXB2 Location	Nef(69-77) DNA(9001..9027)	Nef Epitope Map
Author Location	Nef(69-77)
Epitope	`PVKPQVPLR`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP210: A68:02, B15:10, C*03:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope PVKPQVPLR had a fitness cost ΔE of -2.602 and T cell response was first detected to it at 41d, escape time was 23.61 days.

References

Displaying record number 61104

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HXB2 Location	Nef(74-82) DNA(9016..9042)	Nef Epitope Map
Author Location	Nef(74-82)
Epitope	`VPLRPMTFK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH470: A01:01, A03:01, B08:01, B49:01, C*07:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope VPLRPMTFK had a fitness cost ΔE of -0.782 and T cell response was first detected to it at 41d, escape time was 334.55 days.

References

Displaying record number 61052

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HXB2 Location	Nef(82-90) DNA(9040..9066)	Nef Epitope Map
Author Location	Nef(82-90)
Epitope	`KAAVDLSFF`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP239: A01:01, A29:02, B42:01, B58:01, C06:02, C07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope KAAVDLSFF had a fitness cost ΔE of 1.139 and T cell response was first detected to it at 22d, escape time was 65.8 days.

References

Displaying record number 61069

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HXB2 Location	Nef(82-90) DNA(9040..9066)	Nef Epitope Map
Author Location	Nef(82-90)
Epitope	`KAALDLSHF`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH077: A02:05, B53:01, B57:01, C04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope KAALDLSHF had a fitness cost ΔE of 1.789 and T cell response was first detected to it at 21d, escape time was 8.36 days.

References

Displaying record number 61092

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HXB2 Location	Nef(82-90) DNA(9040..9066)	Nef Epitope Map
Author Location	Nef(82-90)
Epitope	`KAAFDLSFF`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH198: A03:01, A74:01, B08:01, B57, C07:01, C07:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope KAAFDLSFF had a fitness cost ΔE of 3.005 and T cell response was first detected to it at 11d, escape time was 1 days.

References

Displaying record number 61106

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HXB2 Location	Nef(105-115) DNA(9109..9141)	Nef Epitope Map
Author Location	Nef(105-115)
Epitope	`KRREILDLWVY`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH607: A01:01, A03:01, B08:01, B49:01, C*07:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope KRREILDLWVY had a fitness cost ΔE of -4.698 and T cell response was first detected to it at 13d, escape time was 7.26 days.

References

Displaying record number 61076

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HXB2 Location	Nef(107-115) DNA(9115..9141)	Nef Epitope Map
Author Location	Nef(107-115)
Epitope	`REILDLWVY`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH042: A23:01, A30:02, B15:03, B18:01, C02:02, C07:04
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope REILDLWVY had a fitness cost ΔE of -0.513 and T cell response was first detected to it at 4d, escape time was 672 days.

References

Displaying record number 61085

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HXB2 Location	Nef(108-116) DNA(9118..9144)	Nef Epitope Map
Author Location	Nef(108-116)
Epitope	`EILDLWVYH`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH162: A30:01, A34:02, B42:02, B44:03, C04:01, C17:01
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope EILDLWVYH had a fitness cost ΔE of 0.97 and T cell response was first detected to it at 26d, escape time was 61.66 days.

References

Displaying record number 61063

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HXB2 Location	Nef(116-124) DNA(9142..9168)	Nef Epitope Map
Author Location	Nef(116-124)
Epitope	`HTQGYFPDW`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH058: A01:01, A23:01, B14:02, B57, C07:01, C08:02
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope HTQGYFPDW had a fitness cost ΔE of 3.438 and T cell response was first detected to it at 21d, escape time was 35.69 days.

References

Displaying record number 61042

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HXB2 Location	Nef(129-146) DNA(9181..9234)	Nef Epitope Map
Author Location	Nef(129-146)
Epitope	`PGPGVRYPLTFGWCFKLV`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CAP045: A23:01, A29:02, B15:10, B45:01, C16:01, C16:02
Country	South Africa
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope PGPGVRYPLTFGWCFKLV had a fitness cost ΔE of 3.556 and T cell response was first detected to it at 48d, escape time was 392 days.

References

Displaying record number 61082

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HXB2 Location	Nef(178-186) DNA(9328..9354)	Nef Epitope Map
Author Location	Nef(178-186)
Epitope	`REVLIWKFD`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH159: A23:01, A68:02, B18:01, B81:01, C07:04, C18:01
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope REVLIWKFD had a fitness cost ΔE of 0.843 and T cell response was first detected to it at 12d, escape time was 10.58 days.

References

Displaying record number 61059

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HXB2 Location	Nef(187-196) DNA(9355..9384)	Nef Epitope Map
Author Location	Nef(187-196)
Epitope	`SSLAFRHVAR`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH040: A02:01, A31:01, B40:01, B44:02, C03:02, C05:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope SSLAFRHVAR had a fitness cost ΔE of -0.872 and T cell response was first detected to it at 16d, escape time was 1 days.

References

Displaying record number 61100

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HXB2 Location	Nef(188-196) DNA(9358..9384)	Nef Epitope Map
Author Location	Nef(188-196)
Epitope	`QLAHRHMAR`	Epitope Alignment
Subtype	C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH256: A33:01, A68:01, B14:01, B53:01, C04:01, C08:02
Country	Malawi
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope QLAHRHMAR had a fitness cost ΔE of -0.613 and T cell response was first detected to it at 28d, escape time was 86.35 days.

References

Displaying record number 61105

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HXB2 Location	Nef(188-198) DNA(9358..9390)	Nef Epitope Map
Author Location	Nef(188-198)
Epitope	`RLAYQHIAKEK`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH470: A01:01, A03:01, B08:01, B49:01, C*07:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope RLAYQHIAKEK had a fitness cost ΔE of -0.24 and T cell response was first detected to it at 3d, escape time was 1.76 days.

References

Displaying record number 61070

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HXB2 Location	Nef(194-202) DNA(9376..9402)	Nef Epitope Map
Author Location	Nef(194-202)
Epitope	`VAREIHPEF`	Epitope Alignment
Subtype	B
Species (MHC/HLA)	human
Immunogen	HIV-1 infection
Patient MHC/HLA	CH077: A02:05, B53:01, B57:01, C04:01, C*18:01
Country	United States
Experimental methods	CD8 T-cell Elispot - IFNγ, Other
Keywords	computational epitope prediction, escape, acute/early infection, mutation acquisition

Notes

17 patients with acute HIV-1 infection were followed to validate that (1) relative escape rate (2) location and identity of escape mutations and (3) epistatic effects on escape, could be predicted within a host by using a simple model based on population genetics and known fitness measures of HIV polyproteins. In general escape location was found most at residues with the lowest fitness cost and escape time correlates with early detection of mutants when T cell response was first detected.
Epitope VAREIHPEF had a fitness cost ΔE of -3.401 and T cell response was first detected to it at 21d, escape time was 571 days.