Search CTL/CD8+ T-Cell Epitope Database

Found 23 matching records:

Displaying record number 62834

Download this epitope record as JSON.

HXB2 Location	Pol(160-167) RT(5-12) DNA(2562..2585)	Pol Epitope Map
Author Location	RT(5-12)
Epitope	`IETVPVKL`	Epitope Alignment
Epitope Name	IL-8
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphisms E6K & V8I, as well as subtype C consensus V8, were associated with altered RC and are located within best-defined A-list epitope IETVPVK, IL-8, known to bind to B*40:01.
E6K occurred in 19 participant-derived recombinant viruses with a median RC of 0.87, while 382 analogous viruses without E6K had a median RC of 0.92, relative to unmodified NL4-3.
V8I occurred in 14 participant-derived recombinant viruses with a median RC of 0.98, while 468 analogous viruses with consensus V8 had a median RC of 0.92, relative to unmodified NL4-3.

References

Ojwach2018 Doty B. A. Ojwach, Daniel MacMillan, Tarylee Reddy, Vladimir Novitsky, Zabrina L. Brumme, Mark A. Brockman, Thumbi Ndung'u, and Jaclyn K. Mann. Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection. J. Virol., 92(19), 1 Oct 2018. PubMed ID: 29997209. Show all entries for this paper.

Displaying record number 62835

Download this epitope record as JSON.

HXB2 Location	Pol(173-181) RT(18-26) DNA(2601..2627)	Pol Epitope Map
Author Location	RT(18-26)
Epitope	`GPKVKQWPL`	Epitope Alignment
Epitope Name	GL9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism K22R and subtype C consensus K22, were associated with altered RC and are located within best-defined A-list epitope GPKVKQWPL, GL9, known to bind to B*08.
K22R occurred in 6 participant-derived recombinant viruses with a median RC of 1.01, while 473 analogous viruses with consensus K22 had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62836

Download this epitope record as JSON.

HXB2 Location	Pol(188-198) RT(33-43) DNA(2646..2678)	Pol Epitope Map
Author Location	RT(33-43)
Epitope	`ALVEICTEMEK`	Epitope Alignment
Epitope Name	AK11
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism A36E, located within best-defined A-list epitope ALVEICTEMEK (AK11, known to bind to A*02:01/A*03:01), and subtype C consensus T48, located 5 aa downstream from AK11, were associated with altered RC.
A36E occurred in 123 participant-derived recombinant viruses with a median RC of 0.94, while 336 analogous viruses without A36E had a median RC of 0.92, relative to unmodified NL4-3.
Consensus T48 occurred in 458 participant-derived recombinant viruses with a median RC of 0.92, while 22 analogous viruses without T at RT residue 48 had a median RC of 0.95, relative to unmodified NL4-3.

References

Displaying record number 62837

Download this epitope record as JSON.

HXB2 Location	Pol(304-313) RT(149-158) DNA(2994..3023)	Pol Epitope Map
Author Location	RT(149-158)
Epitope	`LPQGWKGSPA`	Epitope Alignment
Epitope Name	LA10
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism A158S and subtype C consensus A158 were associated with altered RC and are located within best-defined A-list epitope LPQGWKGSPA, LA10, known to bind to B*54:01, as well as overlapping epitopes SPAIFQSSM & AIFQSSMTK.
A158S occurred in 25 participant-derived recombinant viruses with a median RC of 0.88, while 453 analogous viruses with consensus A158 had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62838

Download this epitope record as JSON.

HXB2 Location	Pol(311-319) RT(156-164) DNA(3015..3041)	Pol Epitope Map
Author Location	RT(156-164)
Epitope	`SPAIFQSSM`	Epitope Alignment
Epitope Name	SM9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism A158S and subtype C consensus A158 were associated with altered RC and are located within well-defined epitope SPAIFQSSM, SM9, known to bind to B*07, as well as overlapping epitopes LPQGWKGSPA & AIFQSSMTK.
A158S occurred in 25 participant-derived recombinant viruses with a median RC of 0.88, while 453 analogous viruses with consensus A158 had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62839

Download this epitope record as JSON.

HXB2 Location	Pol(313-321) RT(158-166) DNA(3021..3047)	Pol Epitope Map
Author Location	RT(158-166)
Epitope	`AIFQSSMTK`	Epitope Alignment
Epitope Name	AK9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism A158S and subtype C consensus A158 were associated with altered RC and are located within best-defined A-list epitope AIFQSSMTK, AK9, known to bind to A*03:01/A*11:01, as well as overlapping epitopes LPQGWKGSPA & SPAIFQSSM.
A158S occurred in 25 participant-derived recombinant viruses with a median RC of 0.88, while 453 analogous viruses with consensus A158 had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62840

Download this epitope record as JSON.

HXB2 Location	Pol(357-365) RT(202-210) DNA(3153..3179)	Pol Epitope Map
Author Location	RT(202-210)
Epitope	`IEELRQHLL`	Epitope Alignment
Epitope Name	IL-9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism A200E was associated with altered RC and is located 2 aa upstream from best-defined A-list epitope IEELRQHLL, IL-9, known to bind to B*40:01.
A200E occurred in 9 participant-derived recombinant viruses with a median RC of 0.98, while 467 analogous viruses without A200E had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62841

Download this epitope record as JSON.

HXB2 Location	Pol(399-407) RT(244-252) DNA(3279..3305)	Pol Epitope Map
Author Location	RT(244-252)
Epitope	`IVLPEKDSW`	Epitope Alignment
Epitope Name	IW9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphisms V241I & I257V and subtype C consensus V241 & I257 were all associated with altered RC and are located 3 aa upstream and 5 aa downstream from best-defined A-list epitope IVLPEKDSW, IW9, known to bind to B*57:01. Residue 257 is also located within overlapping epitope LVGKLNWASQIY.
Rare V241I occurred in 5 participant-derived recombinant viruses with a substantially reduced median RC of 0.82, while 479 analogous viruses with consensus V241 had a median RC of 0.92, relative to unmodified NL4-3.
Rare I257V occurred in 5 participant-derived recombinant viruses with a substantially reduced median RC of 0.80, while 475 analogous viruses with consensus I257 had a median RC of 0.92, relative to unmodified NL4-3.
Authors suggest V241I & I257V may be novel fitness-costly immune-driven escape mutations.

References

Displaying record number 62842

Download this epitope record as JSON.

HXB2 Location	Pol(415-426) RT(260-271) DNA(3327..3362)	Pol Epitope Map
Author Location	RT(260-271)
Epitope	`LVGKLNWASQIY`	Epitope Alignment
Epitope Name	LY12
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism I257V and subtype C consensus I257 were associated with altered RC and are within best-defined A-list epitope LVGKLNWASQIY, LY12, known to bind to B*15:01. Residue 257 also flanks overlapping epitope IVLPEKDSW.
Rare I257V occurred in 5 participant-derived recombinant viruses with a substantially reduced median RC of 0.80, while 475 analogous viruses with consensus I257 had a median RC of 0.92, relative to unmodified NL4-3. Authors suggest I257V may be a novel fitness-costly immune-driven escape mutation.

References

Displaying record number 62843

Download this epitope record as JSON.

HXB2 Location	Pol(424-432) RT(269-277) DNA(3354..3380)	Pol Epitope Map
Author Location	RT(269-277)
Epitope	`QIYPGIKVR`	Epitope Alignment
Epitope Name	QR9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism P272K and subtype C consensus P272 were associated with altered RC and are within best-defined A-list epitope QIYPGIKVR, QR9, known to bind to A*03:01. Residue 272 is also located within overlapping epitope YPGIKVRQL.
Rare P272K occurred in 5 participant-derived recombinant viruses with a substantially reduced median RC of 0.84, while 350 analogous viruses with consensus P272 had a median RC of 0.93, relative to unmodified NL4-3. Authors suggest P272K may be a novel fitness-costly immune-driven escape mutation.

References

Displaying record number 62844

Download this epitope record as JSON.

HXB2 Location	Pol(426-434) RT(271-279) DNA(3360..3386)	Pol Epitope Map
Author Location	RT(271-279)
Epitope	`YPGIKVRQL`	Epitope Alignment
Epitope Name	YL9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism P272K and subtype C consensus P272 were associated with altered RC and are within well-defined epitope YPGIKVRQL, YL9, known to bind to B*42:01. Residue 272 is also located within overlappping epitope QIYPGIKVR.
Rare P272K occurred in 5 participant-derived recombinant viruses with a substantially reduced median RC of 0.84, while 350 analogous viruses with consensus P272 had a median RC of 0.93, relative to unmodified NL4-3. Authors suggest P272K may be a novel fitness-costly immune-driven escape mutation.

References

Displaying record number 62845

Download this epitope record as JSON.

HXB2 Location	Pol(448-456) RT(293-301) DNA(3426..3452)	Pol Epitope Map
Author Location	RT(293-301)
Epitope	`IPLTEEAEL`	Epitope Alignment
Epitope Name	IL-9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism E297K was associated with altered RC and is located 2 within best-defined A-list epitope IPLTEEAEL, IL-9, known to bind to B*3501 & B*5101.
Rare E297K occurred in 7 participant-derived recombinant viruses with a substantially reduced median RC of 0.80, while 386 analogous viruses without E297K had a median RC of 0.92, relative to unmodified NL4-3. Authors suggest E297K may be a novel fitness-costly immune-driven escape mutation.

References

Displaying record number 62846

Download this epitope record as JSON.

HXB2 Location	Pol(464-473) RT(309-318) DNA(3474..3503)	Pol Epitope Map
Author Location	RT(309-318)
Epitope	`ILKEPVHGVY`	Epitope Alignment
Epitope Name	IY10
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Subtype C consensus K311 was associated with altered RC and is located within RT best-defined A-list epitope ILKEPVHGVY, IY10, known to bind to A*02:01, B*15:01, & C*12:02.
Consensus K311 occurred in 458 participant-derived recombinant viruses with a median RC of 0.92, while 17 analogous viruses without K at residue 311 had a median RC of 0.89, relative to unmodified NL4-3.

References

Displaying record number 62847

Download this epitope record as JSON.

HXB2 Location	Pol(511-521) RT(356-366) DNA(3615..3647)	Pol Epitope Map
Author Location	RT(356-366)
Epitope	`RMRGAHTNDVK`	Epitope Alignment
Epitope Name	RK11
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
RT polymorphism M357R was associated with altered RC and is located within best-defined A-list epitope RMRGAHTNDVK, RK11, known to bind to A*30:02 & A*03:01.
M357R occurred in 171 participant-derived recombinant viruses with a median RC of 0.93, while 299 analogous viruses without M357R had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62848

Download this epitope record as JSON.

HXB2 Location	Pol(793-801) Integrase(78-86) DNA(4461..4487)	Pol Epitope Map
Author Location	Integrase(78-86)
Epitope	`HVASGYIEA`	Epitope Alignment
Epitope Name	HA9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Integrase polymorphism I84M and subtype C consensus I84 were associated with altered RC and are within best-defined A-list epitope HVASGYIEA, HA9, known to bind to B*54:01. Residue 84 is also located within overlapping epitope IEAEVIPAET.
I84M occurred in 89 participant-derived recombinant viruses with a median RC of 0.91, while 363 analogous viruses with consensus I84 had a median RC of 0.93, relative to unmodified NL4-3.

References

Displaying record number 62849

Download this epitope record as JSON.

HXB2 Location	Pol(799-808) Integrase(84-93) DNA(4479..4508)	Pol Epitope Map
Author Location	Integrase(84-93)
Epitope	`IEAEVIPAET`	Epitope Alignment
Epitope Name	IT10
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Integrase polymorphism I84M and subtype C consensus I84 were associated with altered RC and are within best-defined A-list epitope IEAEVIPAET, IT10, known to bind to B*40:02. Residue 84 is also located within overlapping epitope HVASGYIEA.
I84M occurred in 89 participant-derived recombinant viruses with a median RC of 0.91, while 363 analogous viruses with consensus I84 had a median RC of 0.93, relative to unmodified NL4-3.

References

Displaying record number 62850

Download this epitope record as JSON.

HXB2 Location	Pol(829-836) Integrase(114-121) DNA(4569..4592)	Pol Epitope Map
Author Location	Integrase(114-121)
Epitope	`HTDNGSNF`	Epitope Alignment
Epitope Name	HF8
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Polymorphism V112I and subtype C consensus K111, located 2 and 3 aa upstream from integrase best-defined A-list epitope HTDNGSNF (HF8) and polymorphism S119T and subtype C consensus S119, located within HF8, were all associated with altered RC. HF8 is known to bind to C*05.
Consensus K111 occurred in 469 participant-derived recombinant viruses with a median RC of 0.92, while 11 analogous viruses without K at residue 111 had a median RC of 0.97, relative to unmodified NL4-3.
V112I occurred in 445 participant-derived recombinant viruses with a median RC of 0.92, while 26 analogous viruses without V112I had a median RC of 0.89, relative to unmodified NL4-3.
S119T occurred in 33 participant-derived recombinant viruses with a median RC of 0.95, while 403 analogous viruses with consensus S119 had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62851

Download this epitope record as JSON.

HXB2 Location	Pol(838-847) Integrase(123-132) DNA(4596..4625)	Pol Epitope Map
Author Location	Integrase(123-132)
Epitope	`STTVKAACWW`	Epitope Alignment
Epitope Name	SW10
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Polymorphism S119T and subtype C consensus S119 were associated with altered RC and are located 4 aa upstream from integrase best-defined A-list epitope STTVKAACWW (SW10), known to bind to B*57.
S119T occurred in 33 participant-derived recombinant viruses with a median RC of 0.95, while 403 analogous viruses with consensus S119 had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62852

Download this epitope record as JSON.

HXB2 Location	Pol(850-858) Integrase(135-143) DNA(4632..4658)	Pol Epitope Map
Author Location	Integrase(135-143)
Epitope	`IQQEFGIPY`	Epitope Alignment
Epitope Name	IY9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Integrase polymorphism Q136K was associated with altered RC and is located within well-defined epitope IQQEFGIPY, IY9, known to bind to B*1503.
Q136K occurred in 28 participant-derived recombinant viruses with a median RC of 0.88, while 368 analogous viruses without M357R had a median RC of 0.92, relative to unmodified NL4-3.

References

Displaying record number 62853

Download this epitope record as JSON.

HXB2 Location	Pol(912-919) Integrase(197-204) DNA(4818..4841)	Pol Epitope Map
Author Location	Integrase(197-204)
Epitope	`GERIVDII`	Epitope Alignment
Epitope Name	GI8
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Subtype C polymorphism I201V was associated with altered RC and is located within well-defined integrase epitope GI8 known to bind to B*4002. Residue 201 is polymorphic between subtypes and C consensus sequence of GI8 is GERIIDII with I201 vs. GERIVDII with V201 in subtype B.
Rare I201V occurred in 5 participant-derived recombinant viruses with a substantially reduced median RC of 0.83 while 404 analogous viruses without I201V had a median RC of 0.92, relative to unmodified NL4-3. Authors suggest I201V may be a novel fitness-costly immune-driven escape mutation.

References

Displaying record number 62854

Download this epitope record as JSON.

HXB2 Location	Pol(918-926) Integrase(203-211) DNA(4836..4862)	Pol Epitope Map
Author Location	Integrase(203-211)
Epitope	`IIATDIQTK`	Epitope Alignment
Epitope Name	IK9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Integrase polymorphism K211R and subtype C consensus K211 were associated with altered RC and are located within well-defined epitope IIATDIQTK, IY9, known to bind to A*11.
K211R occurred in 53 participant-derived recombinant viruses with a median RC of 0.89, while 414 analogous viruses with consensus K211 had a median RC of 0.93, relative to unmodified NL4-3.

References

Displaying record number 62856

Download this epitope record as JSON.

HXB2 Location	Pol(975-983) Integrase(260-268) DNA(5007..5033)	Pol Epitope Map
Author Location	Integrase(260-268)
Epitope	`VPRRKAKII`	Epitope Alignment
Epitope Name	VI9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Integrase polymorphism K269R and subtype C consensus K269 were associated with altered RC and are located 1 aa downstream from well-defined epitope VPRRKAKII, VI9, known to bind to B*42. Residue 269 is also within overlapping epitope RKAKIIRDY.
K269R occurred in 197 participant-derived recombinant viruses with a median RC of 0.91, while 238 analogous viruses with consensus K269 had a median RC of 0.93, relative to unmodified NL4-3.

References

Displaying record number 62855

Download this epitope record as JSON.

HXB2 Location	Pol(978-986) Integrase(263-271) DNA(5016..5042)	Pol Epitope Map
Author Location	Integrase(263-271)
Epitope	`RKAKIIRDY`	Epitope Alignment
Epitope Name	RY9
Subtype	B, C
Species (MHC/HLA)	human
Immunogen	HIV-1 infection, engineered
Experimental methods	Other, Relative replication capacity assay
Keywords	acute/early infection, HLA associated polymorphism, chronic infection, protective allele

Notes

The in vitro replicative capacity (RC) of recombinant subtype B NL4-3 viruses expressing subtype C RT-integrase sequences derived from recently infected patients correlated positively with log subsequent VL set point and a higher rate of CD4 decline, while the RC of NL4-3 recombinants expressing subtype C RT-integrase sequences derived from chronically infected patients correlated positively with log VL but negatively with CD4 count. Protective & risk HLA alleles were associated with lower and higher RC values, respectively, and the number of HLA-associated polymorphisms in RT correlated positively with RC while the inverse was observed for integrase. About 90% of RT-integrase polymorphisms significantly associated with altered RC occurred inside or within 5 aa of A-list epitopes (LANL HIV Database).
Subtype C polymorphism K269R and subtype C consensus K269 were associated with altered RC and are located within well-defined integrase epitope RY9, known to bind to B*15:03. Residue 269 is polymorphic between subtypes and C consensus sequence of RY9 is RKAKIIKDY with K269 vs. RKAKIIRDY with R269 in subtype B. Residue 269 also flanks overlapping epitope VPRRKAKII.
K269R occurred in 197 participant-derived recombinant viruses with a median RC of 0.91, while 238 analogous viruses with consensus K269 had a median RC of 0.93, relative to unmodified NL4-3.