HIV reservoir quantification using cross-subtype multiplex ddPCR

Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defe...
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Autor*in:	Noah A.J. Cassidy [verfasserIn] Carolyn S. Fish [verfasserIn] Claire N. Levy [verfasserIn] Pavitra Roychoudhury [verfasserIn] Daniel B. Reeves [verfasserIn] Sean M. Hughes [verfasserIn] Joshua T. Schiffer [verfasserIn] Sarah Benki-Nugent [verfasserIn] Grace John-Stewart [verfasserIn] Dalton Wamalwa [verfasserIn] Keith R. Jerome [verfasserIn] Julie Overbaugh [verfasserIn] Florian Hladik [verfasserIn] Dara A. Lehman [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	Virology Genotyping

Übergeordnetes Werk:	In: iScience - Elsevier, 2019, 25(2022), 1, Seite 103615-
Übergeordnetes Werk:	volume:25 ; year:2022 ; number:1 ; pages:103615-

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1016/j.isci.2021.103615

Katalog-ID:	DOAJ086034022

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520			\|a Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest.
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allfields	10.1016/j.isci.2021.103615 doi (DE-627)DOAJ086034022 (DE-599)DOAJe707195846a348508f652a81b92d9da2 DE-627 ger DE-627 rakwb eng Noah A.J. Cassidy verfasserin aut HIV reservoir quantification using cross-subtype multiplex ddPCR 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest. Virology Genotyping Science Q Carolyn S. Fish verfasserin aut Claire N. Levy verfasserin aut Pavitra Roychoudhury verfasserin aut Daniel B. Reeves verfasserin aut Sean M. Hughes verfasserin aut Joshua T. Schiffer verfasserin aut Sarah Benki-Nugent verfasserin aut Grace John-Stewart verfasserin aut Dalton Wamalwa verfasserin aut Keith R. Jerome verfasserin aut Julie Overbaugh verfasserin aut Florian Hladik verfasserin aut Dara A. Lehman verfasserin aut In iScience Elsevier, 2019 25(2022), 1, Seite 103615- (DE-627)1019532106 25890042 nnns volume:25 year:2022 number:1 pages:103615- https://doi.org/10.1016/j.isci.2021.103615 kostenfrei https://doaj.org/article/e707195846a348508f652a81b92d9da2 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221015856 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 25 2022 1 103615-
spelling	10.1016/j.isci.2021.103615 doi (DE-627)DOAJ086034022 (DE-599)DOAJe707195846a348508f652a81b92d9da2 DE-627 ger DE-627 rakwb eng Noah A.J. Cassidy verfasserin aut HIV reservoir quantification using cross-subtype multiplex ddPCR 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest. Virology Genotyping Science Q Carolyn S. Fish verfasserin aut Claire N. Levy verfasserin aut Pavitra Roychoudhury verfasserin aut Daniel B. Reeves verfasserin aut Sean M. Hughes verfasserin aut Joshua T. Schiffer verfasserin aut Sarah Benki-Nugent verfasserin aut Grace John-Stewart verfasserin aut Dalton Wamalwa verfasserin aut Keith R. Jerome verfasserin aut Julie Overbaugh verfasserin aut Florian Hladik verfasserin aut Dara A. Lehman verfasserin aut In iScience Elsevier, 2019 25(2022), 1, Seite 103615- (DE-627)1019532106 25890042 nnns volume:25 year:2022 number:1 pages:103615- https://doi.org/10.1016/j.isci.2021.103615 kostenfrei https://doaj.org/article/e707195846a348508f652a81b92d9da2 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221015856 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 25 2022 1 103615-
allfields_unstemmed	10.1016/j.isci.2021.103615 doi (DE-627)DOAJ086034022 (DE-599)DOAJe707195846a348508f652a81b92d9da2 DE-627 ger DE-627 rakwb eng Noah A.J. Cassidy verfasserin aut HIV reservoir quantification using cross-subtype multiplex ddPCR 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest. Virology Genotyping Science Q Carolyn S. Fish verfasserin aut Claire N. Levy verfasserin aut Pavitra Roychoudhury verfasserin aut Daniel B. Reeves verfasserin aut Sean M. Hughes verfasserin aut Joshua T. Schiffer verfasserin aut Sarah Benki-Nugent verfasserin aut Grace John-Stewart verfasserin aut Dalton Wamalwa verfasserin aut Keith R. Jerome verfasserin aut Julie Overbaugh verfasserin aut Florian Hladik verfasserin aut Dara A. Lehman verfasserin aut In iScience Elsevier, 2019 25(2022), 1, Seite 103615- (DE-627)1019532106 25890042 nnns volume:25 year:2022 number:1 pages:103615- https://doi.org/10.1016/j.isci.2021.103615 kostenfrei https://doaj.org/article/e707195846a348508f652a81b92d9da2 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221015856 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 25 2022 1 103615-
allfieldsGer	10.1016/j.isci.2021.103615 doi (DE-627)DOAJ086034022 (DE-599)DOAJe707195846a348508f652a81b92d9da2 DE-627 ger DE-627 rakwb eng Noah A.J. Cassidy verfasserin aut HIV reservoir quantification using cross-subtype multiplex ddPCR 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest. Virology Genotyping Science Q Carolyn S. Fish verfasserin aut Claire N. Levy verfasserin aut Pavitra Roychoudhury verfasserin aut Daniel B. Reeves verfasserin aut Sean M. Hughes verfasserin aut Joshua T. Schiffer verfasserin aut Sarah Benki-Nugent verfasserin aut Grace John-Stewart verfasserin aut Dalton Wamalwa verfasserin aut Keith R. Jerome verfasserin aut Julie Overbaugh verfasserin aut Florian Hladik verfasserin aut Dara A. Lehman verfasserin aut In iScience Elsevier, 2019 25(2022), 1, Seite 103615- (DE-627)1019532106 25890042 nnns volume:25 year:2022 number:1 pages:103615- https://doi.org/10.1016/j.isci.2021.103615 kostenfrei https://doaj.org/article/e707195846a348508f652a81b92d9da2 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221015856 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 25 2022 1 103615-
allfieldsSound	10.1016/j.isci.2021.103615 doi (DE-627)DOAJ086034022 (DE-599)DOAJe707195846a348508f652a81b92d9da2 DE-627 ger DE-627 rakwb eng Noah A.J. Cassidy verfasserin aut HIV reservoir quantification using cross-subtype multiplex ddPCR 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest. Virology Genotyping Science Q Carolyn S. Fish verfasserin aut Claire N. Levy verfasserin aut Pavitra Roychoudhury verfasserin aut Daniel B. Reeves verfasserin aut Sean M. Hughes verfasserin aut Joshua T. Schiffer verfasserin aut Sarah Benki-Nugent verfasserin aut Grace John-Stewart verfasserin aut Dalton Wamalwa verfasserin aut Keith R. Jerome verfasserin aut Julie Overbaugh verfasserin aut Florian Hladik verfasserin aut Dara A. Lehman verfasserin aut In iScience Elsevier, 2019 25(2022), 1, Seite 103615- (DE-627)1019532106 25890042 nnns volume:25 year:2022 number:1 pages:103615- https://doi.org/10.1016/j.isci.2021.103615 kostenfrei https://doaj.org/article/e707195846a348508f652a81b92d9da2 kostenfrei http://www.sciencedirect.com/science/article/pii/S2589004221015856 kostenfrei https://doaj.org/toc/2589-0042 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_171 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 25 2022 1 103615-
language	English
source	In iScience 25(2022), 1, Seite 103615- volume:25 year:2022 number:1 pages:103615-
sourceStr	In iScience 25(2022), 1, Seite 103615- volume:25 year:2022 number:1 pages:103615-
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Virology Genotyping Science Q
isfreeaccess_bool	true
container_title	iScience
authorswithroles_txt_mv	Noah A.J. Cassidy @@aut@@ Carolyn S. Fish @@aut@@ Claire N. Levy @@aut@@ Pavitra Roychoudhury @@aut@@ Daniel B. Reeves @@aut@@ Sean M. Hughes @@aut@@ Joshua T. Schiffer @@aut@@ Sarah Benki-Nugent @@aut@@ Grace John-Stewart @@aut@@ Dalton Wamalwa @@aut@@ Keith R. Jerome @@aut@@ Julie Overbaugh @@aut@@ Florian Hladik @@aut@@ Dara A. Lehman @@aut@@
publishDateDaySort_date	2022-01-01T00:00:00Z
hierarchy_top_id	1019532106
id	DOAJ086034022
language_de	englisch
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author	Noah A.J. Cassidy
spellingShingle	Noah A.J. Cassidy misc Virology misc Genotyping misc Science misc Q HIV reservoir quantification using cross-subtype multiplex ddPCR
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topic_title	HIV reservoir quantification using cross-subtype multiplex ddPCR Virology Genotyping
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title	HIV reservoir quantification using cross-subtype multiplex ddPCR
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title_full	HIV reservoir quantification using cross-subtype multiplex ddPCR
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author_browse	Noah A.J. Cassidy Carolyn S. Fish Claire N. Levy Pavitra Roychoudhury Daniel B. Reeves Sean M. Hughes Joshua T. Schiffer Sarah Benki-Nugent Grace John-Stewart Dalton Wamalwa Keith R. Jerome Julie Overbaugh Florian Hladik Dara A. Lehman
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title_sort	hiv reservoir quantification using cross-subtype multiplex ddpcr
title_auth	HIV reservoir quantification using cross-subtype multiplex ddPCR
abstract	Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest.
abstractGer	Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest.
abstract_unstemmed	Summary: A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%–33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest.
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title_short	HIV reservoir quantification using cross-subtype multiplex ddPCR
url	https://doi.org/10.1016/j.isci.2021.103615 https://doaj.org/article/e707195846a348508f652a81b92d9da2 http://www.sciencedirect.com/science/article/pii/S2589004221015856 https://doaj.org/toc/2589-0042
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HIV reservoir quantification using cross-subtype multiplex ddPCR

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