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...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004221015856 |
| _version_ | 1828127381946105856 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Noah A.J. Cassidy |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T15:49:40Z |
| format | Article |
| id | doaj.art-e707195846a348508f652a81b92d9da2 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-11T15:49:40Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-e707195846a348508f652a81b92d9da22022-12-22T04:15:26ZengElsevieriScience2589-00422022-01-01251103615HIV reservoir quantification using cross-subtype multiplex ddPCRNoah A.J. Cassidy0Carolyn S. Fish1Claire N. Levy2Pavitra Roychoudhury3Daniel B. Reeves4Sean M. Hughes5Joshua T. Schiffer6Sarah Benki-Nugent7Grace John-Stewart8Dalton Wamalwa9Keith R. Jerome10Julie Overbaugh11Florian Hladik12Dara A. Lehman13Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USADivision of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USADepartment of Obstetrics and Gynecology, University of Washington, Seattle, WA, USAVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USAVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USADepartment of Obstetrics and Gynecology, University of Washington, Seattle, WA, USAVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USADepartment of Global Health, University of Washington, Seattle, WA, USADepartment of Global Health, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USADepartment of Pediatrics and Child Health, University of Nairobi, Kenyatta National Hospital, Nairobi, KenyaVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USADivision of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USADepartment of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USADivision of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2589004221015856VirologyGenotyping |
| spellingShingle | 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 HIV reservoir quantification using cross-subtype multiplex ddPCR iScience Virology Genotyping |
| title | HIV reservoir quantification using cross-subtype multiplex ddPCR |
| title_full | HIV reservoir quantification using cross-subtype multiplex ddPCR |
| title_fullStr | HIV reservoir quantification using cross-subtype multiplex ddPCR |
| title_full_unstemmed | HIV reservoir quantification using cross-subtype multiplex ddPCR |
| title_short | HIV reservoir quantification using cross-subtype multiplex ddPCR |
| title_sort | hiv reservoir quantification using cross subtype multiplex ddpcr |
| topic | Virology Genotyping |
| url | http://www.sciencedirect.com/science/article/pii/S2589004221015856 |
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