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Quantitative Evaluation of Very Low Levels of HIV-1 Reverse Transcriptase by a Novel Highly Sensitive RT-qPCR Assay. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081130. [PMID: 36013309 PMCID: PMC9410348 DOI: 10.3390/life12081130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Based on previous experience in our laboratory, we developed a real-time reverse transcriptase (RT) quantitative PCR (RT-qPCR) assay for the assessment of very low levels of HIV-1 RT activity. The RNA, acting as a template for reverse transcription into cDNA by HIV-1 RT, consisted of a synthetic RNA ad hoc generated by in vitro transcription and included a coding sequence for HSV-1 gD (gD-RNA-synt). Different conditions of variables involved in the RT-qPCR reaction, notably different amounts of gD-RNA-synt, different mixes of the reaction buffer, and different dNTP concentrations, were tested to optimize the assay. The results indicated that the gD-RNA-synt-based RT assay, in its optimized formulation, could detect a specific cDNA reverse transcription even in the presence of 1 × 10-9 U of HIV RT. This achievement greatly improved the sensitivity of the assay over previous versions. In summary, this constructed RT-qPCR assay may be considered a promising tool for providing accurate information on very low HIV-1 RT activity.
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2
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Macchi B, Frezza C, Marino-Merlo F, Minutolo A, Stefanizzi V, Balestrieri E, Cerva C, Sarmati L, Andreoni M, Grelli S, Mastino A. Appraisal of a Simple and Effective RT-qPCR Assay for Evaluating the Reverse Transcriptase Activity in Blood Samples from HIV-1 Patients. Pathogens 2020; 9:pathogens9121047. [PMID: 33322208 PMCID: PMC7763350 DOI: 10.3390/pathogens9121047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022] Open
Abstract
Testing HIV-1 RNA in plasma by PCR is universally accepted as the ultimate standard to confirm diagnosis of HIV-1 infection and to monitor viral load in patients under treatment. However, in some cases, this assay could either underestimate or overestimate the replication capacity of a circulating or latent virus. In the present study, we performed the assessment of evaluating the HIV-1 reverse transcriptase (RT) activity by means of a new assay for the functional screening of the status of HIV-1 patients. To this purpose, we utilized, for the first time on blood samples, an adapted version of a real-time RT quantitative PCR assay, utilized to evaluate the HIV-1-RT inhibitory activity of compounds. The study analyzed blood samples from 28 HIV-1-infected patients, exhibiting a wide range of viremia and immunological values. Results demonstrated that plasma HIV-1 RT levels, expressed as cycle threshold values obtained with the assay under appraisal, were inversely and highly significantly correlated with the plasma HIV-1-RNA levels of the patients. Thus, an HIV-1 RT quantitative PCR assay was created which we describe in this study, and it may be considered as a promising basis for an additional tool capable of furnishing information on the functional virological status of HIV-1-infected patients.
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Affiliation(s)
- Beatrice Macchi
- Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Caterina Frezza
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.F.); (C.C.); (L.S.); (M.A.)
| | - Francesca Marino-Merlo
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy;
| | - Antonella Minutolo
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.M.); (V.S.); (E.B.); (S.G.)
| | - Valeria Stefanizzi
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.M.); (V.S.); (E.B.); (S.G.)
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.M.); (V.S.); (E.B.); (S.G.)
| | - Carlotta Cerva
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.F.); (C.C.); (L.S.); (M.A.)
- Tor Vergata University Hospital, 00133 Rome, Italy
| | - Loredana Sarmati
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.F.); (C.C.); (L.S.); (M.A.)
- Tor Vergata University Hospital, 00133 Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.F.); (C.C.); (L.S.); (M.A.)
- Tor Vergata University Hospital, 00133 Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.M.); (V.S.); (E.B.); (S.G.)
- Tor Vergata University Hospital, 00133 Rome, Italy
| | - Antonio Mastino
- The Institute of Translational Pharmacology, CNR, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-3388658161
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Genome Analysis and Replication Studies of the African Green Monkey Simian Foamy Virus Serotype 3 Strain FV2014. Viruses 2020; 12:v12040403. [PMID: 32268512 PMCID: PMC7232438 DOI: 10.3390/v12040403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/27/2020] [Accepted: 04/01/2020] [Indexed: 01/23/2023] Open
Abstract
African green monkey (AGM) spumaretroviruses have been less well-studied than other simian foamy viruses (SFVs). We report the biological and genomic characterization of SFVcae_FV2014, which was the first foamy virus isolated from an African green monkey (AGM) and was found to be serotype 3. Infectivity studies in various cell lines from different species (mouse, dog, rhesus monkey, AGM, and human) indicated that like other SFVs, SFVcae_FV2014 had broad species and cell tropism, and in vitro cell culture infection resulted in cytopathic effect (CPE). In Mus dunni (a wild mouse fibroblast cell line), MDCK (Madin-Darby canine kidney cell line), FRhK-4 (a fetal rhesus kidney cell line), and MRC-5 (a human fetal lung cell line), SFVcae_FV2014 infection was productive resulting in CPE, and had delayed or similar replication kinetics compared with SFVmcy_FV21 and SFVmcy_FV34[RF], which are two Taiwanese macaque isolates, designated as serotypes 1 and 2, respectively. However, in Vero (AGM kidney cell line) and A549 (a human lung carcinoma cell line), the replication kinetics of SFVcae_FV2014 and the SFVmcy viruses were discordant: In Vero, SFVcae_FV2014 showed rapid replication kinetics and extensive CPE, and a persistent infection was seen in A549, with delayed, low CPE, which did not progress even upon extended culture (day 55). Nucleotide sequence analysis of the assembled SFVcae_FV2014 genome, obtained by high-throughput sequencing, indicated an overall 80–90% nucleotide sequence identity with SFVcae_LK3, the only available full-length genome sequence of an AGM SFV, and was distinct phylogenetically from other AGM spumaretroviruses, corroborating previous results based on analysis of partial env sequences. Our study confirmed that SFVcae_FV2014 and SFVcae_LK3 are genetically distinct AGM foamy virus (FV) isolates. Furthermore, comparative infectivity studies of SFVcae_FV2014 and SFVmcy isolates showed that although SFVs have a wide host range and cell tropism, regulation of virus replication is complex and depends on the virus strain and cell-specific factors.
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Marino-Merlo F, Macchi B, Armenia D, Bellocchi MC, Ceccherini-Silberstein F, Mastino A, Grelli S. Focus on recently developed assays for detection of resistance/sensitivity to reverse transcriptase inhibitors. Appl Microbiol Biotechnol 2018; 102:9925-9936. [PMID: 30269214 DOI: 10.1007/s00253-018-9390-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/23/2022]
Abstract
The biology of HIV is rather complex due to high rate of replication, frequent recombination, and introduction of mutations. This gives rise to a number of distinct variants referred as quasispecies. In addition, the latency within reservoir allows the periodic reactivation of virus replication. The rapid replication of HIV allows immune response escape and establishment of resistance to therapy that can be acquired through drug selection and/or transmitted among individuals. This prompted, over the years, the development of a range of assays aimed to determine drug resistance and sensitivity, to be used both in clinical practice and in antiviral research. Reverse transcriptase (RT) inhibitors have an eminent place among the anti-HIV drugs, being constantly present from the beginning until today in the most commonly used antiviral regimens. This mini-review seeks to provide an up-to-date overview of recent efforts in developing even more reliable and simple methods, of both genotypic and phenotypic types, for specifically detecting drug resistance and sensitivity to RT inhibitors.
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Affiliation(s)
| | - Beatrice Macchi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Antonio Mastino
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Via F. Stagno d'Alcontres 31, 98166, Messina, Italy. .,The Institute of Translational Pharmacology, CNR, Rome, Italy.
| | - Sandro Grelli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
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5
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DeStefano JJ, Alves Ferreira-Bravo I. A highly sensitive aptamer-based HIV reverse transcriptase detection assay. J Virol Methods 2018; 257:22-28. [PMID: 29630943 DOI: 10.1016/j.jviromet.2018.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 03/16/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022]
Abstract
Although many new assays for HIV have been developed, several labs still use simple and reliable radioactivity-based reverse transcriptase (RT) nucleotide incorporation assays for detection and quantification. We describe here a new assay for detection and quantitation of HIV RT activity that is based on a high affinity DNA aptamer to RT. The aptamer is sequestered on 96-well plates where it can bind to RT and other constituents can be removed by extensive washing. Since the aptamer mimics a primer-template, upon radiolabeled nucleotide addition, bound RT molecules can extend the aptamer and the radioactive signal can be detected by standard methods. In addition to being procedurally simple, the assay demonstrated high sensitivity (detection limits for RT and virions were ≤6400 molecules (∼4 × 10-8 units) and ∼100-300 virions, respectively) and was essentially linear over a range of at least 104. Both wild type and drug-resistant forms of HIV-1 RT were detectable as was HIV-2 RT, although there were some modest differences in sensitivity.
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Affiliation(s)
- Jeffrey J DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States; The Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.
| | - Irani Alves Ferreira-Bravo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States; The Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
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6
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Marino-Merlo F, Frezza C, Papaianni E, Valletta E, Mastino A, Macchi B. Development and evaluation of a simple and effective RT-qPCR inhibitory assay for detection of the efficacy of compounds towards HIV reverse transcriptase. Appl Microbiol Biotechnol 2017; 101:8249-8258. [DOI: 10.1007/s00253-017-8544-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
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Fábryová H, Hron T, Kabíčková H, Poss M, Elleder D. Induction and characterization of a replication competent cervid endogenous gammaretrovirus (CrERV) from mule deer cells. Virology 2015. [PMID: 26218214 DOI: 10.1016/j.virol.2015.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Endogenous retroviruses (ERVs) were acquired during evolution of their host organisms after infection and mendelian inheritance in the germline by their exogenous counterparts. The ERVs can spread in the host genome and in some cases they affect the host phenotype. The cervid endogenous gammaretrovirus (CrERV) is one of only a few well-defined examples of evolutionarily recent invasion of mammalian genome by retroviruses. Thousands of insertionally polymorphic CrERV integration sites have been detected in wild ranging mule deer (Odocoileus hemionus) host populations. Here, we describe for the first time induction of replication competent CrERV by cocultivation of deer and human cells. We characterize the physical properties and tropism of the induced virus. The genomic sequence of the induced virus is phylogenetically related to the evolutionarily young endogenous CrERVs described so far. We also describe the level of replication block of CrERV on deer cells and its capacity to establish superinfection interference.
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Affiliation(s)
- Helena Fábryová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic
| | - Tomáš Hron
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic
| | - Hana Kabíčková
- Military Health Institute, Department of Microbiology and Biological Research, 16001 Prague, Czech Republic
| | - Mary Poss
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16801, USA
| | - Daniel Elleder
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic.
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8
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Vermeire J, Naessens E, Vanderstraeten H, Landi A, Iannucci V, Van Nuffel A, Taghon T, Pizzato M, Verhasselt B. Quantification of reverse transcriptase activity by real-time PCR as a fast and accurate method for titration of HIV, lenti- and retroviral vectors. PLoS One 2012; 7:e50859. [PMID: 23227216 PMCID: PMC3515444 DOI: 10.1371/journal.pone.0050859] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/29/2012] [Indexed: 11/19/2022] Open
Abstract
Quantification of retroviruses in cell culture supernatants and other biological preparations is required in a diverse spectrum of laboratories and applications. Methods based on antigen detection, such as p24 for HIV, or on genome detection are virus specific and sometimes suffer from a limited dynamic range of detection. In contrast, measurement of reverse transcriptase (RT) activity is a generic method which can be adapted for higher sensitivity using real-time PCR quantification (qPCR-based product-enhanced RT (PERT) assay). We present an evaluation of a modified SYBR Green I-based PERT assay (SG-PERT), using commercially available reagents such as MS2 RNA and ready-to-use qPCR mixes. This assay has a dynamic range of 7 logs, a sensitivity of 10 nU HIV-1 RT and outperforms p24 ELISA for HIV titer determination by lower inter-run variation, lower cost and higher linear range. The SG-PERT values correlate with transducing and infectious units in HIV-based viral vector and replication-competent HIV-1 preparations respectively. This assay can furthermore quantify Moloney Murine Leukemia Virus-derived vectors and can be performed on different instruments, such as Roche Lightcycler® 480 and Applied Biosystems ABI 7300. We consider this test to be an accurate, fast and relatively cheap method for retroviral quantification that is easily implemented for use in routine and research laboratories.
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Affiliation(s)
- Jolien Vermeire
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Evelien Naessens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Hanne Vanderstraeten
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Alessia Landi
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Veronica Iannucci
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Anouk Van Nuffel
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Massimo Pizzato
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
- * E-mail:
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Ashrafi EH, Paul N. Heat-activatable primers for hot-start PCR and hot-start one-step RT-PCR: endpoint and real-time experiments. ACTA ACUST UNITED AC 2011; Chapter 15:Unit 15.9. [PMID: 19816930 DOI: 10.1002/0471142727.mb1509s88] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hot-start PCR is a technique that improves PCR performance by reducing nonspecific amplification during the initial setup stages of the PCR. This unit describes hot-start PCR protocols which utilize primers containing temperature-sensitive modifications. The introduction of 4-oxo-tetradecyl (OXT) phosphotriester groups onto the 3' end of the primer allows for primer-based hot-start PCR that is amenable for use in a number of PCR-based applications. The protocols described in this unit utilize OXT-modified primers in applications such as standard thermal cycling PCR, fast thermal cycling PCR, multiplex PCR, and one-step reverse-transcription PCR. This method is also advantageous for instances where improved PCR specificity is desired and a hot-start polymerase suitable for your application is not available.
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10
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Abstract
Hot Start activation approaches are increasingly being used to improve the performance of PCR. Since the inception of Hot Start as a means of blocking DNA polymerase extension at lower temperatures, a number of approaches have been developed that target the essential reaction components such as magnesium ion, DNA polymerase, oligonucleotide primers, and dNTPs. Herein, five different Hot Start activation protocols are presented. The first method presents the use of barriers as a means of segregating key reaction components until a Hot Start activation step. The second and third protocols demonstrate Hot Start approaches to block DNA polymerase activity through the use of anti-DNA polymerase antibodies and accessory proteins, respectively. The fourth and fifth protocols utilize thermolabile chemical modifications to the oligonucleotide primers and dNTPs. The results presented demonstrate that all protocols significantly improve the specificity of traditional thermal cycling protocols.
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Affiliation(s)
- Natasha Paul
- Department of Research and Development, TriLink BioTechnologies, Inc., San Diego, CA, USA.
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11
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Hidalgo Ashrafi E, Yee J, Paul N. Selective control of primer usage in multiplex one-step reverse transcription PCR. BMC Mol Biol 2009; 10:113. [PMID: 20042116 PMCID: PMC2811113 DOI: 10.1186/1471-2199-10-113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 12/30/2009] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Multiplex RT-PCR is a valuable technique used for pathogen identification, disease detection and relative quantification of gene expression. The simplification of this protocol into a one-step procedure saves time and reagents. However, intensive PCR optimization is often required to overcome competing undesired PCR primer extension during the RT step.
Results
Herein, we report multiplex one-step RT-PCR experiments in which the PCR primers contain thermolabile phosphotriester modification groups. The presence of these groups minimizes PCR primer extension during the RT step and allows for control of PCR primer extension until the more stringent, elevated temperatures of PCR are reached. Results reveal that the use of primers whose extension can be controlled in a temperature-mediated way provides improved one-step RT-PCR specificity in both singleplex and multiplex reaction formats.
Conclusions
The need for an accurate and sensitive technique to quantify mRNA expression levels makes the described modified primer technology a promising tool for use in multiplex one-step RT-PCR. A more accurate representation of the abundances in initial template sample is feasible with modified primers, as artifacts of biased PCR are reduced because of greater improvements in reaction specificity.
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Khan AS, Ma W, Ma Y, Kumar A, Williams DK, Muller J, Ma H, Galvin TA. Proposed algorithm to investigate latent and occult viruses in vaccine cell substrates by chemical induction. Biologicals 2009; 37:196-201. [DOI: 10.1016/j.biologicals.2009.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 02/02/2009] [Indexed: 10/21/2022] Open
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Ma YK, Khan AS. Evaluation of different RT enzyme standards for quantitation of retroviruses using the single-tube fluorescent product-enhanced reverse transcriptase assay. J Virol Methods 2009; 157:133-40. [PMID: 19186191 DOI: 10.1016/j.jviromet.2009.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2008] [Revised: 12/25/2008] [Accepted: 01/12/2009] [Indexed: 10/21/2022]
Abstract
PCR-based reverse transcriptase (RT) assays are highly sensitive for broad detection of retroviruses. These assays are currently used for demonstrating the absence of retroviral contamination in vaccines and can also be applied to clinical and laboratory research to investigate low-virus replication. A single-tube fluorescent product-enhanced reverse transcriptase assay (STF-PERT) has been published that was highly sensitive for retrovirus detection (<10 virions), with enhanced reproducibility and increased efficiency [Sears, J.F., Khan, A.S., 2003. Single-tube fluorescent product-enhanced reverse transcriptase assay with AmpliWax (STF-PERT) for retrovirus quantitation. J. Virol. Meth. 108, 139-142]. In this report, the step-by-step setup and performance of the STF-PERT assay is described and sensitivity, reproducibility and specificity of the assay reported using three different RTs as standards: avian myeloblastosis virus (AMV) RT, murine leukemia virus (MMLV) RT, and human immunodeficiency virus type 1 (HIV-1) RT. Evaluation of virus stocks showed about 1-2 logs difference in RT detection and retrovirus quantitation with the different RT enzyme standards; in general, virus determination using HIV-1 RT was comparable to using the relevant virus RT.
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Affiliation(s)
- Yun Kun Ma
- Center for Biologics, Evaluation and Research, U.S. Food and Drug Administration, Bethesda, MD 20892, United States
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14
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A one-step SYBR Green I-based product-enhanced reverse transcriptase assay for the quantitation of retroviruses in cell culture supernatants. J Virol Methods 2008; 156:1-7. [PMID: 19022294 DOI: 10.1016/j.jviromet.2008.10.012] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 10/06/2008] [Accepted: 10/13/2008] [Indexed: 11/22/2022]
Abstract
PCR-enhanced reverse transcriptase assays (PERT) are sensitive tools for the detection of retroviruses in biological samples. The adaptation of real-time PCR techniques based on fluorescent probes (F-PERT) has added a reliable quantitative capacity to the assay. In the interest of economy and time, the SYBR Green I-based real-time detection system was used to establish a convenient one-step PERT assay (SG-PERT). This assay can be completed in 2h, is linear over six orders of magnitude and can be used to quantify retroviruses belonging to divergent species, such as the human immunodeficiency virus type 1 (HIV-1), murine leukemia virus (MLV) and prototypic foamy virus (PFV).
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15
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Lee S, Wood O, Tang S, Hu J, Machuca A, Kerby S, Awazi B, Vockley C, Hewlett I. Detection of emerging HIV variants in blood donors from urban areas of Cameroon. AIDS Res Hum Retroviruses 2007; 23:1262-7. [PMID: 17961114 DOI: 10.1089/aid.2006.0301] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The U.S. Food and Drug Administration has licensed several assays for use in donor testing and management of persons with human immunodeficiency virus (HIV) infection. However, the performance of these assays for detection and quantitation of emerging HIV genetic variants has not been studied extensively. We tested 240 human plasma specimens collected from two urban blood centers in Cameroon where HIV genetic diversity and recombinant HIV strains are highly prevalent, using several FDA licensed assays. The testing record in Cameroon indicated that 149 specimens were HIV antibody positive and 91 specimens were negative using a rapid HIV-1/2 antibody assay in routine use in Cameroon blood centers. Both sets of samples were evaluated in the FDA laboratory using four ELISA tests for HIV-1 group M, HIV-1 group O, and HIV-2 antibodies, one IFA for HIV-1 antibody, one Western blot for HIV-1, one HIV-1 p-24 antigen assay, and three nucleic acid tests (NAT). Our results indicate that the assays had high sensitivity for detection of emerging genetic variants, although a small number of samples harboring circulating recombinant forms (CRFs) found in Cameroon were not always consistently detected by a few assays. These findings may be due to the evolving genetic diversity of HIV strains in Cameroon.
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Affiliation(s)
- S. Lee
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, U.S. FDA, Bethesda, Maryland 20852
| | - O. Wood
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, U.S. FDA, Bethesda, Maryland 20852
| | - S. Tang
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, U.S. FDA, Bethesda, Maryland 20852
| | - J. Hu
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, U.S. FDA, Bethesda, Maryland 20852
| | - A. Machuca
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, U.S. FDA, Bethesda, Maryland 20852
| | - S. Kerby
- Product Testing Section, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, U.S. FDA, Bethesda, Maryland 20852
| | - B. Awazi
- Mobile Laboratory, Sanitation and Hygiene, Administration of Health, Cameroon
| | - C. Vockley
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, U.S. FDA, Bethesda, Maryland 20852
| | - I. Hewlett
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, U.S. FDA, Bethesda, Maryland 20852
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Fan XY, Lü GZ, Wu LN, Chen JH, Xu WQ, Zhao CN, Guo SQ. A modified single-tube one-step product-enhanced reverse transcriptase (mSTOS-PERT) assay with heparin as DNA polymerase inhibitor for specific detection of RTase activity. J Clin Virol 2006; 37:305-12. [PMID: 16971176 DOI: 10.1016/j.jcv.2006.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2006] [Revised: 07/03/2006] [Accepted: 08/09/2006] [Indexed: 10/24/2022]
Abstract
BACKGROUND Current regulations and recommendations proposed for the production of vaccines in continuous cell lines of any origin demand that these be free of exogenous viruses, particularly retroviruses. Recently, the ultra-sensitive product-enhanced reverse transcriptase (PERT) assay can be used to detect minute of reverse transcriptase (RTase) in single retroviral particle and is 10(6) times more sensitive than the conventional RTase assays. However, coincidental with this increase in sensitivity is an increase in false-positive reactions derived from contaminating cellular DNA polymerases, which are known to have RTase-like activities. OBJECTIVES To develop a modified single-tube one-step PERT (mSTOS-PERT) assay with improvements on decreasing significantly the level of false-positive reactions, and to evaluate the mSTOS-PERT assay for sensitivity and specificity. STUDY DESIGN Ampliwaxtrade mark was used to compartmentalize the reverse transcription (RT) and PCR step in the same micro-tube with more efficiency and reproducibility, while maintaining the high sensitivity. The DNA amplification products were separated by 2% agarose gel electrophoresis, and then analyzed by non-isotopic Southern blot hybridization. A wide variety of cell lines used in biologicals production were detected to validate the improved mSTOS-PERT assay. RESULTS The detection limit for the mSTOS-PERT assay was at least 10(-9)U, when using AMV-RTase as a positive control. Furthermore, heparin involvement in the RT step can eliminate completely the false-positive PERT signals which are exhibited by cellular polymerases such as DNA-dependent DNA polymerase alpha, gamma released by cell death. Most mammalian cells (MRC-5, Vero, WISH, 2BS, RK-13, MDCK, etc.) are PERT-negative in cell supernatants. Some PERT-positive signals in cell lysates were found to be introduced by the cellular DNA polymerases and could be inhibited specifically by heparin. Chick cells derived from either chick embryo fibroblasts (CEF) or allantoic fluid from SPF embryonated eggs, murine hybridoma cell SP2/0, etc., contained authentic RTase activities, which could not be inactivated by heparin. CONCLUSIONS The improved mSTOS-PERT assay described here may distinguish the genuine RTase activity from cellular polymerases with high sensitivity and specificity, and is rapid and easy to perform to screen for the possible contamination of minute retroviruses in the cell substrates used in vaccine production.
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Affiliation(s)
- Xiao-Yong Fan
- Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200433, China.
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Guidance for Industry: Characterization and Qualification of Cell Substrates and Other Biological Starting Materials Used in the Production of Viral Vaccines for the Prevention and Treatment of Infectious Diseases. Biotechnol Law Rep 2006. [DOI: 10.1089/blr.2006.25.697] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Khan AS, Kumar D. Simian foamy virus infection by whole-blood transfer in rhesus macaques: potential for transfusion transmission in humans. Transfusion 2006; 46:1352-9. [PMID: 16934071 DOI: 10.1111/j.1537-2995.2006.00862.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Cross-species infection of humans with simian foamy virus (SFV) has been reported in European and North American nonhuman primate (NHP) handlers, primarily due to wound injuries involving infected animals in research centers and zoos. Additionally, African hunters have been found to be infected with SFV by exposure to body fluids, blood, or tissues of infected NHPs in the wild. The persistence of infectious virus in peripheral blood mononuclear cells (PBMNC) and the recent identification of some infected blood donors has raised safety concerns regarding potential virus transmission by blood transfusion. STUDY DESIGN AND METHODS SFV infection by blood transfusion was evaluated by whole-blood transfer from two naturally-infected rhesus macaques (designated as D1 and D2) to retrovirus-free monkeys. Blood from D1 was transfused to two recipient monkeys R1 and R2 and from D2 to monkeys R3 and R4. Virus transmission was evaluated by immunoassays, polymerase chain reaction assays, and coculture of PBMNC for SFV isolation. RESULTS SFV infection was seen in R1 and R2 based on development of virus-specific antibodies, identification of SFV sequences in monkey PBMNC, and isolation of infectious virus from PBMNC. Furthermore, both R1 and R2 remained SFV-positive at about 1 year after transfusion, which was the last time tested. No evidence of SFV infection was seen in R3 and R4. CONCLUSION SFV transmission in macaques occurred by transfusion of blood from one of two infected donor animals. These results indicate the potential of SFV transfusion transmission in humans, which may depend on virus-specific or donor-related factors.
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Affiliation(s)
- Arifa S Khan
- Laboratory of Retrovirus Research, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Bethesda, Maryland, USA.
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Delenda C, Gaillard C. Real-time quantitative PCR for the design of lentiviral vector analytical assays. Gene Ther 2006; 12 Suppl 1:S36-50. [PMID: 16231054 DOI: 10.1038/sj.gt.3302614] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
From the recent and emerging concerns for approving lentiviral vector-mediated gene transfer in human clinical applications, several analytical methods have been applied in preclinical models to address the lentiviral vector load in batches, cells or tissues. This review points out the oldest generation methods (blots, RT activity, standard PCR) as well as a full description of the newest real-time quantitative PCR (qPCR) applications. Combinations of primer and probe sequences, which have worked in the lentiviral amplification context, have been included in the effort to dress an exhaustive list. Also, great variations have been observed from interlaboratory results, we have tempted to compare between them the different analytical methods that have been used to consider (i) the titration of lentiviral vector batches, (ii) the absence of the susceptible emerging replicative lentiviruses or (iii) the lentiviral vector biodistribution in the organism.
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Affiliation(s)
- C Delenda
- Genethon, CNRS UMR 8115, 1bis rue de l'Internationale, Evry Cedex, France
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Sinn PL, Sauter SL, McCray PB. Gene therapy progress and prospects: development of improved lentiviral and retroviral vectors--design, biosafety, and production. Gene Ther 2005; 12:1089-98. [PMID: 16003340 DOI: 10.1038/sj.gt.3302570] [Citation(s) in RCA: 219] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Replication defective vectors derived from simple retroviruses or the more complex genomes of lentiviruses continue to offer the advantages of long-term expression, cell and tissue specific tropism, and large packaging capacity for the delivery of therapeutic genes. The occurrence of adverse events caused by insertional mutagenesis in three patients in a gene therapy trial for X-linked SCID emphasizes the potential for problems in translating this approach to the clinic. Several genome-wide studies of retroviral integration are now providing novel insights into the integration site preferences of different vector classes. We review recent developments in vector design, integration, biosafety, and production.
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Affiliation(s)
- P L Sinn
- Program in Gene Therapy, Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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Ambrose Z, Boltz V, Palmer S, Coffin JM, Hughes SH, Kewalramani VN. In vitro characterization of a simian immunodeficiency virus-human immunodeficiency virus (HIV) chimera expressing HIV type 1 reverse transcriptase to study antiviral resistance in pigtail macaques. J Virol 2004; 78:13553-61. [PMID: 15564466 PMCID: PMC533891 DOI: 10.1128/jvi.78.24.13553-13561.2004] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antiviral resistance is a significant obstacle in the treatment of human immunodeficiency virus type 1 (HIV-1)-infected individuals. Because nonnucleoside reverse transcriptase inhibitors (NNRTIs) specifically target HIV-1 reverse transcriptase (RT) and do not effectively inhibit simian immunodeficiency virus (SIV) RT, the development of animal models to study the evolution of antiviral resistance has been problematic. To facilitate in vivo studies of NNRTI resistance, we examined whether a SIV that causes immunopathogenesis in pigtail macaques could be made sensitive to NNRTIs. Two simian-human immunodeficiency viruses (SHIVs) were derived from the genetic background of SIV(mne): SIV-RT-YY contains RT substitutions intended to confer NNRTI susceptibility (V181Y and L188Y), and RT-SHIV(mne) contains the entire HIV-1 RT coding region. Both mutant viruses grew to high titers in vitro but had reduced fitness relative to wild-type SIV(mne). Although the HIV-1 RT was properly processed into p66 and p51 subunits in RT-SHIV(mne) particles, the RT-SHIV(mne) virions had lower levels of RT per viral genomic RNA than HIV-1. Correspondingly, there was decreased RT activity in RT-SHIV(mne) and SIV-RT-YY particles. HIV-1 and RT-SHIV(mne) were similarly susceptible to the NNRTIs efavirenz, nevirapine, and UC781. However, SIV-RT-YY was less sensitive to NNRTIs than HIV-1 or RT-SHIV(mne). Classical NNRTI resistance mutations were selected in RT-SHIV(mne) after in vitro drug treatment and were monitored in a sensitive allele-specific real-time RT-PCR assay. Collectively, these results indicate that RT-SHIV(mne) may be a useful model in macaques for the preclinical evaluation of NNRTIs and for studies of the development of drug resistance in vivo.
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Affiliation(s)
- Zandrea Ambrose
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702-1201, USA
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