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Noorbazargan H, Nadji SA, Mirab Samiee S, Paryan M, Mohammadi-Yeganeh S. Comparison of a new in-house HIV-1 TaqMan real-time PCR and three commercial HIV-1 RNA quantitative assays. Comp Immunol Microbiol Infect Dis 2018; 59:1-7. [PMID: 30290882 DOI: 10.1016/j.cimid.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 07/03/2018] [Accepted: 09/04/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES The aim of this study was to compare the analytical performance of an In-House HIV-1 viral load determination technique with three commercial kits including COBAS® AmpliPrep, RealStar®, and RTA® HIV-1 Real-Time PCR. RESULTS A total of 100 HIV-1 suspicious plasma samples were tested by the In-House TaqMan® Real-Time PCR assay along with the above-mentioned kits. Comparative analysis between In-House and reference method (COBAS® AmpliPrep/COBAS® TaqMan® HIV-1 Test version 2.0) showed high concordance with a mean difference of 0.08 log10 copies/ml. All samples results were within -0.16-0.31 log10 copies/ml. A suitable correlation was obtained with a coefficient (R2) of 0.82 between the In-House assay and RTA® Kit, however, two positive samples were not detected. The lowest agreement was detected with RealStar® HIV Kit 1.0 (R2 = 0.49, r = 0.7). CONCLUSIONS The newly developed method has suitable sensitivity, accuracy, and precision. In addition, it is cost-effective and can be an alternative in all laboratories.
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Affiliation(s)
- Hassan Noorbazargan
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Alireza Nadji
- Virology Research Center (VRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mahdi Paryan
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran.
| | - Samira Mohammadi-Yeganeh
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biotechnology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Du H, Li W, Hao W, Liao X, Li M, Luo S. Taqman real-time PCR assay based on ORFV024 gene for rapid detection of orf infection. Toxicol Mech Methods 2013. [PMID: 23193989 DOI: 10.3109/15376516.2012.753968] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, a TaqMan real-time polymerase chain reaction (PCR) assay was developed to detect and quantify orf virus (ORFV) DNA in infected cell culture and clinical samples. Primers and probes were designed to amplify an 87 bp fragment DNA based on the sequence of ORFV024 gene encoding an NF-κB inhibitor of orf virus. The assay was highly specific and sensitive for ORFV DNA and no cross-reactions were detected with any other poxviruses; the sensitivity was 5 fg or 15 copies of ORFV genomic DNA. Both intra- (1.490 ± 1.261%) and inter-assay (1.958 ± 0.568%) variabilities were within the acceptable range, indicating the high efficiency and reproducibility of the assay. Further, the assay has shown a relative diagnostic sensitivity and specificity of 100%, when compared to B2L gene-based semi-nested PCR. The assay is simple, rapid, specific and sensitive with a wide potential for rapid field diagnosis of orf in sheep and goats.
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Affiliation(s)
- Hongyan Du
- Institute of Antibody Engineering, School of Biotechnology, Southern Medical University , Guangzhou , PR China
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Ten years of external quality assessment of human immunodeficiency virus type 1 RNA quantification. J Clin Microbiol 2012; 50:3614-9. [PMID: 22952265 DOI: 10.1128/jcm.01221-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viral load testing is an essential parameter in guiding antiretroviral therapy for individuals infected with human immunodeficiency virus type 1 (HIV-1). An external quality assessment scheme for the molecular quantification of HIV-1 RNA was introduced by the United Kingdom National External Quality Assessment Service for Microbiology in 2000. Specimen pairs of freeze-dried plasma were distributed to a median of 141 participants three times a year. The aim of this study was to analyze the quantification of HIV-1 RNA results between 2000 and 2010. Overall variability, measured by the standard deviations of all viral load results for each specimen, was below 0.5 log copy/ml (n = 48). When we compared assay results, the medians of the viral load by assay were within a range of 0.25 to 1.08 log copies/ml, with the lowest median values being consistently reported with the Siemens branched-chain DNA assay. The spread of participant results and, hence, differences between assay medians were greater when quantifying non-B subtypes. Laboratories were scored on the proximity of their reported log difference for the specimen pair to the median log difference reported by all laboratories. The overall level of performance with the HIV-1 RNA specimens over the past 10 years has been consistently good, with more than 90% of the participants reporting in the accepted range (median difference, ±0.5 log unit). Future distributions may result in tightening the acceptance levels of quantification and the use of more challenging specimens, including a variety of subtypes, with developments focusing on maintaining the clinical relevance and educational value of the scheme.
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Singer A, Rapireddy S, Ly DH, Meller A. Electronic barcoding of a viral gene at the single-molecule level. NANO LETTERS 2012; 12:1722-8. [PMID: 22352964 PMCID: PMC3572535 DOI: 10.1021/nl300372a] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A new single-molecule approach for rapid and purely electronic discrimination among similar genes is presented. Combining solid-state nanopores and γ-modified synthetic peptide nucleic acid probes, we accurately barcode genes by counting the number of probes attached to each gene and measuring their relative spacing. We illustrate our method by sensing individual genes from two highly similar human immunodeficiency virus subtypes, demonstrating feasibility of a novel, single-molecule diagnostic platform for rapid pathogen classification.
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Affiliation(s)
- Alon Singer
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215
| | - Srinivas Rapireddy
- Department of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - Danith H. Ly
- Department of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - Amit Meller
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215
- Corresponding author.
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Variable influence of mutational patterns in reverse-transcriptase domain on replication capacity of hepatitis B virus isolates from antiviral-experienced patients. Clin Chim Acta 2010; 412:305-13. [PMID: 21056552 DOI: 10.1016/j.cca.2010.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 10/10/2010] [Accepted: 10/29/2010] [Indexed: 12/15/2022]
Abstract
BACKGROUND Various mutations in reverse-transcriptase domain (RT) of hepatitis B virus (HBV) polymerase may develop during antiviral therapy. The influence of these mutational patterns on HBV replication capacity remains to be fully clarified. METHODS Nine clones containing complete HBV genomes were isolated from 5 patients with chronic hepatitis B who had received antiviral treatment. Viral replication capacity was measured by quantitation of HBV replicative intermediates using vector-free transfer of paired mutant and wild-type HBV genomes into human hepatoma cell lines HepG2 and Huh7. HBV pgRNA was quantitated by real-time PCR and Southern blot analysis. RESULTS A real-time PCR assay with high sensitivity and small variation was developed for quantitation of HBV replicative intermediates. Compared to wild-type counterpart, mutant rtL217P produced 1.98-fold higher replicative intermediate level, and mutant rtM204I+rtL217P increased the replicative intermediate level to 1.20 fold. Other mutational patterns (rtV173M, rtA181S/V, rtM204I, rtQ215H, rtL229M, rtN238H, rtV84M+rtA181S+rtM204I, rtV84M+rtM204I, rtA181S+rtM204I, rtA181V+rtL229M, rtQ215H+rtN238H) reduced viral replication capacity to different extents. CONCLUSIONS The study offers a practical measurement assay and novel information for replication features of mutant strains; especially, rtL217P substitution likely represents an energetic replication-compensatory mutation.
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Affiliation(s)
- Xiaonan Yang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and National Engineering Center for BioChip at Shanghai, Shanghai 201203, China;
- Laboratory of Microbial Molecular Physiology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hongliang Yang
- Laboratory of Microbial Molecular Physiology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Microbiology and Parasitology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Guo-Ping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and National Engineering Center for BioChip at Shanghai, Shanghai 201203, China;
- Laboratory of Microbial Molecular Physiology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Belmont JW. Molecular methods. Clin Immunol 2008. [DOI: 10.1016/b978-0-323-04404-2.10101-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Biologie moléculaire et microbiologie clinique en 2007. IMMUNO-ANALYSE & BIOLOGIE SPÉCIALISÉE 2007. [PMCID: PMC7148721 DOI: 10.1016/j.immbio.2006.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
La biologie moléculaire est omniprésente en biologie médicale et plus particulièrement en microbiologie. De nombreux articles démontrent son importance tant dans le domaine du diagnostic que du pronostic, de l'évaluation thérapeutique, de l'épidémiologie ou des risques biologiques naturels ou non. La quantité considérable d'articles sur ce sujet n'apporte pas toujours une réponse évidente sur le rôle de la biologie moléculaire dans un laboratoire de microbiologie qu'il soit hospitalier ou non. Cette revue constitue une synthèse des apports de cette discipline en microbiologie. À partir de cet état des lieux, certaines questions se posent, par exemple : la biologie moléculaire constitue-t-elle un réel apport en microbiologie ? Dans quelles indications prescrire un examen de biologie moléculaire ? Les réponses ne sont pas toujours simples. Elles sont évidentes dans certains cas (l'hépatite C par exemple) et le sont moins dans d'autres, la tuberculose par exemple. Dans la première partie de l'article, nous avons parlé des généralités appliquées à la microbiologie. Dans cette deuxième partie, nous abordons certaines applications, reflets de l'importance prise par la biologie moléculaire en microbiologie.
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Lamoril J, Bogard M, Ameziane N, Deybach JC, Bouizegarène P. Biologie moléculaire et microbiologie clinique en 2007. IMMUNO-ANALYSE & BIOLOGIE SPÉCIALISÉE 2007. [PMCID: PMC7148720 DOI: 10.1016/j.immbio.2006.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
La biologie moléculaire est omniprésente en biologie médicale et plus particulièrement en microbiologie. De nombreux articles démontrent son importance tant dans le domaine du diagnostic que du pronostic, de l'évaluation thérapeutique, de l'épidémiologie ou des risques biologiques naturels ou non. La quantité considérable d'articles sur ce sujet, n'apporte pas toujours une réponse évidente sur le rôle de la biologie moléculaire dans un laboratoire de microbiologie qu'il soit hospitalier ou non. Cette revue constitue une synthèse des apports de cette discipline en microbiologie. À partir de cet état des lieux, certaines questions se posent, par exemple : la biologie moléculaire constitue-t-elle un réel apport en microbiologie ? Dans quelles indications prescrire un examen de biologie moléculaire ? Les réponses ne sont pas toujours simples. Dans cet article composé de deux parties, la première partie aborde les généralités de biologie moléculaire et plus particulièrement les principales techniques utilisées dans le domaine de la microbiologie et la seconde partie à venir traitera des applications.
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Affiliation(s)
- J. Lamoril
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
- Auteur correspondant.
| | - M. Bogard
- Laboratoire de biochimie et biologie moléculaire, centre hospitalier de Meaux, 77100 Meaux, France
| | - N. Ameziane
- Laboratoire de biologie polyvalente, centre hospitalier de Sens, 89100 Sens, France
| | - J.-C. Deybach
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
| | - P. Bouizegarène
- Laboratoire de biochimie et génétique moléculaire, hôpital Louis-Mourier, 178, rue des Renouillers, 92700 Colombes, France
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Leland DS, Ginocchio CC. Role of cell culture for virus detection in the age of technology. Clin Microbiol Rev 2007; 20:49-78. [PMID: 17223623 PMCID: PMC1797634 DOI: 10.1128/cmr.00002-06] [Citation(s) in RCA: 303] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Viral disease diagnosis has traditionally relied on the isolation of viral pathogens in cell cultures. Although this approach is often slow and requires considerable technical expertise, it has been regarded for decades as the "gold standard" for the laboratory diagnosis of viral disease. With the development of nonculture methods for the rapid detection of viral antigens and/or nucleic acids, the usefulness of viral culture has been questioned. This review describes advances in cell culture-based viral diagnostic products and techniques, including the use of newer cell culture formats, cryopreserved cell cultures, centrifugation-enhanced inoculation, precytopathogenic effect detection, cocultivated cell cultures, and transgenic cell lines. All of these contribute to more efficient and less technically demanding viral detection in cell culture. Although most laboratories combine various culture and nonculture approaches to optimize viral disease diagnosis, virus isolation in cell culture remains a useful approach, especially when a viable isolate is needed, if viable and nonviable virus must be differentiated, when infection is not characteristic of any single virus (i.e., when testing for only one virus is not sufficient), and when available culture-based methods can provide a result in a more timely fashion than molecular methods.
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Affiliation(s)
- Diane S Leland
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
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Das A, Spackman E, Senne D, Pedersen J, Suarez DL. Development of an internal positive control for rapid diagnosis of avian influenza virus infections by real-time reverse transcription-PCR with lyophilized reagents. J Clin Microbiol 2006; 44:3065-73. [PMID: 16954228 PMCID: PMC1594697 DOI: 10.1128/jcm.00639-06] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We developed an internal positive control (IPC) RNA to help ensure the accuracy of the detection of avian influenza virus (AIV) RNA by reverse transcription (RT)-PCR and real-time RT-PCR (RRT-PCR). The IPC was designed to have the same binding sites for the forward and reverse primers of the AIV matrix gene as the target amplicon, but it had a unique internal sequence used for the probe site. The amplification of the viral RNA and the IPC by RRT-PCR were monitored with two different fluorescent probes in a multiplex format, one specific for the AIV matrix gene and the other for the IPC. The RRT-PCR test was further simplified with the use of lyophilized bead reagents for the detection of AIV RNA. The RRT-PCR with the bead reagents was more sensitive than the conventional wet reagents for the detection of AIV RNA. The IPC-based RRT-PCR detected inhibitors in blood, kidney, lungs, spleen, intestine, and cloacal swabs, but not allantoic fluid, serum, or tracheal swabs The accuracy of RRT-PCR test results with the lyophilized beads was tested on cloacal and tracheal swabs from experimental birds inoculated with AIV and compared with virus isolation (VI) on embryonating chicken eggs. There was 97 to 100% agreement of the RRT-PCR test results with VI for tracheal swabs and 81% agreement with VI for cloacal swabs, indicating a high level of accuracy of the RRT-PCR assay. The same IPC in the form of armored RNA was also used to monitor the extraction of viral RNA and subsequent detection by RRT-PCR.
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Affiliation(s)
- Amaresh Das
- Southeast Poultry Research Laboratory, Agricultural Research Service, USDA, 934 College Station Rd., Athens, GA 30605, USA
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