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Torres-Salvador F, Ojeda J, Castro C, Gerasimova Y, Chumbimuni-Torres K. A Single Electrochemical Biosensor Designed to Detect Any Virus. Anal Chem 2024; 96:5752-5756. [PMID: 38560822 DOI: 10.1021/acs.analchem.3c05962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Viruses are the primary cause of many infectious diseases in both humans and animals. Various testing methods require an amplification step of the viral RNA sample before detection, with quantitative reverse transcription polymerase chain reaction (RT-qPCR) being one of the most widely used along with lesser-known methods like Nucleic Acid Sequence-Based Amplification (NASBA). NASBA offers several advantages, such as isothermal amplification and high selectivity for specific sequences, making it an attractive option for low-income facilities. In this research, we employed a single electrochemical biosensor (E-Biosensor) designed for potentially detecting any virus by modifying the NASBA protocol. In this modified protocol, a reverse primer is designed with an additional 22-nucleotide sequence (tag region) at the 5'-end, which is added to the NASBA process. This tag region becomes part of the final amplicon generated by NASBA. It can hybridize with a single specific E-Biosensor probe set, enabling subsequent virus detection. Using this approach, we successfully detected three different viruses with a single E-Biosensor design, demonstrating the platform's potential for virus detection.
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Affiliation(s)
| | - Julio Ojeda
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | - Cynthia Castro
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | - Yulia Gerasimova
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | - Karin Chumbimuni-Torres
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
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2
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Nai YH, Doeven EH, Guijt RM. An improved nucleic acid sequence-based amplification method mediated by T4 gene 32 protein. PLoS One 2022; 17:e0265391. [PMID: 35324960 PMCID: PMC8947125 DOI: 10.1371/journal.pone.0265391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/01/2022] [Indexed: 01/06/2023] Open
Abstract
The uptake of Nucleic Acid Sequence-Based Amplification (NASBA) for point of care testing may be hindered by a complexity in the workflow due the requirement of a thermal denaturation step to initiate the cyclic isothermal amplification before the addition of the amplification enzymes. Despite reports of successful enhancement of other DNA and RNA amplification methods using DNA and RNA binding proteins, this has not been reported for NASBA. Here, three single-stranded binding proteins, RecA, Extreme Thermostable Single-stranded binding protein (ET SSB) and T4 gene gp32 protein (gp32), were incorporated in NASBA protocol and used for single pot, one-step NASBA at 41 °C. Indeed, all SSBs showed significantly improved amplifications compared with the 2-step process, but only gp32 showed no non-specific aberrant amplification, and slightly improved the time-to-positivity in comparison with the conventional NASBA. For synthetic HIV-1 RNA, gp32 was found to improve the time-to-positivity (ttp) by average of 13.6% of one-step NASBA and 6.7% of conventional NASBA for the detection of HIV-1 RNA, showing its potential for simplifying the workflow as desirable for point of care applications of NASBA.
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Affiliation(s)
- Yi Heng Nai
- Centre for Regional and Rural Futures, Deakin University, Geelong, Victoria, Australia
- * E-mail: (YHN); (RMG)
| | - Egan H. Doeven
- Centre for Regional and Rural Futures, Deakin University, Geelong, Victoria, Australia
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures, Deakin University, Geelong, Victoria, Australia
- * E-mail: (YHN); (RMG)
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3
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Khan P, Aufdembrink LM, Engelhart AE. Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings. ACS Synth Biol 2020; 9:2861-2880. [PMID: 32966744 PMCID: PMC7552996 DOI: 10.1021/acssynbio.0c00359] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, poses grave threats to both the global economy and health. The predominant diagnostic screens in use for SARS-CoV-2 detection are molecular techniques such as nucleic acid amplification tests. In this Review, we compare current and emerging isothermal diagnostic methods for COVID-19. We outline the molecular and serological techniques currently being used to detect SARS-CoV-2 infection, past or present, in patients. We also discuss ongoing research on isothermal techniques, CRISPR-mediated detection assays, and point-of-care diagnostics that have potential for use in SARS-CoV-2 detection. Large-scale viral testing during a global pandemic presents unique challenges, chief among them the simultaneous need for testing supplies, durable equipment, and personnel in many regions worldwide, with each of these regions possessing testing needs that vary as the pandemic progresses. The low-cost isothermal technologies described in this Review provide a promising means by which to address these needs and meet the global need for testing of symptomatic individuals as well as provide a possible means for routine testing of asymptomatic individuals, providing a potential means of safely enabling reopenings and early monitoring of outbreaks.
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Affiliation(s)
- Pavana Khan
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
| | - Lauren M. Aufdembrink
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
| | - Aaron E. Engelhart
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
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4
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Aufdembrink LM, Khan P, Gaut NJ, Adamala KP, Engelhart AE. Highly specific, multiplexed isothermal pathogen detection with fluorescent aptamer readout. RNA 2020; 26:1283-1290. [PMID: 32482894 PMCID: PMC7430665 DOI: 10.1261/rna.075192.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Isothermal, cell-free, synthetic biology-based approaches to pathogen detection leverage the power of tools available in biological systems, such as highly active polymerases compatible with lyophilization, without the complexity inherent to live-cell systems, of which nucleic acid sequence based amplification (NASBA) is well known. Despite the reduced complexity associated with cell-free systems, side reactions are a common characteristic of these systems. As a result, these systems often exhibit false positives from reactions lacking an amplicon. Here we show that the inclusion of a DNA duplex lacking a promoter and unassociated with the amplicon fully suppresses false positives, enabling a suite of fluorescent aptamers to be used as NASBA tags (Apta-NASBA). Apta-NASBA has a 1 pM detection limit and can provide multiplexed, multicolor fluorescent readout. Furthermore, Apta-NASBA can be performed using a variety of equipment, for example, a fluorescence microplate reader, a qPCR instrument, or an ultra-low-cost Raspberry Pi-based 3D-printed detection platform using a cell phone camera module, compatible with field detection.
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Affiliation(s)
- Lauren M Aufdembrink
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Pavana Khan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nathaniel J Gaut
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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5
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Zhai L, Liu H, Chen Q, Lu Z, Zhang C, Lv F, Bie X. Development of a real-time nucleic acid sequence-based amplification assay for the rapid detection of Salmonella spp. from food. Braz J Microbiol 2018; 50:255-261. [PMID: 30637640 DOI: 10.1007/s42770-018-0002-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 08/01/2017] [Indexed: 11/26/2022] Open
Abstract
Salmonella spp. is one of the most common foodborne infectious pathogen. This study aimed to develop a real-time nucleic acid sequence-based amplification (NASBA) assay for detecting Salmonella in foods. Primers and a molecular beacon targeting the Salmonella-specific xcd gene were designed for mRNA transcription, and 48 Salmonella and 18 non-Salmonella strains were examined. The assay showed a high specificity and low detection limit for Salmonella (7 × 10-1 CFU/mL) after 12 h of pre-enrichment. Importantly, it could detect viable cells. Additionally, the efficacy of the NASBA assay was examined in the presence of pork background microbiota; it could detect Salmonella cells at 9.5 × 103 CFU/mL. Lastly, it was successfully used to detect Salmonella in pork, beef, and milk, and its detection limit was as low as 10 CFU/25 g (mL). The real-time NASBA assay developed in this study may be useful for rapid, specific, and sensitive detection of Salmonella in food of animal origin.
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Affiliation(s)
- Ligong Zhai
- College of Food Science and Technology, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Food and Drug, Anhui Science and Technology University, Fengyang, 233100, People's Republic of China
| | - Hongxia Liu
- College of Food Science and Technology, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qiming Chen
- College of Food Science and Technology, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Chong Zhang
- College of Food Science and Technology, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Fengxia Lv
- College of Food Science and Technology, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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6
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Loukas CM, Mowlem MC, Tsaloglou MN, Green NG. A novel portable filtration system for sampling and concentration of microorganisms: Demonstration on marine microalgae with subsequent quantification using IC-NASBA. Harmful Algae 2018; 75:94-104. [PMID: 29778229 DOI: 10.1016/j.hal.2018.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/19/2018] [Accepted: 03/24/2018] [Indexed: 06/08/2023]
Abstract
This paper presents a novel portable sample filtration/concentration system, designed for use on samples of microorganisms with very low cell concentrations and large volumes, such as water-borne parasites, pathogens associated with faecal matter, or toxic phytoplankton. The example application used for demonstration was the in-field collection and concentration of microalgae from seawater samples. This type of organism is responsible for Harmful Algal Blooms (HABs), an example of which is commonly referred to as "red tides", which are typically the result of rapid proliferation and high biomass accumulation of harmful microalgal species in the water column or at the sea surface. For instance, Karenia brevis red tides are the cause of aquatic organism mortality and persistent blooms may cause widespread die-offs of populations of other organisms including vertebrates. In order to respond to, and adequately manage HABs, monitoring of toxic microalgae is required and large-volume sample concentrators would be a useful tool for in situ monitoring of HABs. The filtering system presented in this work enables consistent sample collection and concentration from 1 L to 1 mL in five minutes, allowing for subsequent benchtop sample extraction and analysis using molecular methods such as NASBA and IC-NASBA. The microalga Tetraselmis suecica was successfully detected at concentrations ranging from 2 × 105 cells/L to 20 cells/L. Karenia brevis was also detected and quantified at concentrations between 10 cells/L and 106 cells/L. Further analysis showed that the filter system, which concentrates cells from very large volumes with consequently more reliable sampling, produced samples that were more consistent than the independent non-filtered samples (benchtop controls), with a logarithmic dependency on increasing cell numbers. This filtering system provides simple, rapid, and consistent sample collection and concentration for further analysis, and could be applied to a wide range of different samples and target organisms in situations lacking laboratories.
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Affiliation(s)
- Christos-Moritz Loukas
- National Oceanography Centre (NOC), University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom; Department of Ocean and Earth Science, University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom.
| | - Matthew C Mowlem
- National Oceanography Centre (NOC), University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom.
| | - Maria-Nefeli Tsaloglou
- National Oceanography Centre (NOC), University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom; Department of Ocean and Earth Science, University of Southampton Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom; Institute for Life Sciences, University of Southampton Highfield Campus, Highfield, Southampton, SO17 1BJ, United Kingdom.
| | - Nicolas G Green
- Institute for Life Sciences, University of Southampton Highfield Campus, Highfield, Southampton, SO17 1BJ, United Kingdom; School of Electronics and Computer Science (ECS), University of Southampton Highfield Campus, Highfield, Southampton, SO17 1BJ, United Kingdom.
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7
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Walker DI, McQuillan J, Taiwo M, Parks R, Stenton CA, Morgan H, Mowlem MC, Lees DN. A highly specific Escherichia coli qPCR and its comparison with existing methods for environmental waters. Water Res 2017; 126:101-110. [PMID: 28930669 DOI: 10.1016/j.watres.2017.08.032] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 05/19/2023]
Abstract
The presence of Escherichia coli in environmental waters is considered as evidence of faecal contamination and is therefore commonly used as an indicator in both water quality and food safety analysis. The long period of time between sample collection and obtaining results from existing culture based methods means that contamination events may already impact public health by the time they are detected. The adoption of molecular based methods for E. coli could significantly reduce the time to detection. A new quantitative real-time PCR (qPCR) assay was developed to detect the ybbW gene sequence, which was found to be 100% exclusive and inclusive (specific and sensitive) for E. coli and directly compared for its ability to quantify E. coli in environmental waters against colony counts, quantitative real-time NASBA (qNASBA) targeting clpB and qPCR targeting uidA. Of the 87 E. coli strains tested, 100% were found to be ybbW positive, 94.2% were culture positive, 100% were clpB positive and 98.9% were uidA positive. The qPCR assays had a linear range of quantification over several orders of magnitude, and had high amplification efficiencies when using single isolates as a template. This compared favourably with qNASBA which showed poor linearity and amplification efficiency. When the assays were applied to environmental water samples, qNASBA was unable to reliably quantify E. coli while both qPCR assays were capable of predicting E. coli concentrations in environmental waters. This study highlights the inability of qNASBA targeting mRNA to quantify E. coli in environmental waters, and presents the first E. coli qPCR assay with 100% target exclusivity. The application of a highly exclusive and inclusive qPCR assay has the potential to allow water quality managers to reliably and rapidly detect and quantify E. coli and therefore take appropriate measures to reduce the risk to public health posed by faecal contamination.
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Affiliation(s)
- David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset, UK.
| | | | - Michael Taiwo
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset, UK
| | - Rachel Parks
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset, UK
| | - Craig A Stenton
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset, UK
| | - Hywel Morgan
- School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
| | | | - David N Lees
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth Laboratory, Weymouth, Dorset, UK
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8
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Abstract
The conservation of plant biosecurity relies on the rapid identification of pathogenic organisms, including viruses. With next-generation sequencing (NGS), it is possible to identify multiple viruses within a metagenomic sample. In this study, we explored the use of electronic probes (e-probes) for the simultaneous detection of 11 recognized citrus viruses. E-probes were designed and screened against raw sequencing data to minimize the bioinformatic processing time required. The e-probes were able to accurately detect their cognate viruses in simulated datasets, without any false negatives or positives. The efficiency of the e-probe-based approach was validated with NGS datasets generated from different RNA preparations: double-stranded RNA (dsRNA) from 'Mexican' lime infected with different Citrus tristeza virus (CTV) genotypes, dsRNA from field samples, and small RNA and total RNA from grapefruit infected with the CTV T3 genotype. A set of probes was made available that is able to accurately detect CTV in sequence data regardless of the input dataset or the genotype that plants are infected with.
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Affiliation(s)
- T L Jooste
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
| | - M Visser
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
| | - G Cook
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
| | - J T Burger
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
| | - H J Maree
- First, second, and fifth authors: Agricultural Research Council, Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute), Stellenbosch, South Africa; first, second, fourth, and fifth authors: Stellenbosch University, Department of Genetics, Stellenbosch, South Africa; and third author: Citrus Research International, Nelspruit, South Africa
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Zhao X, Dong T, Yang Z, Pires N, Høivik N. Compatible immuno-NASBA LOC device for quantitative detection of waterborne pathogens: design and validation. Lab Chip 2012; 12:602-612. [PMID: 22146918 DOI: 10.1039/c1lc20836e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Waterborne pathogens usually pose a global threat to animals and human beings. There has been a growing demand for convenient and sensitive tools to detect the potential emerging pathogens in water. In this study, a lab-on-a-chip (LOC) device based on the real-time immuno-NASBA (immuno-nucleic acid sequence-based amplification) assay was designed, fabricated and verified. The disposable immuno-NASBA chip is modelled on a 96-well ELISA microplate, which contains 43 reaction chambers inside the bionic channel networks. All valves are designed outside the chip and are reusable. The sample and reagent solutions were pushed into each chamber in turn, which was controlled by the valve system. Notably, the immuno-NASBA chip is completely compatible with common microplate readers in a biological laboratory, and can distinguish multiple waterborne pathogens in water samples quantitatively and simultaneously. The performance of the LOC device was demonstrated by detecting the presence of a synthetic peptide, ACTH (adrenocorticotropic hormone) and two common waterborne pathogens, Escherichia coli (E. coli) and rotavirus, in artificial samples. The results indicated that the LOC device has the potential to quantify traces of waterborne pathogens at femtomolar levels with high specificity, although the detection process was still subject to some factors, such as ribonuclease (RNase) contamination and non-specific adsorption. As an ultra-sensitive tool to quantify waterborne pathogens, the LOC device can be used to monitor water quality in the drinking water system. Furthermore, a series of compatible high-throughput LOC devices for monitoring waterborne pathogens could be derived from this prototype with the same design idea, which may render the complicated immuno-NASBA assays convenient to common users without special training.
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Affiliation(s)
- Xinyan Zhao
- Department of Micro and Nano Systems Technology, Faculty of Engineering and Marine Sciences, Vestfold University College, Tønsberg, Box 2243, N-3103, Norway
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10
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Dimov IK, Kijanka G, Park Y, Ducrée J, Kang T, Lee LP. Integrated microfluidic array plate (iMAP) for cellular and molecular analysis. Lab Chip 2011; 11:2701-10. [PMID: 21709914 PMCID: PMC4143330 DOI: 10.1039/c1lc20105k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Just as the Petri dish has been invaluable to the evolution of biomedical science in the last 100 years, microfluidic cell assay platforms have the potential to change significantly the way modern biology and clinical science are performed. However, an evolutionary process of creating an efficient microfluidic array for many different bioassays is necessary. Specifically for a complete view of a cell response it is essential to incorporate cytotoxic, protein and gene analysis on a single system. Here we present a novel cellular and molecular analysis platform, which allows access to gene expression, protein immunoassay, and cytotoxicity information in parallel. It is realized by an integrated microfluidic array plate (iMAP). The iMAP enables sample processing of cells, perfusion based cell culture, effective perturbation of biologic molecules or drugs, and simultaneous, real-time optical analysis for different bioassays. The key features of the iMAP design are the interface of on-board gravity driven flow, the open access input fluid exchange and the highly efficient sedimentation based cell capture mechanism (∼100% capture rates). The operation of the device is straightforward (tube and pump free) and capable of handling dilute samples (5-cells per experiment), low reagent volumes (50 nL per reaction), and performing single cell protein and gene expression measurements. We believe that the unique low cell number and triple analysis capabilities of the iMAP platform can enable novel dynamic studies of scarce cells.
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Affiliation(s)
- Ivan K. Dimov
- Biomedical Diagnostics Institute, NCSR, Dublin City University, Glasnevin, Dublin, 9, Ireland
- Department of Biomedical Engineering, Universidad de Valparaíso, Chile; Tel: +56 32 2686848
| | - Gregor Kijanka
- Biomedical Diagnostics Institute, NCSR, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Younggeun Park
- Biomolecular Nanotechnology Center, Berkeley Sensor and Actuator Center, Department of Bioengineering, University of California, Berkeley, USA. Tel: +1-510-642-5855
| | - Jens Ducrée
- Biomedical Diagnostics Institute, NCSR, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Taewook Kang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Korea
| | - Luke P. Lee
- Biomolecular Nanotechnology Center, Berkeley Sensor and Actuator Center, Department of Bioengineering, University of California, Berkeley, USA. Tel: +1-510-642-5855
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11
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Kommedal Ø, Lekang K, Langeland N, Wiker HG. Characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16S rRNA gene followed by DNA sequencing and RipSeq analysis. J Med Microbiol 2011; 60:927-936. [PMID: 21436365 PMCID: PMC3168215 DOI: 10.1099/jmm.0.028373-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The standard use of a single universal broad-range PCR in direct 16S rDNA sequencing from polybacterial samples leaves the minor constituents at risk of remaining undetected because all bacterial DNA will be competing for the same reagents. In this article we introduce a set of three broad-range group-specific 16S rDNA PCRs that together cover the clinically relevant bacteria and apply them in the investigation of 25 polybacterial clinical samples. Mixed DNA chromatograms from samples containing more than one species per primer group were analysed using RipSeq Mixed (iSentio, Norway), a web-based application for the interpretation of chromatograms containing up to three different species. The group-specific PCRs reduced complexity in the resulting DNA chromatograms and made the assay more sensitive in situations with unequal species concentrations. Together this allowed for identification of a significantly higher number of bacterial species than did standard direct sequencing with a single universal primer pair and RipSeq analysis (95 vs 51). The method could improve microbiological diagnostics for important groups of patients and can be established in any laboratory with experience in direct 16S rDNA sequencing.
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Affiliation(s)
- Øyvind Kommedal
- Section for Microbiology and Immunology, The Gade Institute, University of Bergen, 5020 Bergen, Norway
| | - Katrine Lekang
- Institute of Biology, University of Bergen, 5020 Bergen, Norway
| | - Nina Langeland
- Institute of Medicine, University of Bergen, 5020 Bergen, Norway
| | - Harald G. Wiker
- Section for Microbiology and Immunology, The Gade Institute, University of Bergen, 5020 Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, 5021 Bergen, Norway
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12
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Forbi JC, Gabadi S, Iperepolu HO, Esona MD, Agwale SM. Quantification of human immunodeficiency virus-1 viral load using nucleic acid sequence-based amplification (NASBA) in north central Nigeria. Niger J Clin Pract 2010; 13:284-287. [PMID: 20857786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND Viral load (VL) quantification is considered an integral part of the standard care in human immunodeficiency virus (HIV) infected individuals but in Nigeria as in most of sub-Saharan Africa, this has not reached the majority ofpatients. METHODS We report the first field application of the NucliSens EasyQ HIV-1 platform for the real time quantification of HIV-1 VL combining NASBA amplification and real time detection with molecular beacons among HIV-1 infected individuals in north central Nigeria where the predominant HIV-1 subtypes are CRF02_AG and G. CD4+ counts were enumerated using a fluorescence-activated cell sorter system. RESULTS Of one hundred and forty nine (n=149) plasma sample from patients with mean age of 32 years and made up of 77 males and 72 females, fifty {n=50 (37.9%); 28 males and 22 females} had VLs below the lower detection limit (LDL=25 IU/ml) set by the assay while eighty-two {n=82 (62.1%); 39 males and 43 females} had VL levels above the LDL. Furthermore, 13 of 82 (15.9%) patients with viral loads above the LDL had VLs between 26-1000 IU/ml while 69 (84.1%) had VLs of 1001-2,400,000 IU/ml. 17 (11.4%) of the samples could not be analyzed due to poor viral amplification. Among individuals with both CD4+ and VL results (n=56), those with CD4+ of 1-418 cell/microl presented with higher VL usually above 45,000 IU/ml when compared with those with CD4+ of over 500 cell/microl. CONCLUSION Our findings highlight the pattern, usefulness and feasibility ofVL quantification by NucliSens EasyQ in monitoring HIV-1 patients in Nigeria.
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Affiliation(s)
- J C Forbi
- Virology Research Laboratory, Innovative Biotech-Abuja/Keffi, Nigeria.
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Matovu E, Mugasa CM, Ekangu RA, Deborggraeve S, Lubega GW, Laurent T, Schoone GJ, Schallig HD, Büscher P. Phase II evaluation of sensitivity and specificity of PCR and NASBA followed by oligochromatography for diagnosis of human African trypanosomiasis in clinical samples from D.R. Congo and Uganda. PLoS Negl Trop Dis 2010; 4:e737. [PMID: 20625557 PMCID: PMC2897845 DOI: 10.1371/journal.pntd.0000737] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 05/20/2010] [Indexed: 12/05/2022] Open
Abstract
Background The polymerase chain reaction (PCR) and nucleic acid sequence-based amplification (NASBA) have been recently modified by coupling to oligochromatography (OC) for easy and fast visualisation of products. In this study we evaluate the sensitivity and specificity of the PCR-OC and NASBA-OC for diagnosis of Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense human African trypanosomiasis (HAT). Methodology and Results Both tests were evaluated in a case-control design on 143 HAT patients and 187 endemic controls from the Democratic Republic of Congo (DRC) and Uganda. The overall sensitivity of PCR-OC was 81.8% and the specificity was 96.8%. The PCR-OC showed a sensitivity and specificity of 82.4% and 99.2% on the specimens from DRC and 81.3% and 92.3% on those from Uganda. NASBA-OC yielded an overall sensitivity of 90.2%, and a specificity of 98.9%. The sensitivity and specificity of NASBA-OC on the specimens from DRC was 97.1% and 99.2%, respectively. On the specimens from Uganda we observed a sensitivity of 84.0% and a specificity of 98.5%. Conclusions/Significance The tests showed good sensitivity and specificity for the T. b. gambiense HAT in DRC but rather a low sensitivity for T. b. rhodesiense HAT in Uganda. Diagnosis plays a central role in the control of human African trypanosomiasis (HAT) whose mainstay in disease control is chemotherapy. However, accurate diagnosis is hampered by the absence of sensitive techniques for parasite detection. Without concentrating the blood, detection thresholds can be as high as 10,000 trypanosomes per milliliter of blood. The polymerase chain reaction (PCR) and nucleic acid sequence-based amplification (NASBA) are promising molecular diagnostics that generally yield high sensitivity and could improve case detection. Recently, these two tests were coupled to oligochromatography (OC) for simplified and standardized detection of amplified products, eliminating the need for electrophoresis. In this study, we evaluated the diagnostic accuracy of these two novel tests on blood specimens from HAT patients and healthy endemic controls from D.R. Congo and Uganda. Both tests exhibited good sensitivity and specificity compared to the current diagnostic tests and may be valuable tools for sensitive and specific parasite detection in clinical specimens. These standardized molecular test formats open avenues for improved case detection, particularly in epidemiological studies and in disease diagnosis at reference centres.
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Affiliation(s)
- Enock Matovu
- Department of Veterinary Parasitology and Microbiology, Makerere University, Kampala, Uganda.
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Mader A, Riehle U, Brandstetter T, Stickeler E, zur Hausen A, Rühe J. Microarray-based amplification and detection of RNA by nucleic acid sequence based amplification. Anal Bioanal Chem 2010; 397:3533-41. [PMID: 20596698 DOI: 10.1007/s00216-010-3892-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 05/21/2010] [Accepted: 05/29/2010] [Indexed: 11/25/2022]
Abstract
Nucleic acid sequence based amplification (NASBA) is a versatile in vitro nucleic acid amplification method. In this work, RNA amplification and labeling by NASBA and microarray analysis are combined in a one-step process. The NASBA reaction is performed in direct contact with capture probes. These probes are bound to surface-attached hydrogel spots generated at the chip surfaces by using a simple printing and UV irradiation process. Five gene expression and SNP parameters with known relevance in breast cancer diagnostics were chosen to demonstrate that multiplex NASBA-on-microarray analysis is possible. A minimum amount of 10 pg of total RNA was shown to be sufficient for the detection of the reference parameter RPS18, which demonstrates that the detection limit of the microarray-based NASBA assays theoretically allows single-cell assays to be performed.
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Affiliation(s)
- Andreas Mader
- Institute of Pathology, Freiburg University Medical Center, Breisacher Strasse 115a, 79106 Freiburg, Germany
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15
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Heijnen L, Medema G. Method for rapid detection of viable Escherichia coli in water using real-time NASBA. Water Res 2009; 43:3124-32. [PMID: 19476965 DOI: 10.1016/j.watres.2009.04.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 02/12/2009] [Accepted: 04/16/2009] [Indexed: 05/16/2023]
Abstract
A rapid real-time NASBA method was developed for detection of Escherichia coli in water samples. In this method, a fragment of the clpB-mRNA is amplified and a specific molecular beacon probe is used to detect the amplified mRNA fragment during the NASBA reaction. The method was shown to be specific and sensitive (1 viable E. coli in 100ml) and can be performed within 3-4h. Different inactivation processes (starvation, heat, UV-irradiation and chlorine) were employed to study the relationship between culturability and the ability to detect E. coli using NASBA. Detection of clpB-mRNA correlated with culturability after starvation or chlorine treatment. After UV-irradiation or heat-inactivation, detection of the increase in production of clpB-mRNA in viable E. coli cells after heat-shock induction correlated with culturability. Application of the NASBA method on tap water, treated sewage and surface water samples showed that culture and NASBA yielded comparable results in these different matrices. This study demonstrates that the NASBA method has high potential as a rapid test for microbiological water quality monitoring.
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Affiliation(s)
- Leo Heijnen
- KWR, Watercycle Research Institute, P.O. Box 1072, 3430 BB Nieuwegein, The Netherlands.
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16
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Dimov IK, Garcia-Cordero JL, O'Grady J, Poulsen CR, Viguier C, Kent L, Daly P, Lincoln B, Maher M, O'Kennedy R, Smith TJ, Ricco AJ, Lee LP. Integrated microfluidic tmRNA purification and real-time NASBA device for molecular diagnostics. Lab Chip 2008; 8:2071-8. [PMID: 19023470 DOI: 10.1039/b812515e] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We demonstrate the first integrated microfluidic tmRNA purification and nucleic acid sequence-based amplification (NASBA) device incorporating real-time detection. The real-time amplification and detection step produces pathogen-specific response in < 3 min from the chip-purified RNA from 100 lysed bacteria. On-chip RNA purification uses a new silica bead immobilization method. On-chip amplification uses custom-designed high-selectivity primers and real-time detection uses molecular beacon fluorescent probe technology; both are integrated on-chip with NASBA. Present in all bacteria, tmRNA (10Sa RNA) includes organism-specific identification sequences, exhibits unusually high stability relative to mRNA, and has high copy number per organism; the latter two factors improve the limit of detection, accelerate time-to-positive response, and suit this approach ideally to the detection of small numbers of bacteria. Device efficacy was demonstrated by integrated on-chip purification, amplification, and real-time detection of 100 E. coli bacteria in 100 microL of crude lysate in under 30 min for the entire process.
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Affiliation(s)
- Ivan K Dimov
- Biomedical Diagnostics Institute, National Centre for Sensor Research, Research & Engineering Building, Dublin City University, Glasnevin, Dublin 9, Ireland
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17
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Lamhoujeb S, Fliss I, Ngazoa SE, Jean J. Evaluation of the persistence of infectious human noroviruses on food surfaces by using real-time nucleic acid sequence-based amplification. Appl Environ Microbiol 2008; 74:3349-55. [PMID: 18378643 PMCID: PMC2423024 DOI: 10.1128/aem.02878-07] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 03/24/2008] [Indexed: 11/20/2022] Open
Abstract
Noroviruses (NoV) are the major cause of nonbacterial gastroenteritis. However, there is no published study to ascertain their survival on foodstuffs which are directly related to human health risk. In the present study, we developed a rapid, simple, and sensitive real-time nucleic acid sequence-based amplification (NASBA) combined with an enzymatic treatment for distinguishing infectious from noninfectious human NoV. The developed method was validated using spiked ready-to-eat food samples. When feline calicivirus (FCV) was used as a NoV surrogate in the preliminary assays, it appeared more sensitive to heat inactivation and enzymatic pretreatment than the human NoV. This suggests that FCV may not be an ideal model for studying NoV. Our results reveal clearly that the developed enzymatic pretreatment/real-time NASBA combination successfully distinguished the infectious from heat-inactivated NoV. Moreover, we demonstrate that NoV survived for at least 10 days on refrigerated ready-to-eat foods, such as lettuce and turkey. However, the survival rate was higher on turkey than on lettuce, probably because of their different surface natures. The approach developed in this study may be suitable for more in-depth studies of the persistence and inactivation of human NoV and may be applied to other nonculturable RNA viruses. Moreover, the evaluation of infectious NoV survival provided valuable information concerning its persistence on ready-to-eat food.
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Affiliation(s)
- Safaa Lamhoujeb
- Institut des Nutraceutiques et des Aliments Fonctionnels, Université Laval, Québec, Québec G1K 7P4, Canada
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18
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Deiman B, Schrover C, Moore C, Westmoreland D, van de Wiel P. Rapid and highly sensitive qualitative real-time assay for detection of respiratory syncytial virus A and B using NASBA and molecular beacon technology. J Virol Methods 2007; 146:29-35. [PMID: 17614146 DOI: 10.1016/j.jviromet.2007.05.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 05/24/2007] [Accepted: 05/31/2007] [Indexed: 11/25/2022]
Abstract
The performance of a sensitive and specific qualitative respiratory syncytial virus (RSV) assay based on NASBA technology and real-time molecular beacon detection is presented. Very low detection limits for both RSV A and RSV B were determined: 95% detection hit-rate of 95 and 47 copies/input in isolation for RSV A and RSV B, respectively. RSV was detected in a wide variety of clinical samples including respiratory swabs, nasopharyngeal aspirates (NPA), bronchoalveolar lavages (BAL), endotracheal secretions, and sputum samples. In total 779 clinical samples were tested and a valid result was obtained for 765 (RSV NASBA assay), 765 (cell culture), and 529 (rapid direct immunofluorescence testing (IF)) samples. Of these samples, 229 (RSV NASBA assay), 61 (cell culture), and 122 (IF) samples were positive for RSV. In addition, 106 samples were reported as RSV negative using the NOW RSV assay (Binax). Subsequent testing using the RSV NASBA assay demonstrated that 32 (30%) of these samples were RSV positive. The RSV NASBA assay includes a homologous internal control, which offers a high degree of standardization and quality control. When the RSV NASBA assay was performed on the NucliSens EasyQ platform (bioMérieux), test results of 48 sample extracts were obtained in less than 2h.
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Affiliation(s)
- B Deiman
- BioMerieux bv, Boseind 15, P.O. Box 84, 5280 AB Boxtel and Wales Specialist Virology Centre, Netherlands.
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19
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Costa AM, Lamb D, Garland SM, Tabrizi SN. Evaluation of LightCycler as a platform for nucleic acid sequence-based amplification (NASBA) in real-time detection of enteroviruses. Curr Microbiol 2007; 56:80-3. [PMID: 17909885 DOI: 10.1007/s00284-007-9043-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 08/04/2007] [Indexed: 10/22/2022]
Abstract
The nucleic acid sequence-based amplification (NASBA) assay has been demonstrated to be more sensitive for detection of enteroviruses (EV) than RT-PCR. Many laboratories, however, do not have a dedicated instrument for the NASBA assay. This study aimed to evaluate the use of the Roche LightCycler as a platform for performing the NASBA assay for detection of EV. A diverse subgenera of EV were used to assess the specificity of the NASBA assay, including coxsackie, echovirus, poliovirus, and other enteroviruses together with related and unrelated viruses, including rhinovirus, respiratory syncytial virus, herpes simplex virus, adenovirus, influenza virus A, and cytomegalovirus. All species of EV tested were successfully detected using NASBA and no cross reactivity with other viruses was observed. Using serial dilutions of EV to assess sensitivity, the NASBA assay was compared to an in-house EV RT-PCR assay. The NASBA assay demonstrated a higher level of sensitivity. Fifty-one clinical samples positive for EV by viral culture were also evaluated. All NASBA results obtained were concordant with viral culture results. This study confirmed that the NASBA assay for the detection of EV could be readily performed on the LightCycler and easily incorporated into the workflow of a diagnostic laboratory equipped with a LightCycler, thereby eliminating the need for additional instrumentation.
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Affiliation(s)
- Anna-Maria Costa
- Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, 132 Grattan Street, Carlton 3053, Victoria, Australia.
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20
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Gu J, Xie Z, Gao Z, Liu J, Korteweg C, Ye J, Lau LT, Lu J, Gao Z, Zhang B, McNutt MA, Lu M, Anderson VM, Gong E, Yu ACH, Lipkin WI. H5N1 infection of the respiratory tract and beyond: a molecular pathology study. Lancet 2007; 370:1137-45. [PMID: 17905166 PMCID: PMC7159293 DOI: 10.1016/s0140-6736(07)61515-3] [Citation(s) in RCA: 283] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
BACKGROUND Human infection with avian influenza H5N1 is an emerging infectious disease characterised by respiratory symptoms and a high fatality rate. Previous studies have shown that the human infection with avian influenza H5N1 could also target organs apart from the lungs. METHODS We studied post-mortem tissues of two adults (one man and one pregnant woman) infected with H5N1 influenza virus, and a fetus carried by the woman. In-situ hybridisation (with sense and antisense probes to haemagglutinin and nucleoprotein) and immunohistochemistry (with monoclonal antibodies to haemagglutinin and nucleoprotein) were done on selected tissues. Reverse-transcriptase (RT) PCR, real-time RT-PCR, strand-specific RT-PCR, and nucleic acid sequence-based amplification (NASBA) detection assays were also undertaken to detect viral RNA in organ tissue samples. FINDINGS We detected viral genomic sequences and antigens in type II epithelial cells of the lungs, ciliated and non-ciliated epithelial cells of the trachea, T cells of the lymph node, neurons of the brain, and Hofbauer cells and cytotrophoblasts of the placenta. Viral genomic sequences (but no viral antigens) were detected in the intestinal mucosa. In the fetus, we found viral sequences and antigens in the lungs, circulating mononuclear cells, and macrophages of the liver. The presence of viral sequences in the organs and the fetus was also confirmed by RT-PCR, strand-specific RT-PCR, real-time RT-PCR, and NASBA. INTERPRETATION In addition to the lungs, H5N1 influenza virus infects the trachea and disseminates to other organs including the brain. The virus could also be transmitted from mother to fetus across the placenta.
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Affiliation(s)
- Jiang Gu
- Infectious Disease Centre, Peking University, Beijing, China.
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Abstract
Given the causal relation between a persistent high-risk human papillomavirus (hrHPV) infection and the development of high-grade cervical intraepithelial neoplasia (CIN) and cervical cancer, hrHPV testing has been advocated in addition to cytology for the detection of clinically relevant cervical lesions. HrHPV testing is thought to improve cervical screening algorithms, the management of women with cytologically equivocal smears, and the management of women treated for high grade CIN. In this chapter we discuss different methods for HPV detection and genotyping and their respective applications.
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Affiliation(s)
- Antoinette A. T. P. Brink
- VU University medical centerDepartment of PathologySection Molecular PathologyDe Boelelaan 11171081 HV AmsterdamThe Netherlands
| | - Peter J. F. Snijders
- VU University medical centerDepartment of PathologySection Molecular PathologyDe Boelelaan 11171081 HV AmsterdamThe Netherlands
| | - Chris J. L. M. Meijer
- VU University medical centerDepartment of PathologySection Molecular PathologyDe Boelelaan 11171081 HV AmsterdamThe Netherlands
- *Chris J. L. M. Meijer:
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Patterson SS, Smith MW, Casper ET, Huffman D, Stark L, Fries D, Paul JH. A nucleic acid sequence-based amplification assay for real-time detection of norovirus genogroup II. J Appl Microbiol 2007; 101:956-63. [PMID: 16968307 DOI: 10.1111/j.1365-2672.2006.02934.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To use molecular beacon based nucleic acid sequence-based amplification (NASBA) to develop a rapid, sensitive, specific detection method for norovirus (NV) genogroupII (GII). METHODS AND RESULTS A method to detect NV GII from environmental samples using real-time NASBA was developed. This method was routinely sensitive to 100 copies of target RNA and intermittent amplification occurred with as few as 10 copies. Quantitative estimates of viral load were possible over at least four orders of magnitude. CONCLUSIONS The NASBA method described here is a reliable and sensitive assay for the detection of NV. This method has the potential to be linked to a handheld NASBA device that would make this real-time assay a portable and inexpensive alternative to bench-top, lab-based assays. SIGNIFICANCE AND IMPACT OF THE STUDY The development of the real-time NASBA assay described here has resulted in a simple, rapid (<1 h), convenient testing format for NV. To our knowledge, this is the first example of a molecular beacon based NASBA assay for NV.
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Affiliation(s)
- S S Patterson
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
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Tung SK, Teng LJ, Vaneechoutte M, Chen HM, Chang TC. Identification of species of Abiotrophia, Enterococcus, Granulicatella and Streptococcus by sequence analysis of the ribosomal 16S-23S intergenic spacer region. J Med Microbiol 2007; 56:504-513. [PMID: 17374892 DOI: 10.1099/jmm.0.47027-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The feasibility of sequence analysis of the ribosomal 16S-23S intergenic spacer region (ITS) was evaluated for identification of 24 species of Streptococcus, one species of Abiotrophia, 18 species of Enterococcus and three species of Granulicatella. As GenBank currently lacks ITS sequence entries for many species of these four genera, the ITS sequences of 38 type strains were first sequenced and submitted to GenBank to facilitate species identification of these genera. Subsequently, the ITS sequences of 217 strains (84 reference strains and 133 clinical isolates) were determined and species identification was made by blast search for homologous sequences in public databases. Species other than Streptococcus contained multiple ITS fragments and only the shortest fragment was analysed. A total of 25 isolates (11.5 %) produced discrepant identification by ITS sequencing. The 25 discordant strains were analysed further by sequencing of the 16S rRNA gene for species clarification, and 21 were found to be identified correctly by ITS sequence analysis. The correct identification rate by ITS sequencing was 98.2 % (213/217). Several closely related enterococcal and streptococcal species/subspecies contained specific ITS signature sequences that were useful for differentiating these bacteria. In conclusion, ITS sequencing provides a useful approach towards identifying this group of pathogens on a molecular platform alongside 16S rRNA gene sequencing.
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Affiliation(s)
- Sheng Kai Tung
- Department of Medical Laboratory Science and Biotechnology, School of Medicine, National Cheng Kung University, 1 University Road, Tainan 701, Taiwan, ROC
| | - Lee Jene Teng
- School of Medical Technology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Mario Vaneechoutte
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium
| | - Hung Mo Chen
- Division of Clinical Microbiology, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan, ROC
| | - Tsung Chain Chang
- Department of Medical Laboratory Science and Biotechnology, School of Medicine, National Cheng Kung University, 1 University Road, Tainan 701, Taiwan, ROC
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Criado-Fornelio A. A review of nucleic-acid-based diagnostic tests for Babesia and Theileria, with emphasis on bovine piroplasms. Parassitologia 2007; 49 Suppl 1:39-44. [PMID: 17691606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Nucleic acid-based methods offer a variety of tools for the detection of parasites. This field of veterinary and medical sciences is rapidly evolving, leading to greater sensitivity and higher throughput. One of the reasons justifying such a fast development is the fact that tests targeting several taxa can be created. The present article deals with the applications of molecular diagnostics of tick-borne diseases in Parasitology. Special attention is given to Babesia and Theileria species infecting livestock. The commonly used molecular methods in diagnostic of tick-transmitted hematic protozoa are the following: (i) final time polymerase chain reaction; (ii) reverse line blotting (RLB); (iii) real time PCR, based on SYBR Green or probe fluorescence; (iv) isothermal amplification methods: loop-mediated amplification (LAMP) and self sustaining sequence replication (3SR, also named as "Nucleic Acid Sequence Based Amplification", NASBA, or Transcription Mediated Amplification, TMA). In general, none of these methods could be considered better than another. Their score in diagnostic applications greatly depends on the laboratory size. Small-scale laboratories handling few samples may find final time PCR a cheap alternative. On the contrary, large-scale laboratories prefer methods amenable to automation, like RLB, PCR-ELISA or qPCR.
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Affiliation(s)
- A Criado-Fornelio
- Parasitology Laboratory, Microbiology and Parasitology Department, University of Alcalá, Alcalá de Henares, Spain.
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Molden T, Kraus I, Skomedal H, Nordstrøm T, Karlsen F. PreTect HPV-Proofer: real-time detection and typing of E6/E7 mRNA from carcinogenic human papillomaviruses. J Virol Methods 2007; 142:204-12. [PMID: 17379322 DOI: 10.1016/j.jviromet.2007.01.036] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2006] [Revised: 01/29/2007] [Accepted: 01/31/2007] [Indexed: 11/17/2022]
Abstract
Monitoring human papillomavirus (HPV) E6/E7 mRNA expression may provide an accurate and informative diagnostic approach for detection of oncogene activity related to the development of severe dysplasia or cervical carcinoma. A multiplex nucleic acid sequence based amplification (NASBA) assay, utilizing molecular beacon probes for real-time detection was developed for the identification of E6/E7 mRNA from HPV types 16, 18, 31, 33 and 45. The assay is called PreTect HPV-Proofer and this report describes the development and the analytical performance of the assay. The reproducibility of PreTect HPV-Proofer with regard to a positive result was found to be between 96 and 100%, depending on HPV type. The melting temperature for the different molecular beacons was in the range of 48-55 degrees C, indicating conformational stability, i.e. the molecular beacons will not get activated by the 41 degrees C annealing temperature, but will be activated by the annealing to the target itself. The limit of detection for HPV 16 was ten SiHa or CaSki cells and for HPV 18 one HeLa cell. No cross reactivity was observed with E6/E7 mRNA from the other tested HPV types. mRNA from cervical cells was also successfully amplified after more than one year of storage. In conclusion, the PreTect HPV-Proofer assay, individually identifying E6/E7 mRNA expression from five carcinogenic HPV types, is a reproducible assay that may serve as a valuable tool in monitoring HPV infections producing proteins with a transforming potential.
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Affiliation(s)
- Tor Molden
- Institute of Pathology, Rikshospitalet University Hospital, 0027 Oslo, Norway.
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Fykse EM, Skogan G, Davies W, Olsen JS, Blatny JM. Detection of Vibrio cholerae by real-time nucleic acid sequence-based amplification. Appl Environ Microbiol 2007; 73:1457-66. [PMID: 17220262 PMCID: PMC1828771 DOI: 10.1128/aem.01635-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 12/20/2006] [Indexed: 12/17/2022] Open
Abstract
A multitarget molecular beacon-based real-time nucleic acid sequence-based amplification (NASBA) assay for the specific detection of Vibrio cholerae has been developed. The genes encoding the cholera toxin (ctxA), the toxin-coregulated pilus (tcpA; colonization factor), the ctxA toxin regulator (toxR), hemolysin (hlyA), and the 60-kDa chaperonin product (groEL) were selected as target sequences for detection. The beacons for the five different genetic targets were evaluated by serial dilution of RNA from V. cholerae cells. RNase treatment of the nucleic acids eliminated all NASBA, whereas DNase treatment had no effect, showing that RNA and not DNA was amplified. The specificity of the assay was investigated by testing several isolates of V. cholerae, other Vibrio species, and Bacillus cereus, Salmonella enterica, and Escherichia coli strains. The toxR, groEL, and hlyA beacons identified all V. cholerae isolates, whereas the ctxA and tcpA beacons identified the O1 toxigenic clinical isolates. The NASBA assay detected V. cholerae at 50 CFU/ml by using the general marker groEL and tcpA that specifically indicates toxigenic strains. A correlation between cell viability and NASBA was demonstrated for the ctxA, toxR, and hlyA targets. RNA isolated from different environmental water samples spiked with V. cholerae was specifically detected by NASBA. These results indicate that NASBA can be used in the rapid detection of V. cholerae from various environmental water samples. This method has a strong potential for detecting toxigenic strains by using the tcpA and ctxA markers. The entire assay including RNA extraction and NASBA was completed within 3 h.
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Affiliation(s)
- Else M Fykse
- Norwegian Defence Research Establishment, P.O. Box 25, N-2027 Kjeller, Norway.
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Nadal A, Coll A, Cook N, Pla M. A molecular beacon-based real time NASBA assay for detection of Listeria monocytogenes in food products: role of target mRNA secondary structure on NASBA design. J Microbiol Methods 2007; 68:623-32. [PMID: 17258831 DOI: 10.1016/j.mimet.2006.11.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Revised: 11/06/2006] [Accepted: 11/20/2006] [Indexed: 11/20/2022]
Abstract
A molecular beacon-based real-time NASBA (QNASBA) assay for detection and identification of Listeria monocytogenes has been developed. A correlation between targeting highly accessible mRNA sequences and QNASBA efficiency and sensitivity was demonstrated. The assay targets a sequence from the mRNA transcript of the hly gene which is specific for this bacterium; and includes an internal amplification control to disclose failure of the reaction. It was fully selective and consistently detected down to 100 target molecules and 40 L. monocytogenes exponentially growing cells per reaction. In addition, it was capable of accurate quantification of target RNA molecules independently of the presence of DNA in the sample. In combination with a short RNase treatment prior to nucleic acids extraction our QNASBA specifically detected viable L. monocytogenes cells. It was successfully applied to rapid detection of this pathogen in meat and salmon products, and is therefore a useful tool for the study of L. monocytogenes in food samples. We finally discuss considerations of target secondary structure with regard to development of NASBA assays.
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Affiliation(s)
- Anna Nadal
- Institute of Food and Agricultural Technology, University of Girona, E-17071 Girona, Spain
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Olmos A, Bertolini E, Cambra M. Isothermal amplification coupled with rapid flow-through hybridisation for sensitive diagnosis of Plum pox virus. J Virol Methods 2007; 139:111-5. [PMID: 17092572 DOI: 10.1016/j.jviromet.2006.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 09/13/2006] [Accepted: 09/19/2006] [Indexed: 11/22/2022]
Abstract
A nucleic acid sequence-based amplification method coupled with rapid flow-through hybridisation (NASBA-FH) was developed for diagnosis of Plum pox virus (PPV). The sensitivity level achieved by NASBA-FH was 10 times higher than that obtained by Co-PCR and 1000 times higher than the sensitivity afforded by RT-PCR. In addition, samples from 262 stone-fruit trees collected during winter and spring seasons were analysed. These samples were tested using methods recommended by the European and Mediterranean Plant Protection Organization to detect PPV (DASI-ELISA, RT-PCR and Co-PCR) and by NASBA-FH. Winter PPV diagnostic results by ELISA and NASBA-FH coincided in 90.8%, while ELISA and PCR-based methods coincided in 91.6% and PCR-based methods with NASBA-FH agreed in 95.4%. In spring, diagnostic results were similar with all the molecular techniques, which agreed with ELISA results for 98.8% of the trees. NASBA-FH was able to detect more positive infections in winter, which were later confirmed in spring. These results indicate that NASBA-FH is a suitable molecular method for routine PPV detection in the winter and spring. This user-friendly isothermal RNA amplification coupled with a very fast flow-through hybridisation (15 min) opens up new possibilities for rapid and reliable diagnosis of a variety of pathogens.
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Affiliation(s)
- Antonio Olmos
- Laboratorio de Virología e Inmunología, Departamento de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada-Náquera Km 5, 46113 Moncada, Valencia, Spain.
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de Vries PJ, van der Meide WF, Godfried MH, Schallig HDFH, Dinant HJ, Faber WR. Quantification of the response to miltefosine treatment for visceral leishmaniasis by QT-NASBA. Trans R Soc Trop Med Hyg 2006; 100:1183-6. [PMID: 16678871 DOI: 10.1016/j.trstmh.2006.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Revised: 12/20/2005] [Accepted: 01/05/2006] [Indexed: 11/16/2022] Open
Abstract
A male patient with psoriatic arthritis and visceral Leishmania infantum infection was treated with oral miltefosine 50 mg three times a day for 4 weeks at the Academic Medical Center, Amsterdam, The Netherlands. Miltefosine plasma concentrations were measured with liquid chromatography/mass spectrometry. The parasite load was followed by quantitative nucleic acid sequence-based amplification (QT-NASBA) assay in blood. Miltefosine elicited a prompt therapeutic effect. After an initial worsening of symptoms and an increase of QT-NASBA values during the first week, recovery was rapidly achieved. QT-NASBA values declined exponentially and were negative after 6 weeks. Miltefosine plasma concentrations continued to accumulate during the 4 weeks of treatment. The terminal elimination half-life was 14.8 days.
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Affiliation(s)
- P J de Vries
- Academic Medical Center, Division of Infectious Diseases, Tropical Medicine & AIDS, Meibergdreef 9, Amsterdam, The Netherlands.
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Starkey WG, Smail DA, Bleie H, Muir KF, Ireland JH, Richards RH. Detection of infectious salmon anaemia virus by real-time nucleic acid sequence based amplification. Dis Aquat Organ 2006; 72:107-13. [PMID: 17140133 DOI: 10.3354/dao072107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We have developed a real-time nucleic acid sequence based amplification (NASBA) procedure for detection of infectious salmon anaemia virus (ISAV). Primers were designed to target a 124 nucleotide region of ISAV genome segment 8. Amplification products were detected in real-time with a molecular beacon (carboxyfluorescin [FAM]-labelled and methyl-red quenched) that recognised an internal region of the target amplicon. Amplification and detection were performed at 41 degrees C for 90 min in a Corbett Research Rotorgene. The real-time NASBA assay was compared to a conventional RT-PCR for ISAV detection. From a panel of 45 clinical samples, both assays detected ISAV in the same 19 samples. Based on the detection of a synthetic RNA target, the real-time NASBA procedure was approximately 100x more sensitive than conventional RT-PCR. These results suggest that real-time NASBA may represent a useful diagnostic procedure for ISAV.
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Affiliation(s)
- William G Starkey
- Department of Virology, Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK.
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Rutjes SA, van den Berg HHJL, Lodder WJ, de Roda Husman AM. Real-time detection of noroviruses in surface water by use of a broadly reactive nucleic acid sequence-based amplification assay. Appl Environ Microbiol 2006; 72:5349-58. [PMID: 16885286 PMCID: PMC1538714 DOI: 10.1128/aem.00751-06] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Noroviruses are the most common agents causing outbreaks of viral gastroenteritis. Outbreaks originating from contaminated drinking water and from recreational waters have been described. Due to a lack of cell culture systems, noroviruses are detected mostly by molecular methods. Molecular detection assays for viruses in water are often repressed by inhibitory factors present in the environment, like humic acids and heavy metals. To study the effect of environmental inhibitors on the performance of nucleic acid sequence-based amplification (NASBA), we developed a real-time norovirus NASBA targeting part of the RNA-dependent RNA polymerase (RdRp) gene. Specificity of the assay was studied with 33 divergent clones that contained part of the targeted RdRp gene of noroviruses from 15 different genogroups. Viral RNA originated from commercial oysters, surface waters, and sewage treatment plants in The Netherlands. Ninety-seven percent of the clones derived from human noroviruses were detected by real-time NASBA. Two clones containing animal noroviruses were not detected by NASBA. We compared the norovirus detection by real-time NASBA with that by conventional reverse transcriptase PCR (RT-PCR) with large-volume river water samples and found that inhibitory factors of RT-PCR had little or no effect on the performance of the norovirus NASBA. This consequently resulted in a higher sensitivity of the NASBA assay than of the RT-PCR. We show that by combining an efficient RNA extraction method with real-time NASBA the sensitivity of norovirus detection in water samples increased at least 100 times, which consequently has implications for the outcome of the infectious risk assessment.
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Affiliation(s)
- Saskia A Rutjes
- National Institute of Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Antonie van Leeuwenhoeklaan 9, 3720 BA Bilthoven, The Netherlands.
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Mens PF, Schoone GJ, Kager PA, Schallig HDFH. Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification. Malar J 2006; 5:80. [PMID: 17018138 PMCID: PMC1592503 DOI: 10.1186/1475-2875-5-80] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Accepted: 10/03/2006] [Indexed: 11/11/2022] Open
Abstract
Background Decisions concerning malaria treatment depend on species identification causing disease. Microscopy is most frequently used, but at low parasitaemia (<20 parasites/μl) the technique becomes less sensitive and time consuming. Rapid diagnostic tests based on Plasmodium antigen detection do often not allow for species discrimination as microscopy does, but also become insensitive at <100 parasites/μl. Methods This paper reports the development of a sensitive and specific real-time Quantitative Nucleic Acid Sequence Based Amplification (real-time QT-NASBA) assays, based on the small-subunit 18S rRNA gene, to identify the four human Plasmodium species. Results The lower detection limit of the assay is 100 – 1000 molecules in vitro RNA for all species, which corresponds to 0.01 – 0.1 parasite per diagnostic sample (i.e. 50 μl of processed blood). The real-time QT-NASBA was further evaluated using 79 clinical samples from malaria patients: i.e. 11 Plasmodium. falciparum, 37 Plasmodium vivax, seven Plasmodium malariae, four Plasmodium ovale and 20 mixed infections. The initial diagnosis of 69 out of the 79 samples was confirmed with the developed real-time QT-NASBA. Re-analysis of seven available original slides resolved five mismatches. Three of those were initially identified as P. malariae mono-infection, but after re-reading the slides P. falciparum was found, confirming the real-time QT-NASBA result. The other two slides were of poor quality not allowing true species identification. The remaining five discordant results could not be explained by microscopy, but may be due to extreme low numbers of parasites present in the samples. In addition, 12 Plasmodium berghei isolates from mice and 20 blood samples from healthy donors did not show any reaction in the assay. Conclusion Real-time QT-NASBA is a very sensitive and specific technique with a detection limit of 0.1 Plasmodium parasite per diagnostic sample (50 μl of blood) and can be used for the detection, identification and quantitative measurement of low parasitaemia of Plasmodium species, thus making it an effective tool for diagnostic purposes and useful for epidemiological and drug studies.
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Affiliation(s)
- Petra F Mens
- Koninklijk Instituut voor de Tropen (KIT)/Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ Amsterdam, The Netherlands
- Academic Medical Centre, Division of Infectious Diseases, Tropical Medicine and AIDS, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Gerard J Schoone
- Koninklijk Instituut voor de Tropen (KIT)/Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ Amsterdam, The Netherlands
| | - Piet A Kager
- Academic Medical Centre, Division of Infectious Diseases, Tropical Medicine and AIDS, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Henk DFH Schallig
- Koninklijk Instituut voor de Tropen (KIT)/Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ Amsterdam, The Netherlands
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McClernon DR, Vavro C, St Clair M. Evaluation of a real-time nucleic acid sequence-based amplification assay using molecular beacons for detection of human immunodeficiency virus type 1. J Clin Microbiol 2006; 44:2280-2. [PMID: 16757640 PMCID: PMC1489398 DOI: 10.1128/jcm.02187-05] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the performance characteristics of a new, real-time nucleic acid sequence-based amplification (NASBA) assay that incorporates molecular beacon technology for detection of human immunodeficiency virus type 1 (HIV-1). The quantitative results were comparable to those obtained with three leading commercially available assays. The analytical sensitivity was 37 IU/ml. The NASBA assay detected clinically relevant recombinant viruses and all group M HIV-1 subtypes.
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Affiliation(s)
- D R McClernon
- Clinical Virology Department, GlaxoSmithKline, Research Triangle Park, NC 27709-3398, USA.
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Moore C, Valappil M, Corden S, Westmoreland D. Enhanced clinical utility of the NucliSens EasyQ RSV A+B Assay for rapid detection of respiratory syncytial virus in clinical samples. Eur J Clin Microbiol Infect Dis 2006; 25:167-74. [PMID: 16534566 DOI: 10.1007/s10096-006-0112-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The aim of the present study was to compare traditional methods for the detection of respiratory syncytial virus with a newly developed commercial assay based on real-time nucleic acid sequence based amplification. Respiratory syncytial virus is a major cause of severe respiratory infection in infants and in certain groups of older children and adults. Treatment options are limited, but a rapid diagnosis improves patient management and infection control. The rapid diagnosis of respiratory syncytial virus currently relies on antigen detection assays. These tests are limited to use in certain good-quality types of samples, which are rarely obtained from adult patients. Molecular-based assays for the detection of respiratory syncytial virus are shown to be highly sensitive, specific, and more rapid than cell culture techniques. This retrospective study compared traditional laboratory techniques for the detection of respiratory syncytial virus in 508 respiratory samples collected during the winter months of 2003-2004 against the recently developed, commercially available NucliSens EasyQ Respiratory Syncytial Virus A+B assay (bioMérieux, Marcy l'Etoile, France), which is based on real-time nucleic acid sequence based amplification using molecular beacons and an internal control. Using traditional techniques, the prevalence of respiratory syncytial virus in the samples tested was found to be 21%. Using the real-time nucleic acid sequence-based amplification assay, an additional 41 samples from patients with a clinically diagnosed respiratory illness were found to be positive for respiratory syncytial virus. The NucliSens EasyQ assay was shown to be sensitive and specific for the detection of respiratory syncytial virus A+B in different types of respiratory samples. Moreover, the time required to complete the assay was <4 h, so results could be obtained on the same day as sample receipt in the laboratory.
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Affiliation(s)
- C Moore
- Wales Specialist Virology Centre, National Public Health Service for Wales Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff, CF 14 4XW, UK.
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Kou XX, Wu QP, Fan HY. [Study on Rotavirus detection by nucleic acid sequence based amplification]. Wei Sheng Wu Xue Bao 2006; 46:328-30. [PMID: 16736602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Rotavirus is one of the major cause of the viral gastroenteritis throughout the world. A nucleic acid sequence-based amplification(NASBA) technique for the detection of rotavirus in faecal specimens was developed and compared to the RT-PCR technique. Primers were designed according to the high conserved region of VP7 gene. Amplicons were detected by denaturating agarose gel, and then demonstrated by Northern hybridization with digoxigenin-labeled oligonucleotide probe. The anticipative specific amplification product is 392bp,and no nonspecific products appear even the concentration of nontarget nucleic acid as high as 1 microg/microL. A detection limit of 50 pg target RNA/mL is obtained when the optimal amplification time of 3h used.The NASBA assay will be a favourable alternative to RT-PCR for the investigation of rotavirus outbreaks as a routine diagnostic test in the near future because it is shown to be highly sensitive, specific and do not require specialized equipment.
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Affiliation(s)
- Xiao-Xi Kou
- Guangdong Instisute of Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, China.
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Loens K, Goossens H, de Laat C, Foolen H, Oudshoorn P, Pattyn S, Sillekens P, Ieven M. Detection of rhinoviruses by tissue culture and two independent amplification techniques, nucleic acid sequence-based amplification and reverse transcription-PCR, in children with acute respiratory infections during a winter season. J Clin Microbiol 2006; 44:166-71. [PMID: 16390965 PMCID: PMC1351952 DOI: 10.1128/jcm.44.1.166-171.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five hundred seventeen consecutive nasopharyngeal aspirates were collected between October 1998 and May 1999 for episodes of acute respiratory tract infections in children presenting at the University Hospital of Antwerp. Culture and nucleic acid amplification techniques--nucleic acid sequence-based amplification (NASBA) and reverse transcription-PCR (RT-PCR)--were applied to detect rhinoviruses (RVs). Other respiratory viruses were detected by immunofluorescence (IF) analysis of the specimens and IF analysis of shell vial cultures. Among the 517 specimens, 219 viral agents were identified. They were, in decreasing order, rhinoviruses (93 [18.0%]), respiratory syncytial virus (76 [14.7%]), adenoviruses (16 [3.1%]), influenza viruses (15 [2.9%]), enteroviruses (15 [2.9%]), and herpes simplex virus (4 [0.8%]). For the evaluation of rhinovirus detection, culture positivity and/or a positive reaction in the two independent amplification methods was used as an expanded "gold standard." Based on this standard, the sensitivity, specificity, positive predictive value, and negative predictive value of culture were 44.7, 100, 100, and 99.8%, and those of NASBA and RT-PCR were 85.1, 98.3, 83.3, and 98.5% and 82.9, 93.4, 55.7, and 98.2%, respectively. NASBA and RT-PCR produced comparable results and were significantly more sensitive than virus culture. RVs showed the highest incidence in acute respiratory tract infections in children.
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Affiliation(s)
- K Loens
- Department of Medical Microbiology, University of Antwerp, Wilrijk, Belgium.
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Lamy PJ, Verjat T, Paye M, Servanton AC, Grenier J, Leissner P, Mougin B. NASBA: a novel approach to assess hormonal receptors and ERBB2 status in breast cancer. Clin Chem Lab Med 2006; 44:3-12. [PMID: 16375577 DOI: 10.1515/cclm.2006.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In human breast cancer, estrogen receptor-alpha (ERalpha), progesterone receptor (PR) and human epidermal growth factor receptor (ERBB2) status are currently determined using different techniques. We propose to assess the mRNA expression of these three clinically relevant markers using a unique technique, real-time nucleic acid sequence-based amplification (NASBA). Gene expression of hormone receptors was analyzed and compared to the cytosolic functional protein content as determined with a ligand binding assay (LBA), while ERBB2 mRNA expression was compared to quantitative PCR and ELISA. We observed that the three markers are significantly overexpressed at the mRNA level in positive tumors, as measured by DNA- or protein-based techniques. Biostatistical analysis of the receiver operating characteristic (ROC) curve demonstrated high concordance between NASBA and LBA [area under the curve (AUC) for ROC of 0.899] and showed that ERalpha status could be predicted using the molecular assay with a sensitivity of 72.7% and a specificity of 93.5%. Similar results were obtained for PR (AUC ROC 0.938, sensitivity 75.3%, specificity 100%). Moreover, excellent concordance was observed between NASBA, quantitative PCR and ELISA with respect to ERBB2 (AUC ROC 0.92, sensitivity 90%, specificity 89.7%; and AUC ROC 0.98, sensitivity 100%, specificity 91.5%, respectively). These results suggest that NASBA is well suited for assessing ER, PR and ERBB2 status in breast tumor samples. This approach is rapid, highly sensitive and a standardized method that could be complementary to the existing techniques, especially for small tumors.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Female
- Gene Expression Regulation, Neoplastic/genetics
- Hormones/metabolism
- Humans
- Middle Aged
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Self-Sustained Sequence Replication/methods
- Time Factors
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Affiliation(s)
- Pierre-Jean Lamy
- Laboratoire de Biologie Spécialisée, Centre Régional de Lutte contre le Cancer, Montpellier, France
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Cools I, Uyttendaele M, D'Haese E, Nelis HJ, Debevere J. Development of a real-time NASBA assay for the detection of Campylobacter jejuni cells. J Microbiol Methods 2006; 66:313-20. [PMID: 16443295 DOI: 10.1016/j.mimet.2005.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 12/14/2005] [Accepted: 12/19/2005] [Indexed: 11/22/2022]
Abstract
The objectives of this study were the development of a real-time NASBA assay for the detection of Campylobacter jejuni mRNA and the evaluation of its potential to determine the viability of the detected C. jejuni cells. A set of specific primers and probes was chosen to amplify the mRNA of the tuf-gene and the GTPase-gene. Only the tuf-assay was able to detect as low as 10(2) cells per NASBA reaction and was specific for Campylobacter. However, as the assay was able to detect dead cells, it cannot be used to demonstrate the viability of C. jejuni cells. The tuf-gene mRNA is no good viability indicator due to its stability.
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Affiliation(s)
- Ils Cools
- Laboratory of Food Microbiology and Food Preservation, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Gent, Belgium
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Lau LT, Fung YWW, Yu ACH. Detection of animal viruses using nucleic acid sequence-based amplification (NASBA). Dev Biol (Basel) 2006; 126:7-15; discussion 323. [PMID: 17058476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
As seen in recent avian influenza outbreaks in Asia, prevention is the key to fighting infectious disease successfully. Efficient disease surveillance systems on the basis of molecular diagnostics will help monitor the emergence of viruses in the early stage and thus prompt containment measures can be in place to minimize disease spread. Here we describe and review molecular diagnostics focusing on nucleic acid sequence-based amplification (NASBA) technology in detecting viruses causing animal diseases, such as avian influenza, foot-and-mouth disease, and Newcastle disease. NASBA offers high sensitivity, specificity, accuracy, and speed of availability of results, and NASBA would be the most applicable molecular diagnostics for disease surveillance and control.
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Affiliation(s)
- L T Lau
- Hong Kong DNA Chips Ltd, Hang Tung Resources Centre, Shau Kei Wan, China
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Sawyer J, Wakeley P, West D, Fearnley C, Anderson S, Flowers M, Webster K, Errington J, Williams R. Practical experiences of moving molecular diagnostics into routine use at the Veterinary Laboratories Agency. Dev Biol (Basel) 2006; 126:89-97; discussion 324-5. [PMID: 17058484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The practical bench application of molecular tests (here defined as nucleic acid-based tests) in a routine testing situation is not without its challenges. This paper outlines the approaches we take at the Veterinary Laboratories Agency (VLA) and highlights some of the practical issues which we have found to be important for the successful introduction and use of molecular tests in a routine testing environment. The potential advantages of molecular tests, and factors which dictate which tests are adopted for routine testing, are discussed before giving some examples of molecular tests in routine use at the VLA. The instrumentation, reagents and assays we use are outlined, followed by sections of how we approach validation and how we manage and resource the transfer of molecular tests into routine use.
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Affiliation(s)
- J Sawyer
- Veterinary Laboratories Agency, Biotechnology Department Weybridge, Addlestone, UK.
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Abd el-Galil KH, el-Sokkary MA, Kheira SM, Salazar AM, Yates MV, Chen W, Mulchandani A. Real-time nucleic acid sequence-based amplification assay for detection of hepatitis A virus. Appl Environ Microbiol 2005; 71:7113-6. [PMID: 16269748 PMCID: PMC1287728 DOI: 10.1128/aem.71.11.7113-7116.2005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A nucleic acid sequence-based amplification (NASBA) assay in combination with a molecular beacon was developed for the real-time detection and quantification of hepatitis A virus (HAV). A 202-bp, highly conserved 5' noncoding region of HAV was targeted. The sensitivity of the real-time NASBA assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, with only HAV positively identified. When combined with immunomagnetic separation, the NASBA assay successfully detected as few as 10 PFU from seeded lake water samples. Due to its isothermal nature, its speed, and its similar sensitivity compared to the real-time RT-PCR assay, this newly reported real-time NASBA method will have broad applications for the rapid detection of HAV in contaminated food or water.
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Rutjes SA, Italiaander R, van den Berg HHJL, Lodder WJ, de Roda Husman AM. Isolation and detection of enterovirus RNA from large-volume water samples by using the NucliSens miniMAG system and real-time nucleic acid sequence-based amplification. Appl Environ Microbiol 2005; 71:3734-40. [PMID: 16000783 PMCID: PMC1169005 DOI: 10.1128/aem.71.7.3734-3740.2005] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Concentration of water samples is a prerequisite for the detection of the low virus levels that are present in water and may present a public health hazard. The aim of this study was to develop a rapid, standardized molecular method for the detection of enteroviruses in large-volume surface water samples, using a concentration method suitable for the detection of infectious viruses as well as virus RNA. Concentration of water was achieved by a conventional filter adsorption-elution method and ultrafiltration, resulting in a 10,000-fold concentration of the sample. Isolation of virus RNA by a silica-based RNA extraction method was compared with the nonmagnetic and magnetic NucliSens RNA isolation methods. By using the silica-based RNA extraction method in two out of five samples, enterovirus RNA was detected, whereas four out of five samples were positive following RNA isolation with magnetic silica beads. Moreover, estimated RNA levels increased at least 100 to 500 times. Furthermore, we compared enterovirus detection by an in-house reverse transcription (RT)-PCR with a novel commercially available real-time nucleic acid sequence-based amplification (NASBA) assay. We found that the rapid real-time NASBA assay was slightly less sensitive than our in-house RT-PCR. The advantages, however, of a commercial real-time NASBA assay, like the presence of an internal control RNA, standardization, and enormous decrease in turnaround time, makes it an attractive alternative to RT-PCR.
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Affiliation(s)
- Saskia A Rutjes
- National Institute for Public Health and the Environment (RIVM), Microbiological Laboratory for Health Protection (MGB), Health-Related Water Microbiology, P.O. Box 1/Antonie van Leeuwenhoeklaan 9, 3720 BA Bilthoven, The Netherlands.
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Landry ML, Garner R, Ferguson D. Real-time nucleic acid sequence-based amplification using molecular beacons for detection of enterovirus RNA in clinical specimens. J Clin Microbiol 2005; 43:3136-9. [PMID: 16000425 PMCID: PMC1169110 DOI: 10.1128/jcm.43.7.3136-3139.2005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time nucleic acid sequence-based amplification (NASBA) using molecular beacon technology (NASBA-beacon) was compared to standard NASBA with postamplification hybridization using electrochemiluminescently labeled probes (NASBA-ECL) for detection of enteroviruses (EV) in 133 cerebrospinal fluid and 27 stool samples. NASBA-ECL and NASBA-beacon were similar in sensitivity, detecting 55 (100%) and 52 (94.5%) EV-positive samples, respectively. There were no false positives. Both NASBA assays were significantly more sensitive than culture. Real-time NASBA-beacon reagents and equipment rental were more expensive than those for NASBA-ECL; however, time to result was shortened by 1.5 h, hands-on time was reduced by 25 min, and the assay was much simpler for technologists to learn and perform.
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Affiliation(s)
- Marie L Landry
- Department of Laboratory Medicine, P.O. Box 208035, Yale University School of Medicine, New Haven, CT 06520-8035, USA.
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Ginocchio CC, Zhang F, Malhotra A, Manji R, Sillekens P, Foolen H, Overdyk M, Peeters M. Development, technical performance, and clinical evaluation of a NucliSens basic kit application for detection of enterovirus RNA in cerebrospinal fluid. J Clin Microbiol 2005; 43:2616-23. [PMID: 15956374 PMCID: PMC1151940 DOI: 10.1128/jcm.43.6.2616-2623.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The combination of nucleic acid sequence-based amplification and electrochemiluminescence detection was used to develop an internally controlled, highly sensitive and specific assay for the detection of enterovirus (EV) RNA in cerebrospinal fluid (CSF). The analytical performance of the assay was determined using both in vitro-transcribed EV RNAs and viral culture isolates. The sensitivity of the assay was 10 EV RNA copies per amplification reaction. The assay detected all enteroviral isolates tested with no cross-reactivity to 21 nonenteroviral species, including rhinovirus and parechovirus. The clinical performance of the assay was evaluated by testing 992 CSF specimens collected from adult and pediatric patients. NucliSens EV results from a subset of 327 CSF samples were compared to viral culture of nasopharyngeal specimens and rectal swabs (n = 195) and/or CSF (n = 212). Of the 212 CSF samples, 96 samples were positive by either the NucliSens EV assay (94/96; 97.9%) or culture (63/96; 65.6%), and 61/96 (63.5%) were positive by both methods. The inclusion of an EV-specific internal control monitored the entire process, including the efficiency of nucleic acid extraction, amplification, and detection. In total, only five blood-clotted CSF samples (0.5%) were inhibited. The NucliSens EV assay demonstrated superior sensitivity over viral culture (P < 0.001), excellent specificity, clear delineation of positive samples, and minimal amplification inhibition.
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Affiliation(s)
- Christine C Ginocchio
- North Shore-Long Island Jewish Health System Laboratories, 10 Nevada Drive, Lake Success, NY 11042, USA.
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Ayele W, Baar MPD, Goudsmit J, Kliphuis A, Tilahun T, Dorigo-Zetsma W, Wolday D, Abebe A, Mengistu Y, Pollakis G. Surveillance technology for HIV-1 subtype C in Ethiopia: an env-based NASBA molecular beacon assay to discriminate between subcluster C and C'. J Virol Methods 2005; 130:22-9. [PMID: 16040135 DOI: 10.1016/j.jviromet.2005.05.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 05/20/2005] [Accepted: 05/23/2005] [Indexed: 11/26/2022]
Abstract
Forty-nine samples with known C2V3 sequences were used for the evaluation of an env-based molecular beacon assay to distinguish between the two genetic subclusters C and C' which characterize the HIV-1 epidemic in Ethiopia. Two subcluster C and two subcluster C' beacons targeting two different loci in the C2V3 region were developed. Using a three beacon-based (2C and 1C'=C prime), isothermal amplification assay, concordance with DNA sequencing was achieved for 43 (87.8%) samples. Sensitivity was 81.8% and specificity 97.4% for subcluster C beacons. For the subcluster C' beacon, a sensitivity of 97% and a specificity of 87.5% was achieved. Five samples were ambiguous by sequencing of which two samples were subcluster C' by the beacon assay and one subcluster C. Two of the samples remained ambiguous with different beacon-pair combinations as well. From samples with a clear C or C' phylogeny by sequencing, three were undetected by the first-line beacon genotyping assay. Genotype ambiguity was resolved in the three samples using beacon pair combinations restricted to each targeted locus. The beacons were evaluated further in a panel including all HIV-1 subtypes. Four of five subtype C isolates were identified correctly, and no cross-reactivity was observed with other subtypes.
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Affiliation(s)
- Workenesh Ayele
- Ethio-Netherlands AIDS Research Project at Ethiopian Health and Nutrition Research Institute (EHNRI), P.O. Box 1242, Addis Abeba, Ethiopia.
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Gulliksen A, Solli LA, Drese KS, Sörensen O, Karlsen F, Rogne H, Hovig E, Sirevåg R. Parallel nanoliter detection of cancer markers using polymer microchips. Lab Chip 2005; 5:416-20. [PMID: 15791339 DOI: 10.1039/b415525d] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A general multipurpose microchip technology platform for point-of-care diagnostics has been developed. Real-time nucleic acid sequence-based amplification (NASBA) for detection of artificial human papilloma virus (HPV) 16 sequences and SiHa cell line samples was successfully performed in cyclic olefin copolymer (COC) microchips, incorporating supply channels and parallel reaction channels. Samples were distributed into 10 parallel reaction channels, and signals were simultaneously detected in 80 nl volumes. With a custom-made optical detection unit, the system reached a sensitivity limit of 10(-6) microM for artificial HPV 16 sequences, and 20 cells microl(-1) for the SiHa cell line. This is comparable to the detection limit of conventional readers, and clinical testing of biological samples in polymer microchips using NASBA is therefore possible.
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Lambert AJ, Nasci RS, Cropp BC, Martin DA, Rose BC, Russell BJ, Lanciotti RS. Nucleic acid amplification assays for detection of La Crosse virus RNA. J Clin Microbiol 2005; 43:1885-9. [PMID: 15815013 PMCID: PMC1081376 DOI: 10.1128/jcm.43.4.1885-1889.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 10/22/2004] [Accepted: 12/20/2004] [Indexed: 11/20/2022] Open
Abstract
We report the development of nucleic acid sequence-based amplification (NASBA) and quantitative real-time reverse transcription (RT)-PCR assays for the detection of La Crosse (LAC) virus in field-collected vector mosquito samples and human clinical samples. The sensitivities of these assays were compared to that of a standard plaque assay in Vero cells. The NASBA and quantitative real-time RT-PCR assays demonstrated sensitivities greater than that of the standard plaque assay. The specificities of these assays were determined by testing a battery of reference strain viruses, including representative strains of LAC virus and other arthropod-borne viruses. Additionally, these assays were used to detect LAC viral RNA in mosquito pool samples and human brain tissue samples and yielded results within less than 4 h. The NASBA and quantitative real-time RT-PCR assays detect LAC viral RNA in a sensitive, specific, and rapid manner; these findings support the use of these assays in surveillance and diagnostic laboratory systems.
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Affiliation(s)
- Amy J Lambert
- Division of Vector-Borne Infectious Diseases, National Centers for Infectious Diseases, CDC, Rampart Rd., Fort Collins, CO 80521, USA.
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Capaul SE, Gorgievski-Hrisoho M. Detection of enterovirus RNA in cerebrospinal fluid (CSF) using NucliSens EasyQ Enterovirus assay. J Clin Virol 2005; 32:236-40. [PMID: 15722029 DOI: 10.1016/j.jcv.2004.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2004] [Indexed: 10/26/2022]
Abstract
Rapid detection of enterovirus (EV) infections is essential in the management of aseptic meningitis. Molecular approaches have opened the way to such rapid, but also specific and sensitive, diagnostic tests. The aim of this study was to compare the performance of the CE marked NucliSens EasyQ Enterovirus assay with an in-house two-step RT-PCR assay using cerebrospinal fluid (CSF) and throat swab samples. In addition, specificity was tested with clinical isolates positive for viruses with clinical importance in CSF samples. For nucleic acid extraction, the NucliSens miniMAG and NucliSens magnetic extraction reagents were used. Subsequently real-time nucleic acid sequence-based amplification (NASBA) RNA amplification was performed using NucliSens EasyQ basic kit reagents and NucliSens EasyQ Enterovirus reagents. An EV-specific internal homologous control (IC) RNA was used to monitor the entire NucliSens EasyQ procedure at the individual sample level. No IC but an external inhibition control was available for the RT-PCR method. For the NucliSens EasyQ procedure, amplification and real-time detection reactions were carried out in the NucliSens EasyQ analyzer. The real-time NASBA enterovirus detection was based on NASBA amplification and real-time molecular beacon technology. Data were analyzed using the manufacturer's software on the NucliSens EasyQ analyzer. For the in-house assay, RT-PCR amplicons were detected using agarose gel analysis. The analysis of clinical samples positive for HSV-1, HSV-2, adenovirus, CMV, VZV, mumps and rhinovirus were all negative by NucliSens EasyQ Enterovirus assay. Three rhinovirus samples were, however, strongly positive in RT-PCR. A total of 141 clinical samples were retrospectively tested, including 126 cerebrospinal fluid (CSF) samples and 15 throat swabs. The 91 CSF samples were negative by both methods, 31 CSF samples and 14 throat swab samples were positive by both methods. The four CSF samples were positive by RT-PCR only. One throat swab sample was negative in NucliSens EasyQ but positive in RT-PCR. The sensitivity and specificity of both methods seem to be more or less comparable. However, the in-house RT-PCR assay appears to amplify some rhinovirus strains and should therefore not be used for throat swab samples. NucliSens EasyQ Enterovirus assay gave more invalid results than the in-house RT-PCR, which is obvious taken into account the difference in quality control between the CE marked NucliSens EasyQ Enterovirus assay and the in-house enterovirus assay. The NucliSens EasyQ procedure can be completed within 5h versus 9.5h for the RT-PCR. NucliSens EasyQ Enterovirus assay showed to be a standardized, rapid, specific, sensitive and reliable procedure for the detection of enterovirus RNA.
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Affiliation(s)
- S E Capaul
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, CH-3010 Bern, Switzerland.
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Schneider P, Wolters L, Schoone G, Schallig H, Sillekens P, Hermsen R, Sauerwein R. Real-time nucleic acid sequence-based amplification is more convenient than real-time PCR for quantification of Plasmodium falciparum. J Clin Microbiol 2005; 43:402-5. [PMID: 15635001 PMCID: PMC540116 DOI: 10.1128/jcm.43.1.402-405.2005] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Determination of the number of malaria parasites by routine or even expert microscopy is not always sufficiently sensitive for detailed quantitative studies on the population dynamics of Plasmodium falciparum, such as intervention or vaccine trials. To circumvent this problem, two more sensitive assays, real-time quantitative nucleic acid sequence-based amplification (QT-NASBA) and real-time quantitative PCR (QT-PCR) were compared for quantification of P. falciparum parasites. QT-NASBA was adapted to molecular beacon real-time detection technology, which enables a reduction of the time of analysis and of contamination risk while retaining the specificity and sensitivity of the original assay. Both QT-NASBA and QT-PCR have a sensitivity of 20 parasites/ml of blood, but QT-PCR requires a complicated DNA extraction procedure and the use of 500 microl of venous blood to achieve this sensitivity, compared to 50 microl of finger prick blood for real-time QT-NASBA. Both techniques show a significant correlation to microscopic parasite counts, and the quantification results of the two real-time assays are significantly correlated for in vitro as well as in vivo samples. However, in comparison to real-time QT-PCR, the results of real-time QT-NASBA can be obtained 12 h earlier, with relatively easy RNA extraction and use of finger prick blood samples. The prospective development of multiplex QT-NASBA for detection of various P. falciparum developmental stages increases the value of QT-NASBA for malaria studies. Therefore, for studies requiring sensitive and accurate detection of P. falciparum parasites in large numbers of samples, the use of real-time QT-NASBA is preferred over that of real-time QT-PCR.
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Affiliation(s)
- Petra Schneider
- University Medical Centre Nijmegen, Medical Microbiology 188, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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Schneider P, Schoone G, Schallig H, Verhage D, Telgt D, Eling W, Sauerwein R. Quantification of Plasmodium falciparum gametocytes in differential stages of development by quantitative nucleic acid sequence-based amplification. Mol Biochem Parasitol 2005; 137:35-41. [PMID: 15279949 DOI: 10.1016/j.molbiopara.2004.03.018] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2003] [Revised: 02/25/2004] [Accepted: 03/17/2004] [Indexed: 11/22/2022]
Abstract
Two quantitative nucleic acid sequence-based amplification assays (QT-NASBA) based on Pfs16 and Pfs25, have been developed to quantify sexual stage commitment and mature gametocytes of Plasmodium falciparum. Pfs16 mRNA is expressed in all sexual forms including sexually committed ring stages while expression of Pfs25 mRNA is restricted to late stage gametocytes. Both assays showed a sensitivity of one sexual stage parasite/microl of blood. Blood samples from experimentally infected non-immune human volunteers were tested for Plasmodium falciparum by standard microscopy, a previously developed asexual 18S rRNA QT-NASBA, Pfs16 and Pfs25 mRNA QT-NASBA. Pfs16 QT-NASBA was positive in 9 out of 10 volunteers within 48 h after first detection of 18S rRNA, mostly before or at the day of positive microscopy. In contrast, the Pfs25 mRNA QT-NASBA was negative during the 28 days of follow-up, but consistently positive in gametocyte samples from naturally infected Kenyan patients. These data suggest that sexual stage commitment can occur early in the blood-stage infection without successful maturation into infectious gametocytes. In conclusion, Pfs16 and Pfs25 QT-NASBA assays in combination with a previously developed asexual stage QT-NASBA allow for the separate quantification of all developmental stages present in the circulation. The application of sexual stage QT-NASBA assays may contribute to a better understanding of the biology and epidemiology of malaria transmission.
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Affiliation(s)
- Petra Schneider
- Department of Medical Microbiology, University Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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