A role for arrays in clinical virology: fact or fiction?

Clewley, Jonathan P.

doi:10.1016/j.jcv.2003.08.002

Cited by 37 publications

(16 citation statements)

References 97 publications

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“…Other arrays have been described for the rapid detection and serotyping of acute respiratory disease-associated adenoviruses (83), and for the simultaneous detection of herpesviruses, enteroviruses, and flaviviruses (84). Comprehensive microarrays representing the most up-to-date sequence information for all viral families have much promise for the detection of previously unidentified viruses, provided these have sufficient homology to the known viral sequences (85).…”

Section: Pan-viral Dna Microarraysmentioning

confidence: 99%

Molecular Amplification Methods in Diagnostic Virology

Whiley¹,

Sloots²

2010

Infectious Disease and Therapy

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Conventional PCR Detection MethodsPCR product detection was traditionally performed by direct visualization of the product using agarose gel electrophoresis with DNA-binding fluorescent dyes such as ethidium bromide. Gel-based methods, although laborious and dependent on subjective result interpretation, are still widely used in diagnostic virology, particularly for PCR-based sequencing and typing (10). In addition, gel-based visualization of PCR product remains an effective way for troubleshooting problems encountered using alternative detection methods. Thus, most diagnostic laboratories maintain gel-based methods to some extent.Enzyme immunoassays, including the enzyme-linked immunosorbent assay (ELISA), provided the first key advancement in PCR detection methodology. Briefly, the PCR-ELISA system used a colorimetric microtiter plate probe-based capture system whereby a 5 biotinylated oligonucleotide probe targeting a DNA sequence internal to the primers was used to capture Lennette's Laboratory Diagnosis of Viral Infections Downloaded from informahealthcare.com by Kainan University on 05/16/15For personal use only. MOLECULAR AMPLIFICATION METHODS IN DIAGNOSTIC VIROLOGY 21PCR product to streptavidin-coated wells (11). A major advantage of the PCR-ELISA over gel-based techniques is that it is objective, minimizing the potential for interpretation errors. In addition, the technology is particularly suitable for multiplex PCR reactions (discussed below) (12). PCR-ELISA was extensively used in "home-brew" assays as well as in several commercial assays targeting a variety of important viral pathogens, including human immunodeficiency virus (7) and hepatitis C virus (13). However, the PCR-ELISA technology has now been largely superseded by real-time PCR. Real-Time PCR DetectionThe advent of real-time PCR probably represents the greatest leap in DNA amplification technology since the development of PCR itself, and real-time PCR has been the key advancement in revolutionizing diagnostic virology. Briefly, real-time PCR is achieved through the use of fluorescent detection technology. Fluorescent molecules are added to a PCR reaction mix and interact with the PCR product to produce an increase in fluorescent signal when PCR amplification occurs. Monitoring of the fluorescent output is achieved through real-time PCR instrumentation, which measures the fluorescent signal during or following each thermal cycle. Thus, PCR amplification is monitored in "real-time," providing numerous advantages over conventional detection methods. From a practical perspective, real-time PCR removes the need for a separate detection step, which significantly reduces PCR result turnaround times and decreases staff hands on time. Also, the system is closed (i.e., reactions do not need to be opened for detection), reducing the potential for carryover contamination. The technology also provides an additional key performance characteristic, in that it has an extremely broad dynamic range for virus detection making it highly suitable for viral quan...

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Section: Pan-viral Dna Microarraysmentioning

confidence: 99%

Molecular Amplification Methods in Diagnostic Virology

Whiley¹,

Sloots²

2010

Infectious Disease and Therapy

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“…Real-time PCR is helping formulate answers to this and other questions by defining the fitness of the host though quantitation of the immune response to infection and antimicrobial therapies and also as a tool to quantify the damage caused. While micro-array technologies provide a comprehensive snap-shot of the state of the host or invading microbe's transcriptome, arrays do not permit reliable quantitation of the target change over a broad dynamic range (Lockhart and Winzeler, 2000;Clewley, 2004;Lucchini et al, 2001). Real-time PCR has increasingly become the method of choice for validating and further characterising experimental data generated by micro-arrays and is the favoured tool for determining gene transcript abundance in basic research, molecular medicine and biotechnology.…”

Section: Vvvvvv Host Immunity: Measuring the Response To A Microbementioning

confidence: 99%

Real-time Fluorescent PCR Techniques to Study Microbial–Host Interactions

Mackay

Arden

Nitsche

2004

Methods in Microbiology

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“…In addition to their already widespread use in differential gene expression experiments, DNA microarrays are increasingly being explored for use in diagnostic applications (3,23,28). Current applications of interest include the identification of risk for genetic diseases such as cancer, the detection of drug resistance in a wide variety of species, and the identification and subtyping of viral pathogens (28).…”

mentioning

confidence: 99%

Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus

et al. 2006

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DNA microarrays have proven to be powerful tools for gene expression analyses and are becoming increasingly attractive for diagnostic applications, e.g., for virus identification and subtyping. The selection of appropriate sequences for use on a microarray poses a challenge, particularly for highly mutable organisms such as influenza viruses, human immunodeficiency viruses, and hepatitis C viruses. The goal of this work was to develop an efficient method for mining large databases in order to identify regions of conservation in the influenza virus genome. From these regions of conservation, capture and label sequences capable of discriminating between different viral types and subtypes were selected. The salient features of the method were the use of phylogenetic trees for data reduction and the selection of a relatively small number of capture and label sequences capable of identifying a broad spectrum of influenza viruses. A detailed experimental evaluation of the selected sequences is described in a companion paper. The software is freely available under the General Public License at http://www.colorado.edu/chemistry/RGHP/software/.

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A role for arrays in clinical virology: fact or fiction?

Cited by 37 publications

References 97 publications

Molecular Amplification Methods in Diagnostic Virology

Molecular Amplification Methods in Diagnostic Virology

Real-time Fluorescent PCR Techniques to Study Microbial–Host Interactions

Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus

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