Electronic microarray assays for avian influenza and Newcastle disease virus

Lung, Oliver; Beeston, Anne; Ohene-Adjei, Samuel; Pasick, John; Hodko, Dalibor; Hughes, Kimberley Burton; Furukawa-Stoffer, Tara L.; Fisher, Mathew; Deregt, Dirk

doi:10.1016/j.jviromet.2012.07.005

Cited by 13 publications

(24 citation statements)

References 32 publications

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“…The combination of Reverse Transcription real-time, digital PCR with Sanger sequencing or applications of Next Generation Sequencing and oligonucleotide microarrays can give great results, but they are expensive and highly demanding for trained technician and elaborate equipment [39, 66, 67]. As an alternative, many protocols, based on techniques like restriction endonuclease analyses, peptide nucleic acid with gold nanoparticles assay, phage-capturing dot blot, in situ hybridization, RT-PCR, and probe-based real-time RT-PCR, were proposed [68–72].…”

Section: Discussionmentioning

confidence: 99%

Detection of Newcastle Disease Virus Minor Genetic Variants by Modified Single-Stranded Conformational Polymorphism Analysis

Rąbalski

Śmietanka

Minta

et al. 2014

BioMed Research International

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Newcastle disease and Avian Influenza are considered to be the most dangerous fowl diseases which may cause huge economic losses. Newcastle disease is caused by the enveloped, and single-stranded RNA virus (NDV, APMV-1; belonging to Paramyxoviridae family), which can be further divided into sixteen different genotypes grouped into five pathotypes according to their pathogenicity. It has been reported that low pathogenic virus can greatly increase its pathogenicity even during a single passage. Additionally, due to the widespread use of live vaccines, a mixture of two or more different viruses in one sample can be detected. Hence, there is a great need for establishment of fast, inexpensive, sensitive, and relatively simple diagnostic method for multistrain and quasispecies detection of NDV infection. In this paper we describe a diagnostic method based on RT-PCR followed by a modified version of single-stranded conformational polymorphism analysis using short DNA fragments of gene encoding viral F protein. The method allows for rapid diagnosis of genetic variant emerging from previously stable population which may prevent the spread of the pathogenic viral variant.

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Section: Discussionmentioning

confidence: 99%

Detection of Newcastle Disease Virus Minor Genetic Variants by Modified Single-Stranded Conformational Polymorphism Analysis

Rąbalski

Śmietanka

Minta

et al. 2014

BioMed Research International

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“…In contrast, AIV typing microarray tests can detect and provide additional information about the subtype detected in positive clinical samples compared with that obtained using realtime-PCR [20]. In contrast, AIV typing microarray tests can detect and provide additional information about the subtype detected in positive clinical samples compared with that obtained using realtime-PCR [20].…”

Section: Conventional Methods: Elisa and Pcrmentioning

confidence: 96%

Advanced nanotechnologies in avian influenza: Current status and future trends – A review

Moulick

Richtera

Milosavljević

et al. 2017

Analytica Chimica Acta

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In the last decade, the control of avian influenza virus has experienced many difficulties, which have caused major global agricultural problems that have also led to public health consequences. Conventional biochemical methods are not sufficient to detect and control agricultural pathogens in the field due to the growing demand for food and subsidiary products; thus, studies aiming to develop potent alternatives to conventional biochemical methods are urgently needed. In this review, emerging detection systems, their applicability to diagnostics, and their therapeutic possibilities in view of nanotechnology are discussed. Nanotechnology-based sensors are used for rapid, sensitive and cost-effective diagnostics of agricultural pathogens. The application of different nanomaterials promotes interactions between these materials and the virus, which enables researchers to construct portable electroanalytical biosensing analyser that should effectively detect the influenza virus. The present review will provide insights into the guidelines for future experiments to develop better techniques to detect and control influenza viruses.

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“…PCR primer and capture probe sequences were either identified from the literature, then used with or without modifications or were newly designed (Tables and ). Primer and probe design were performed as described previously (Lung et al., , ) using AlleleID ® v. 7.7 (Premier BioSoft International, Palo Alto, CA, USA), Clone Manager v 9.0 software (Scientific and Educational Software, Cary, NC, USA) and BioEdit (http://www.mbio.ncsu.edu/BioEdit/bioedit.html) using all publicly available sequences from NCBI. Primers were tested in silico using IDT's OligoAnalyzer 3.1 (http://www.idtdna.com/calc/analyzer), and any primers with self‐ and hetero‐dimers with a ΔG ≥ −11 kcal/mole were modified or screened out.…”

Section: Methodsmentioning

confidence: 99%

“… Reverse primers contain a complimentary tag sequence for Red Universal Reporter probe at the 5′ end (Lung et al., ). …”

Section: Methodsmentioning

confidence: 99%

“…The cartridge was washed five more times with His/Proclin ® buffer, incubated at 40°C for 60 s and washed once with high salt buffer (HSB, Nexogen Inc.). Hybridized amplicons were detected using a fluoresceinated reporter probe resuspended in HSB at 1 μM final concentration and a touchdown passive reporting protocol as described previously (Lung et al., ). All electronic microarray hybridizations were performed in duplicate, and a non‐template PCR control (NTC) was included in all experiments.…”

Section: Methodsmentioning

confidence: 99%

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A multiplex reverse transcription PCR and automated electronic microarray assay for detection and differentiation of seven viruses affecting swine

Erickson

Fisher

Furukawa-Stoffer

et al. 2017

Transbound Emerg Dis

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Microarray technology can be useful for pathogen detection as it allows simultaneous interrogation of the presence or absence of a large number of genetic signatures. However, most microarray assays are labour-intensive and time-consuming to perform. This study describes the development and initial evaluation of a multiplex reverse transcription (RT)-PCR and novel accompanying automated electronic microarray assay for simultaneous detection and differentiation of seven important viruses that affect swine (foot-and-mouth disease virus [FMDV], swine vesicular disease virus [SVDV], vesicular exanthema of swine virus [VESV], African swine fever virus [ASFV], classical swine fever virus [CSFV], porcine respiratory and reproductive syndrome virus [PRRSV] and porcine circovirus type 2 [PCV2]). The novel electronic microarray assay utilizes a single, user-friendly instrument that integrates and automates capture probe printing, hybridization, washing and reporting on a disposable electronic microarray cartridge with 400 features. This assay accurately detected and identified a total of 68 isolates of the seven targeted virus species including 23 samples of FMDV, representing all seven serotypes, and 10 CSFV strains, representing all three genotypes. The assay successfully detected viruses in clinical samples from the field, experimentally infected animals (as early as 1 day post-infection (dpi) for FMDV and SVDV, 4 dpi for ASFV, 5 dpi for CSFV), as well as in biological material that were spiked with target viruses. The limit of detection was 10 copies/μl for ASFV, PCV2 and PRRSV, 100 copies/μl for SVDV, CSFV, VESV and 1,000 copies/μl for FMDV. The electronic microarray component had reduced analytical sensitivity for several of the target viruses when compared with the multiplex RT-PCR. The integration of capture probe printing allows custom onsite array printing as needed, while electrophoretically driven hybridization generates results faster than conventional microarrays that rely on passive hybridization. With further refinement, this novel, rapid, highly automated microarray technology has potential applications in multipathogen surveillance of livestock diseases.

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Electronic microarray assays for avian influenza and Newcastle disease virus

Cited by 13 publications

References 32 publications

Detection of Newcastle Disease Virus Minor Genetic Variants by Modified Single-Stranded Conformational Polymorphism Analysis

Detection of Newcastle Disease Virus Minor Genetic Variants by Modified Single-Stranded Conformational Polymorphism Analysis

Advanced nanotechnologies in avian influenza: Current status and future trends – A review

A multiplex reverse transcription PCR and automated electronic microarray assay for detection and differentiation of seven viruses affecting swine

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