Multiplex RT-PCR detection and microarray typing of vesicular disease viruses

Lung, Oliver; Fisher, Mathew; Beeston, Anne; Hughes, Kimberley Burton; Clavijo, Alfonso; Goolia, Melissa; Pasick, John; Mauro, William; Deregt, Dirk

doi:10.1016/j.jviromet.2011.05.023

Cited by 37 publications

(31 citation statements)

References 27 publications

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“…A multiplex RT‐PCR assay, combined with microarray typing, was used to detect and type all serotypes of FMDV and vesicular stomatitis virus in one test protocol (Lung et al., ). Another multiplex PCR assay was able to screen samples for six different porcine pathogens that can present with similar clinical signs, including FMDV (Wernike et al., ).…”

Section: Introductionmentioning

confidence: 99%

Global Foot-and-Mouth Disease Research Update and Gap Analysis: 4 - Diagnostics

Knight-Jones

Robinson

Charleston

et al. 2016

Transbound Emerg Dis

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SummaryThis study assessed knowledge gaps in foot-and-mouth disease (FMD) research in the field of diagnostics. The study took the form of a literature review combined with research updates collected in 2014 from 33 institutes from around the world. Findings were used to identify priority areas for future FMD research.Molecular and genetic technologies, including sequencing, are developing at an increasing rate both in terms of capability and affordability. These advances potentiate progress in many other fields of research, from vaccine development to epidemiology. The development of RT-LAMP represents an important breakthrough allowing greater use and access to molecular diagnostics. It is now possible to determine virus serotype using PCR, although only for certain virus pools, continued progress is needed to cover the global spectrum of FMD viruses. Progress has also been made in the development of pen-side rapid diagnostics, some with the ability to determine serotype. However, further advances in pen-side serotype or strain determination would benefit both FMD-free countries and endemic countries with limited access to wellresourced laboratories.Novel sampling methods that show promise include air sampling and baited ropes, the latter may aid sampling in wildlife and swine. Studies of infrared thermography for the early detection of FMD have not been encouraging, although investigations are ongoing. Multiplex tests have been developed that are able to simultaneously screen for multiple pathogens with similar clinical signs. Crucial for assessing FMDV freedom, tests exist to detect animals that have been infected with FMDV regardless of vaccination status; however, limitations exist, particularly when testing previously vaccinated animals. Novel vaccines are being developed with complementary DIVA tests for this purpose. Research is also needed to improve the current imprecise approaches to FMD vaccine matching.The development of simple, affordable tests increases access to FMD diagnostics, greatly benefiting regions with limited laboratory capacity.

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Section: Introductionmentioning

confidence: 99%

Global Foot-and-Mouth Disease Research Update and Gap Analysis: 4 - Diagnostics

Knight-Jones

Robinson

Charleston

et al. 2016

Transbound Emerg Dis

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“…Following PCR, amplicons were visualized either on the QIAxcel instrument (Qiagen) or on a 1% agarose gel. The remainder of the amplified products were fluorescently labelled using the ARES Alexa Fluor 647 Labelling Kit (Life Technologies) as previously described [44]. Briefly, following amplification, PCR products were hydrolyzed to remove RNA and then purified using DNA Clean and Concentrator spin columns (Zymo Research, Irvine, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

“…Capture probe printing, hybridization, washing and reporting were performed as previously described [44]. Briefly, probes in 15 μL Pronto!…”

Section: Methodsmentioning

confidence: 99%

Microarray for Identification of the Chiropteran Host Species of Rabies Virus in Canada

et al. 2013

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Species identification through genetic barcoding can augment traditional taxonomic methods, which rely on morphological features of the specimen. Such approaches are especially valuable when specimens are in poor condition or comprise very limited material, a situation that often applies to chiropteran (bat) specimens submitted to the Canadian Food Inspection Agency for rabies diagnosis. Coupled with phenotypic plasticity of many species and inconclusive taxonomic keys, species identification using only morphological traits can be challenging. In this study, a microarray assay with associated PCR of the mitochondrial cytochrome c oxidase subunit I (COI) gene was developed for differentiation of 14 bat species submitted to the Canadian Food Inspection Agency from 1985–2012 for rabies diagnosis. The assay was validated with a reference collection of DNA from 153 field samples, all of which had been barcoded previously. The COI gene from 152 samples which included multiple specimens of each target species were successfully amplified by PCR and accurately identified by the microarray. One sample that was severely decomposed failed to amplify with PCR primers developed in this study, but amplified weakly after switching to alternate primers and was accurately typed by the microarray. Thus, the chiropteran microarray was able to accurately differentiate between the 14 species of Canadian bats targeted. This PCR and microarray assay would allow unequivocal identification to species of most, if not all, bat specimens submitted for rabies diagnosis in Canada.

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“…Primers (SVA_W_4F and SVA_W_4R) were designed for the SVA amplification (Table S1). Previously reported primers were used to amplify the other vesicular disease viruses (Lung et al., ). The test results demonstrated that all three vesicular fluids and six of nine coronary band samples were PCR positive for SVA.…”

Section: The Studymentioning

confidence: 99%