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Open AccessArticle

Validation of a Preformulated, Field Deployable, Recombinase Polymerase Amplification Assay for Phytophthora Species

1
Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
2
Ottawa Plant Laboratory, Canadian Food Inspection Agency, 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada
3
Plant Pest Diagnostics Branch, California Department of Food and Agriculture, Sacramento, CA 95832, USA
4
Crop Improvement and Protection Research Unit, U.S. Department of Agriculture Agricultural Research Service, Salinas, CA 93905, USA
*
Authors to whom correspondence should be addressed.
Plants 2020, 9(4), 466; https://doi.org/10.3390/plants9040466
Received: 22 February 2020 / Revised: 27 March 2020 / Accepted: 1 April 2020 / Published: 7 April 2020
(This article belongs to the Special Issue Detection and Diagnostics of Fungal and Oomycete Plant Pathogens)
Recombinase polymerase amplification (RPA) assays are valuable molecular diagnostic tools that can detect and identify plant pathogens in the field without time-consuming DNA extractions. Historically, RPA assay reagents were commercially available as a lyophilized pellet in microfuge strip tubes, but have become available in liquid form more recently—both require the addition of primers and probes prior to use, which can be challenging to handle in a field setting. Lyophilization of primers and probes, along with RPA reagents, contained within a single tube limits the risk of contamination, eliminates the need for refrigeration, as the lyophilized reagents are stable at ambient temperatures, and simplifies field use of the assays. This study investigates the potential effect of preformulation on assay performance using a previously validated Phytophthora genus-specific RPA assay, lyophilized with primers and probes included with the RPA reagents. The preformulated lyophilized Phytophthora RPA assay was compared with a quantitative polymerase chain reaction (qPCR) assay and commercially available RPA kits using three qPCR platforms (BioRad CFX96, QuantStudio 6 and Applied Biosystems ViiA7) and one isothermal platform (Axxin T16-ISO RPA), with experiments run in four separate labs. The assay was tested for sensitivity (ranging from 500 to 0.33 pg of DNA) and specificity using purified oomycete DNA, as well as crude extracts of Phytophthora-infected and non-infected plants. The limit of detection (LOD) using purified DNA was 33 pg in the CFX96 and ViiA7 qPCR platforms using the preformulated kits, while the Axxin T16-ISO RPA chamber and the QuantStudio 6 platform could detect down to 3.3 pg with or without added plant extract. The LOD using a crude plant extract for the BioRad CFX96 was 330 pg, whereas the LOD for the ViiA7 system was 33 pg. These trials demonstrate the consistency and uniformity of pathogen detection with preformulated RPA kits for Phytophthora detection when conducted by different labs using different instruments for measuring results. View Full-Text
Keywords: diagnostics; isothermal amplification; oomycetes; point of care diagnostics diagnostics; isothermal amplification; oomycetes; point of care diagnostics
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MDPI and ACS Style

McCoy, A.G.; Miles, T.D.; Bilodeau, G.J.; Woods, P.; Blomquist, C.; Martin, F.N.; Chilvers, M.I. Validation of a Preformulated, Field Deployable, Recombinase Polymerase Amplification Assay for Phytophthora Species. Plants 2020, 9, 466.

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