Diagnostic activities for plant pests
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NPDN Newsletter | National Plant Diagnostic Network

August Highlights of the newsletter:

• Emerald ash borer found in Kansas
• NPDN Regional Directors awards recipients
• Diagnostic tip: isolating Phialophora gregata
• USDA seeking comment on chrysanthemum white rust
• National Repository tips

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Diagnostic activities for plant pests
Information on diagnostic activities on pests and diseases of plants follow the activities of EPPO Panels on diagnostics
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EPPO and Diagnostics for plant pests of quarantine significance

EPPO and Diagnostics for plant pests of quarantine significance | Diagnostic activities for plant pests | Scoop.it

 

'Diagnostic activities for plant pests' is maintained by the Secretariat of the European and Mediterranean Plant Protection Organization (EPPO) and its aim is to share information on diagnostics.

 

EPPO is an intergovernmental organization created in 1951 which currently has 50 member countries. EPPO is responsible for harmonization and cooperation among the National Plant Protection Organizations (official authorities) of its member countries. EPPO helps its members in their efforts to protect plant health in agriculture, forestry and the uncultivated environment (standard-setting activities and exchange of information).

 

EPPO has established a programme on diagnostics since 1992

view the approved diagnostic protocols on the EPPO official website:

http://archives.eppo.int/EPPOStandards/diagnostics.htm

 

On this website, a page dedicated to EPPO activities on diagnostics is also available at: http://www.eppo.int/QUARANTINE/diagnostic_activities.htm

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The EPPO Secretariat maintains other scoop.it magazines onPest Risk Analysis (http://www.scoop.it/t/pest-risk-analysis) Pest Alerts (http://www.scoop.it/t/pest-alerts), Invasive Alien Plants (http://www.scoop.it/t/invasive-alien-plants), Video of plant pests (http://www.scoop.it/t/pests-on-videos), Communication on pests (http://www.scoop.it/t/communication-and-citizen-sciences-on-pests-and-invasive-alien-species)

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Isolation of the bacterium Xylella fastidiosa from plant samples Anses LSV Angers

This video presents the preparation of plant samples for the isolation of Xylella fastidiosa and gives some tips.
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Short report of the last Panel on Diagnostics in Bacteriology 2016-06-01/02

Short report of the last Panel on Diagnostics in Bacteriology 2016-06-01/02 | Diagnostic activities for plant pests | Scoop.it
Read a short report of the last Panel meeting in June where the three diagnostic protocols were finalized and later proposed for adoption. All three protocols are now approved and the one on Xylella fastidiosa is available through the EPPO Global Database. 
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EPPO Bulletin - Revised protocol on Xylella fastidiosa (PM 7/24 (2))

EPPO Bulletin - Revised protocol on Xylella fastidiosa (PM 7/24 (2)) | Diagnostic activities for plant pests | Scoop.it
The revised protocol on Xylella fastidiosa (PM 7/24 (2))  has been published and is available as early view. It should be noted that as more experience with the diagnostic of Xylella fastidiosa will be gathered in the coming months, the EPPO Secretariat intends to schedule a review of the Protocol at the next Panel on Diagnostics in Bacteriology in 2017-05.
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Development of reverse transcription loop-mediated isothermal amplification assay as a simple detection method of Chrysanthemum stem necrosis virus in chrysanthemum and tomato

Development of reverse transcription loop-mediated isothermal amplification assay as a simple detection method of Chrysanthemum stem necrosis virus in chrysanthemum and tomato | Diagnostic activities for plant pests | Scoop.it
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Xylella in Apulia: an EFSA review found no evidence of multiple types

Xylella in Apulia: an EFSA review found no evidence of multiple types | Diagnostic activities for plant pests | Scoop.it
Read the EFSA Statement on diversity of Xylella fastidiosa subsp pauca in Apulia
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Euroreference

Euroreference | Diagnostic activities for plant pests | Scoop.it
The Euroreference magazine is now available in a new formula, produced jointly by a group of agencies from several Member States of the European Union. Euroreference is a European journal created by ANSES in 2009. It deals specifically with reference activities in the areas of animal health, plant health, and food and drinking water safety. Its new formula is based on an editorial committee of 15 European partners, making the new Euroreference a collective publication devoted to better dissemination of knowledge at the European and international scales. It offers scientific and technical articles of interest to health protection laboratories and agencies involved in reference activities in Europe. Euroreference is thus designed to help enhance efficiency in European reference activities.
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Generic RT-PCR tests for detection and identification of tospoviruses

A set of tests for generic detection and identification of tospoviruses has been developed. Based on a multiple sequence alignment of the nucleocapsid gene and its 5′ upstream untranslated region sequence from 28 different species, primers were designed for RT-PCR detection of tospoviruses from all recognized clades, i.e. the American, Asian and Eurasian clades, and from the small group of distinct and floating species. Pilot experiments on isolates from twenty different species showed that the designed primer sets successfully detected all species by RT-PCR, as confirmed by nucleotide sequence analysis of the amplicons. In a final optimized design, the primers were applied in a setting of five RT-PCR tests. Seven different tospoviruses were successfully identified from diagnostic samples and in addition a non-described tospovirus species from alstroemeria plants. The results demonstrate that the newly developed generic RT-PCR tests provide a relevant tool for broad detection and identification of tospoviruses in plant quarantine and diagnostic laboratories.
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An EPPO Diagnostic protocl on generic detection of tospoviruses is in preparation (it will also include specifc tospoviruses)
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Short report of the last EPPO Panel on Diagnostics and Quality Assurance

Short report of the last EPPO Panel on Diagnostics and Quality Assurance | Diagnostic activities for plant pests | Scoop.it
Read this short report to learn about the topics discussed during the last Panel 
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New EPPO Diagnotic protocols published- EPPO Bulletin -

New EPPO Diagnotic protocols published- EPPO Bulletin - | Diagnostic activities for plant pests | Scoop.it
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PM 7/123 (1) Phytophthora lateralis 
PM 7/124 (1) Spodoptera littoralis, Spodoptera litura, Spodoptera frugiperda, Spodoptera eridania 
PM 7/125 (1) ELISA tests for viruses 
PM 7/126 (1) Electron microscopy in diagnosis of plant viruses

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Inter-laboratory comparison of four RT-PCR based methods for the generic detection of pospiviroids in tomato leaves and seeds - Online First - Springer

Inter-laboratory comparison of four RT-PCR based methods for the generic detection of pospiviroids in tomato leaves and seeds - Online First - Springer | Diagnostic activities for plant pests | Scoop.it

Four pospiviroid detection methods
consisting of a pair of RT-PCR (ANSES 1-2), a pair of
real time RT-PCR (Botermans 1-2) and two single RTPCR
methods (Luigi and Olivier) were evaluated for
their relative accuracy, diagnostic sensitivity, diagnostic
specificity, analytical sensitivity and reproducibility
through a comparison in eight laboratories. All detection
methods were tested on 13 tomato leaf and nine tomato
seed samples as well as on 100-fold dilutions of the
corresponding RNA extracts. Two different RNA extraction
kits and three combinations of RNA extraction
and RT-PCR kits were assessed. According to the statistical
analysis of the results, ANSES 1-2 method provided
the best performance criteria whatever the matrix

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An EPPO  diagnostic protocol on the generic detection of pospiviroids is in preparation 

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Free online training course on classification and identification of Arthropods and Nematodes opening soon!

Free online training course on classification and identification of Arthropods and Nematodes opening soon! | Diagnostic activities for plant pests | Scoop.it
This MOOC (in French and English) will deliver 5 weeks of course material and other pedagogical activities covering the following topics: Classification of arthropods and nematodes Collection and trapping methods Morphological and molecular identification methods Application of these integrative concepts for agroecosystem management through case studies
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Quarantine Regulations and the Impact of Modern Detection Methods - Annual Review of Phytopathology, 54(1):189

Producers worldwide need access to the best plant varieties and cultivars available to be competitive in global markets. This often means moving plants across international borders as soon as they are available. At the same time, quarantine agencies are tasked with minimizing the risk of introducing exotic pests and pathogens along with imported plant material, with the goal to protect domestic agriculture and native fauna and flora. These two drivers, the movement of more plant material and reduced risk of pathogen introduction, are at odds. Improvements in large-scale or next-generation sequencing (NGS) and bioinformatics for data analysis have resulted in improved speed and accuracy of pathogen detection that could facilitate plant trade with reduced risk of pathogen movement. There are concerns to be addressed before NGS can replace existing tools used for pathogen detection in plant quarantine and certification programs. Here, we discuss the advantages and possible pitfalls of this technology for meeting the needs of plant quarantine and certification.
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A very good article on NGS , plant quarantine and certification
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Rapid loop-mediated isothermal amplification assays for grapevine yellows phytoplasmas on crude leaf-vein homogenate has the same performance as qPCR

Rapid loop-mediated isothermal amplification assays for grapevine yellows phytoplasmas on crude leaf-vein homogenate has the same performance as qPCR | Diagnostic activities for plant pests | Scoop.it
A fluorescence-based real-time loop-mediated isothermal amplification (LAMP) assay for ‘Candidatus Phytoplasama solani’ (Bois noir phytoplasma; BNp) detection was developed and optimised for rapid lab
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10th Meeting of the Panel on Diagnostics in Nematology

10th Meeting of the Panel on Diagnostics in Nematology | Diagnostic activities for plant pests | Scoop.it
Read a summary on the main issues discussed during the last meeting of the EPPO Panel on Diagnostics in Nematology
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A robust and specific real-time PCR tool for the detection of Phytophthora lateralis in plant tissues

A robust and specific real-time PCR tool for the detection of Phytophthora lateralis in plant tissues | Diagnostic activities for plant pests | Scoop.it

Phytophthora lateralis is an oomycete responsible for Port-Orford Cedar (Chamaecyparis lawsoniana) dieback and mortality.

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Behind the scenes at one of Australia's biggest and oldest insect collections

Behind the scenes at one of Australia's biggest and oldest insect collections | Diagnostic activities for plant pests | Scoop.it
From the beauty of iridescent blue butterflies to tiny, unassuming brown beetles, there is a story behind every one of the estimated 650,000 specimens in one of Australia's oldest insect collections.
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EPPO Bulletin - Volume 46, Issue 2 - August 2016 - Wiley Online Library

EPPO Bulletin - Volume 46, Issue 2 - August 2016 - Wiley Online Library | Diagnostic activities for plant pests | Scoop.it
Revised EPPO diagnostic protocols published! they are freely available online
PM 7/41 (3) Meloidogyne chitwoodi and Meloidogyne fallax
PM 7/103 (2) Meloidogyne enterolobii 
PM 7/42 (3) Clavibacter michiganensis subsp. michiganensis 
PM 7/60 (2) Pantoea stewartii subsp. stewartii 
PM 7/77 (2) Documentation and reporting on a diagnosis 
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dPCR EXPERIENCE WORKSHOP Practical workshop on different dPCR platforms 5th – 7th October 2016, National Institute of Biology, Ljubljana, Slovenia

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A training course on digital PCR
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A revision of the EPPO Diagnostic Protocol on Xylella fastidiosa sent for EPPO Member Country Consultation 

A revision of the EPPO Diagnostic Protocol on Xylella fastidiosa sent for EPPO Member Country Consultation  | Diagnostic activities for plant pests | Scoop.it
A revised version of the EPPO Diagnostic Protocol on Xylella fastidiosa was prepared by an Expert Working Group and in consultation with experts from Brazil and North America (see section acknowledgements for details).
This revised Standard has been sent for Country Consultation.  According to the EPPO Standard setting procedures comment should only be made through the National Plant Protection Organization official contact point . 
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A revision of the EPPO Diagnostic Protocol on Xylella fastidiosa sent for EPPO Member Country Consultation
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PM 7/079 (2) Grapevine flavescence dorée phytoplasma -  published

PM 7/079 (2) Grapevine flavescence dorée phytoplasma -  published | Diagnostic activities for plant pests | Scoop.it
A revision of the EPPO Diagnostic Protocol on Grapevine flavescence dorée phytoplasma  has been published in the EPPO bulletin. 
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New molecular tests included
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Testa - EPPO Conference on diagnostics for plant pests

Testa - EPPO Conference on diagnostics for plant pests | Diagnostic activities for plant pests | Scoop.it

The EPPO-TESTA Conference was organized in Angers on 2015-11-30/12-02 at the kind invitation of the Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail (ANSES, FR) and of the Groupe d'Etude et de contrôle des Variétés et des Semences (GEVES, FR)

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Read the summary of the meeting and the main conclusions and recommendations

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Assessment of a new qPCR tool for the detection and identification of the root-knot nematode Meloidogyne enterolobii by an international test performance study - Springer

Assessment of a new qPCR tool for the detection and identification of the root-knot nematode Meloidogyne enterolobii by an international test performance study - Springer | Diagnostic activities for plant pests | Scoop.it
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Simultaneous detection of Clavibacter michiganensis subsp. michiganensis, Pepino mosaic virus and Mexican papita viroid by non-radioactive molecular hybridization using a unique polyprobe - Springer

Simultaneous detection of Clavibacter michiganensis subsp. michiganensis, Pepino mosaic virus and Mexican papita viroid by non-radioactive molecular hybridization using a unique polyprobe - Springer | Diagnostic activities for plant pests | Scoop.it

Clavibacter michiganensis subsp. michiganensis, Pepino mosaic virus, and Mexican papita viroidare three economically important pathogens that infect tomato crops. In this work, a polyprobe (poly-3) was developed and evaluated for the simultaneous detection of these pathogens in tomato plants by non-isotopic molecular hybridization. The endpoint detection limit of the poly-3 with C. michiganensis subsp. michiganensis cell cultures was 106 CFU/ml. No differences were found in terms of the sensitivity and specificity when the individual riboprobes were compared to the poly-3 for the detection of the three pathogens. The analysis of 80 tomato field samples by the poly-3 and RT-PCR techniques rendered the same number of positive samples for each pathogen. As far as we know this is the first time that three pathogens with very different life cycle styles (bacteria, virus and viroid) are simultaneously detected in a single assay. The possibility of using this poly-3 technology for the routine diagnosis of field tomato samples is discussed.

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