Diagnostic activities for plant pests
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ID Source

ID Source | Diagnostic activities for plant pests | Scoop.it

ID Source is a gateway to websites that help you identify plant pests, diseases, and weeds. Searchable for ID Aids on a pest by name, geographic region, commodity affected, and more. Developed through collaboration between USDA's Center for Plant Health Science and Technology (CPHST) and Colorado State University.

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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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Assessment of the genetic diversity of Xylella fastidiosa in imported ornamental Coffea arabica plants Bergsma-Vlami et al. 2017

Assessment of the genetic diversity of Xylella fastidiosa in imported ornamental Coffea arabica plants Bergsma-Vlami et al. 2017 | Diagnostic activities for plant pests | Scoop.it

A study has been performed in order to assess the presence of Xylella fastidiosa in imported ornamental plants, among them Olea europeae, Coffea arabica, and Nerium oleander.

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A diagnostic protocol has been developed - PM7/24.
http://onlinelibrary.wiley.com/doi/10.1111/epp.12327/epdf
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Isolation of Xylella fastidiosa from plant stem tissues - PONTEPROJECT

Isolation of Xylella fastidiosa from plant stem tissues - PONTEPROJECT | Diagnostic activities for plant pests | Scoop.it
A video showing the procedure to isolate Xylella fastidiosa from host plant stem tissues. The video was made in the laboratories of CNR-IPSP, Bari, Italy.
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Another video for the isolation of Xylella fastidiosa from plant material (see previous soop it for the one prepared by Anses (FR) 
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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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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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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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Several subspecies and sequence types are associated with the emergence of Xylella fastidiosa in natural settings in France Denance et al. 2017

Several subspecies and sequence types are associated with the emergence of Xylella fastidiosa in natural settings in France Denance et al. 2017 | Diagnostic activities for plant pests | Scoop.it

Xylella fastidiosa is a plant pathogenic bacterium emerging in Europe. In France its emergence has been evidenced through interceptions of contaminated coffee plants and in 2015 by the survey of natural settings. The first French contaminated focus was detected in 2015 in Corsica; then almost 300 foci and nearly 30 plant species were declared contaminated, with Polygala myrtifolia remaining the principal host suffering from severe leaf scorches. We report on the diversity of X. fastidiosa identified in France in 2015. Multilocus sequence analysis/typing revealed the presence of mainly X. fastidiosa subsp. multiplex ST6 and ST7. A focus of subspecies pauca ST53 was identified in mainland France; one sample contaminated by X. fastidiosa subsp. sandyi ST76, one novel recombinant, and co-infections of different isolates in individual samples were also identified, but could not be confirmed by successive samplings indicating limited or transient contaminations. Koch's postulates were fulfilled for two isolates of X. fastidiosa subsp. multiplex on P. myrtifolia one being ST6 and the other ST7. Comparative genomics of the genome sequences of three French isolates (one ST6 and two ST7), with available sequences revealed that unlike the American Dixon strain, the French ST6 and ST7 strains are devoid of a plasmid encoding a complete type IV secretion system. Other differences regarding phage sequences were highlighted. Altogether, our results suggest that the emergence of X. fastidiosa in France is linked to several introduction events of diverse strains from different subspecies.

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A diagnostic protocol has been developed - PM 7/24. 
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A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies | Virology  | Massart et al 2017

A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies | Virology  |  Massart et al 2017 | Diagnostic activities for plant pests | Scoop.it
Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time is also faced with substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.
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Use of Nested and Real-Time PCR for the Detection of Ceratocystis fagacearum in the Sapwood of Diseased Oak Species in Minnesota Yang & Juzwik 2017

Use of Nested and Real-Time PCR for the Detection of Ceratocystis fagacearum in the Sapwood of Diseased Oak Species in Minnesota Yang & Juzwik 2017 | Diagnostic activities for plant pests | Scoop.it
Oak wilt caused by Ceratocystis fagacearum is a significant disease of Quercus spp. in the eastern United States. Early and accurate detection of the pathogen is particularly important when disease control is planned. Nested and real-time polymerase chain reaction (PCR) methods utilizing fungal DNA extracted from sapwood drill shavings of red, bur, and white oak at different stages of disease development were compared with culture-based detection from sapwood. The pathogen was detected in all (n = 3) actively wilting branches of each of nine red oak trees using all three methods. The lowest detection rate (33% of assayed branches; 6 of 8 trees) for actively wilting branches was found for white oak using isolation while nested PCR had a branch detection rate of 100% (8 of 8 trees) and real-time PCR of 87% (8 of 8 trees) for the same samples. For both bur and white oak, the pathogen was not detected by isolation in branches over 1 year after their death but was detected using both PCR methods. Only the PCR assays detected the fungus in sapwood samples underlying remnants of sporulation mats (n = 21; 90%, nested and 62%, real-time) on red oak. These PCR methods offer several significant improvements for laboratory-based detection methods of C. fagacearum.
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4th meeting of the EPPO Panel on Diagnostics in Entomology
Paris, 2016-11-29/12-01

4th meeting of the EPPO Panel on Diagnostics in Entomology<br/>Paris, 2016-11-29/12-01 | Diagnostic activities for plant pests | Scoop.it

Read a short report of the  4th meeting of the EPPO Panel on Diagnostics in Entomology
Paris, 2016-11-29/12-01

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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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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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