Progress 05/01/20 to 04/30/23
Outputs
Target Audience:Diagnostic assay developers and scientists with plant pathogen collections. American Phytopathological Society. Industries that rely on accurate diagnoses based on well-validated assays (importers, exporters, seed companies). Plant diagnostic laboratory personnel. USDA Animal Plant Health Inspection Service and State Plant regulatory laboratories. Researchers who conduct plant pathogen phyllogenetic research and holders of extensive pathogen type collections and genomic sequence data. Changes/Problems:Covid caused the project to be conducted entirely via Zoom sessions, which in hindsight was a blessing. We had more people hours and deliberation remotely than if we had tried to hold in-person meetings. What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?The concept of DAVN was presented at National and International conferences: The American Phytopathological Society Annual Meeting, Pittsburgh, Pennsylvania, August 8, 2022; National Plant Diagnostic Network (NPDN) National Meeting, UC Davis, Davis, California, April 26 - 30, 2022. Further, the participants were divided into 6 writing teams: The Need and a Vision for a diagnostic assay validation network - We propose the development of a Diagnostic Assay Validation Network (DAVN) system to provide coordinating resources at the national level and harmonize with our partners at the international level. State of the Field of Plant-Pathogen Diagnostic Assay Development and Validation - Evaluated 115 publications in peer-reviewed plant pathology journals from the past decade, reporting the development of new plant pathogen diagnostic assays, and collected data on the level of validation performed during performance testing of each assay. The objective of this study was to use this subsample to represent the status of the field and determine to what extent these published assays have been validated. The survey of publications finds that those detailing an appropriate and robust diagnostic assay validation process were few in number. Terminology and Guidelines for Diagnostic Assay Development and Validation: A Proposal for Best Practices - To increase awareness of common pitfalls and gaps encountered during this process with the goal of increased success in technology transfer. Recommendations are given for improving the efficiency and quality of test development through improved coordination among stakeholders. Knowledge Gaps, Research Needs, and Opportunities in Plant Disease Diagnostics Assay Development and Validation - These assessments should take into consideration the new technological and analytical advances available, the establishment of shared material, and data resources that will accelerate and facilitate progress in diagnostics development and validation. Here, we highlight some of the research opportunities available, in the context of anticipated needs. Communications Ecosystem to Support the Assay Validation Community - A Concept - A communications ecosystem to facilitate the sharing of such resources, as well as, to provide access to taxon and technology expertise will greatly accelerate the development, validation, and reliability of trusted diagnostic tests to support plant biosecurity, specifically, and plant health, in general. Standards of Diagnostic Validation: Recommendations for Reference Collections - recommend a framework for coordinated development, long-term maintenance, and accessibility of curated sets of pathogen data representing cultures and other reference material, that could serve the needs of pathogen diagnostics development, population studies, and resistance breeding efforts. A Focus Issue on PhytoFrontiers was developed which attracted >30 articles/perspectives/reviews. In total, 26 articles have been accepted and many of them are already in First Look. This PhytoFrontiers Focus Issue was developed not only to house the Perspectives derived from discussions among a large group of experts over several years during the NIFA seed grant but also to create a space for other perspectives and research papers specific to plant disease diagnostic assay validation. The primary objective of the Focus Issue was to raise awareness about the importance of assay validation for diagnostic accuracy. Among the peer-reviewed 16 research contributions to be included in the Focus Issue, across different diagnostic methods, manuscripts appeared describing validation research for three fungi, three Oomycetes, four viruses and a viroid, fruit flies and two nematodes, and five bacterial species. Sample matrices included soil, woody stems, leaves, fruits, tubers, and seeds. Methods were described for detection and diagnostics with sequencing and bioinformatic analysis, conventional PCR, rt qPCR, Recombinase polymerase amplification, and PMAqPCR. This range of taxa, sample matrices, and diagnostic platforms and methods provides a sobering snapshot of the sheer breadth of the needs of the plant health community for accurate and reliable diagnostic tools. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The DALN Seed Grant was designed to work toward a common understanding of the framework for a Diagnostic Assay Laboratory Network among subject matter experts in the field of plant pathology. We have had 50+ meetings for the development of a grant proposal for the Diagnostic Assay Validation Network (DAVN). These meetings included 3 plenary sessions and numerous meetings of the different groups that were formed with the 30 participants we had. The aim was to develop a consensus for a national and sustainable system for Plant Disease Validation Research. Plenary session number 1- October 01, 2020, had 31 participants. Objectives were to 'socialize' the ideas concerning diagnostic assay validation and to establish 4 working groups: a. Assay Validation Research & Statistics, b. Diagnostic Assay Development, c. Reference Collections, and d. IT framework. Plenary session number 2 - December 10, 2020, was attended by 26 participants. Report outs were obtained from the above-mentioned 4 groups (details mentioned in Annual Report - 2021) and the participants were reassorted on the area of their work expertise into 3 groups: a. Virus and Viroids, b. Bacteria and Phytoplasma, c. True Fungi and Stramenopiles Plenary session number 3 - March 11-12, 2021, had 25 participants. Objectives were to complete the planning phase of the effort to build consensus among experts. Organize the next phase of work including proposal development and publications. The content of the report outs recommended process of validation, validation research needs and gaps, gaps in extension/outreach, and solutions to address those gaps. Here is the list of resource/knowledge gaps that were identified: Diversity of target pathogens and hosts, Sampling strategy to reduce variation in sample quality, Extraction from tissues: the inhibitor problem, Best practices in diagnostic assay validation research, Continual improvement and verification of assay performance, (National?) strategy for inclusivity/exclusivity selections, Qualitative project rating system for the level of validation, Resource system OMICS, voucher specimens, a database of informative oligos, Linkage of population genetics data to the diagnostic community. A consensus framework as a logic model was designed from the numerous workshops and meetings that will be worked towards achieving the goals of the project: An online portal housing all the assays and connecting the plant pathology community, Uniformity, synchronization, and harmonization in validation research, Engaged plant pathology community, operation, and sustainability of DAVN. The concept of DAVN was presented at National and International conferences: The American Phytopathological Society Annual Meeting, Pittsburgh, Pennsylvania, August 8, 2022; National Plant Diagnostic Network (NPDN) National Meeting, UC Davis, Davis, California, April 26 - 30, 2022. Further, the participants were divided into 6 writing teams: The Need and a Vision for a diagnostic assay validation network - We propose the development of a Diagnostic Assay Validation Network (DAVN) system to provide coordinating resources at the national level and harmonize with our partners at the international level. State of the Field of Plant-Pathogen Diagnostic Assay Development and Validation - Evaluated 115 publications in peer-reviewed plant pathology journals from the past decade, reporting the development of new plant pathogen diagnostic assays, and collected data on the level of validation performed during performance testing of each assay. The objective of this study was to use this subsample to represent the status of the field and determine to what extent these published assays have been validated. The survey of publications finds that those detailing an appropriate and robust diagnostic assay validation process were few in number. Terminology and Guidelines for Diagnostic Assay Development and Validation: A Proposal for Best Practices - To increase awareness of common pitfalls and gaps encountered during this process with the goal of increased success in technology transfer. Recommendations are given for improving the efficiency and quality of test development through improved coordination among stakeholders. Knowledge Gaps, Research Needs, and Opportunities in Plant Disease Diagnostics Assay Development and Validation - These assessments should take into consideration the new technological and analytical advances available, the establishment of shared material, and data resources that will accelerate and facilitate progress in diagnostics development and validation. Here, we highlight some of the research opportunities available, in the context of anticipated needs. Communications Ecosystem to Support the Assay Validation Community - A Concept - A communications ecosystem to facilitate the sharing of such resources, as well as, to provide access to taxon and technology expertise will greatly accelerate the development, validation, and reliability of trusted diagnostic tests to support plant biosecurity, specifically, and plant health, in general. Standards of Diagnostic Validation: Recommendations for Reference Collections - recommend a framework for coordinated development, long-term maintenance, and accessibility of curated sets of pathogen data representing cultures and other reference material, that could serve the needs of pathogen diagnostics development, population studies, and resistance breeding efforts. A Focus Issue on PhytoFrontiers was developed which attracted >30 articles/perspectives/reviews. In total, 26 articles have been accepted and many of them are already in First Look. This PhytoFrontiers Focus Issue was developed not only to house the Perspectives derived from discussions among a large group of experts over several years during the NIFA seed grant but also to create a space for other perspectives and research papers specific to plant disease diagnostic assay validation. The primary objective of the Focus Issue was to raise awareness about the importance of assay validation for diagnostic accuracy. Among the peer-reviewed 16 research contributions to be included in the Focus Issue, across different diagnostic methods, manuscripts appeared describing validation research for three fungi, three Oomycetes, four viruses and a viroid, fruit flies and two nematodes, and five bacterial species. Sample matrices included soil, woody stems, leaves, fruits, tubers, and seeds. Methods were described for detection and diagnostics with sequencing and bioinformatic analysis, conventional PCR, rt qPCR, Recombinase polymerase amplification, and PMAqPCR. This range of taxa, sample matrices, and diagnostic platforms and methods provides a sobering snapshot of the sheer breadth of the needs of the plant health community for accurate and reliable diagnostic tools.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Cardwell, K.F., Harmon, C.L., Luster D.G., Stack, J.P., Hyten, A.M., Sharma P., and Nakhla, M.K. Need and Vision for a Diagnostic Assay Validation Network. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack. https://doi.org/10.1094/PHYTOFR-05-22-0056-FI
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Sharma, P. and Luster, G.L. 2022 Perspective: State of the Field of Plant Pathogen Diagnostic Assay Development and Validation. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack. https://doi.org/10.1094/PHYTOFR-05-22-0054-FI
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Stack, J.P. and Cardwell, K.F. 2022. Communications Ecosystem to Support the Assay Validation Community: a Concept. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack. https://doi.org/10.1094/PHYTOFR-05-22-0055-FI
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Geiser, D.M., Martin, F.N., Espindola, A.S., Brown J.K., Bell, T.H., Yang, Y., and Kang, S. 2023. Knowledge Gaps, Research Needs, and Opportunities in Plant Disease Diagnostics Assay Development and Validation https://doi.org/10.1094/PHYTOFR-05-22-0057-FI
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2023
Citation:
Groth-Helms, D., Rivera, Y., Martin, F., Arif, M., Sharma, P., and Castlebury, L.A. 2023 Terminology and Guidelines for Diagnostic Assay Development and Validation: A Proposal for Best Practices. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack. Accepted Aug 22nd, 2022, to be published with the Focus issue
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack. https://apsjournals.apsnet.org/doi/epdf/10.1094/PHYTOFR-3-1
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Progress 05/01/21 to 04/30/22
Outputs
Target Audience:Diagnostic assay developers and scientists with plant pathogen collections. American Phytopathological Society. Industries that rely on accurate diagnoses based on well-validated assays (importers, exporters, seed companies). Plant diagnostic laboratory personnel. USDA Animal Plant Health Inspection Service and State Plant regulatory laboratories Changes/Problems:Due to Covid-19, we had to shift from in-person meetings to all remote. We have shifted funds from travel to greater facilitation and IT management. The final remaining funds from this project will be used to cover page charges for the publications in Phytofrontiers. What opportunities for training and professional development has the project provided?Early career scientists have been involved in the project and are slated to have several publications for related research. How have the results been disseminated to communities of interest?Six policy papers are to be published in the APS journal Phytofrontiers. APS is fully engaged so outreach will be streamlined through the participation of the APS publications board. A Special Focus Issue on Diagnostic Assay Development and Validation (https://apsjournals.apsnet.org/diagnosticassays_focusissue) has been organized to publish in Phytofrontiers. Some 28-30 concept notes, literature reviews, and research papers on the topic of assay validation are undergoing revision or have already been published online in First Look. This effort is a direct outcome of the NIFA project on the Diagnostic Assay Laboratory Network. This focus issue will reach plant pathologists around the world and is expected to have a high impact factor. What do you plan to do during the next reporting period to accomplish the goals?The final work of this project is to get the Phytofrontiers focus issue bundled and published as an e-book. The book will come out early in 2023, although all of the articles that make it through review and revision will be published individually online as well.
Impacts
What was accomplished under these goals?
The specific objective of this Seed Grant is to prepare for the creation of DALN by: 1. Identifying key players in diagnostic assay development, validation, and reference collections; 2. Identifying resources and processes that can be shared or developed; 3. Preparing to forge a consensus on relevant models for tiers of validation, statistical processes, pathogen equivalence, databases of reference standards, and by identifying key statisticians, epidemiologists, and validation experts; and 4. Starting to compile inventories of validated assays. Objective 1: Network of Diagnostic Assay Developers Objective 2: Network of Diagnostic Assay Validators and Specialists and online tools designed Objective 3: Create a consensus framework with core experts in each arena
Publications
- Type:
Books
Status:
Published
Year Published:
2022
Citation:
Bailey, K. L., & Cardwell, K. F. (2022). Looking to the Future: Advancing Tactical Sciences for the Biosecurity Toolbox. In K. Cardwell, & K. Bailey (Ed.), Tactical Sciences for Biosecurity in Animal and Plant Systems (pp. 362-374). IGI Global. https://doi.org/10.4018/978-1-7998-7935-0.ch011
- Type:
Book Chapters
Status:
Published
Year Published:
2022
Citation:
Bulluck, R., Meade, B. J., Cardwell, K. F., & Bailey, K. L. (2022). Response and Recovery Tactics. In K. Cardwell, & K. Bailey (Ed.), Tactical Sciences for Biosecurity in Animal and Plant Systems (pp. 293-322). IGI Global. https://doi.org/10.4018/978-1-7998-7935-0.ch009
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2022
Citation:
Cardwell, K.F., Harmon, C.L., Luster D.G., Stack, J.P., Hyten, A.M., Sharma P., and Nakhla, M.K. Need and Vision for a Diagnostic Assay Validation Network. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2022
Citation:
Stack, J.P. and Cardwell, K.F. 2022. Communications Ecosystem to Support the Assay Validation Community: a Concept. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2022
Citation:
Groth-Helms, D., Rivera, Y., Martin, F., Arif, M., Sharma, P., and Castlebury, L.A. 2022 Terminology and Guidelines for Diagnostic Assay Development and Validation: A Proposal for Best Practices. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2022
Citation:
Sharma, P. and Luster, G.L. 2022 Perspective: State of the Field of Plant Pathogen Diagnostic Assay Development and Validation. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2022
Citation:
Harmon, C.L., Castlebury, L.A., Sharma, P. 2022. Standards of Diagnostic Validation: Recommendations for Reference Collections. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
Dang, T., Wang, H., Espindola, A.S., Habiger, J., Vidalakis, G, and Cardwell K.F. 2022. Development and statistical validation of e-probe diagnostic nucleic acid analysis (EDNA) detection assays for the detection of citrus pathogens from raw high throughput sequencing data. Phytofrontiers Special Focus Issue: Diagnostic Assay Development and Validation: The Science of Getting it Right, eds Cardwell, Sharma, Harmon and Stack.
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Progress 05/01/20 to 04/30/21
Outputs
Target Audience:Diagnostic assay developers and scientists with plant pathogen collections. Changes/Problems:Due to Covid-19, we had to shift from in-person meetings to all remote. We have shifted funds from travel to greater facilitation and IT management. What opportunities for training and professional development has the project provided?There are early-career scientists engaged in working group activities. How have the results been disseminated to communities of interest?The CC anticipates writing a number of policy papers to be published in APS journals. APS is fully engaged so that outreach will be streamlined through the participation of the APS publications board. What do you plan to do during the next reporting period to accomplish the goals?During the Dec 10, 2020, plenary meeting, the participants were re-assorted into 3 new working groups to work through case studies according to taxa: 1 viroids and viruses; 2. fungi and stramenopiles; and 3. Bacteria and phytoplasmas. The output of these working groups will be defined as wet lab research that is needed for the future of diagnostic tool development. These groups are tasked to report out in the March 11 remote plenary meeting. Expected outputs: 1. defined knowledge gaps and recommendations for specific research and 2. an analysis of potential interoperability of validation protocols within taxa. The CC will propose and get feedback on the matrix of terms and tiers that will be proposed based on consensus and define the needed state of knowledge. Also, a statistical committee review will work on the research steps that will be needed to get to each Tier. There is a lot of diversity in the terms used, so DALN will impose some structure on the language and terminology to be used in the diagnostic assay development and validation. Will work with American Phytopathological Society (APS) to develop a sustainability plan for DALN IT platform. March 12, during a final Plenary meeting, we will seek consensus on draft tiers of validation and terminology. The following steps will be writing and publishing four policy papers, hold another meeting with APS public policy board, and writing the next Tactical Sciences grant proposal.
Impacts
What was accomplished under these goals?
DALN Grant is working towards a common framework for a Diagnostic Assay Laboratory Network among subject matter experts in the field of plant pathology. The format is to have 4 remote plenary sessions (2 in 2020 and 2 in 2021) with working groups operating on specific tasks leading up to each meeting. Convening committee: Grant PIs, Cardwell and Harmon, and OSU faculty Sharma, 2 regional NPDN directors, 1 APHIS PPQ laboratory director, 1 ARS research scientist, and a USDA APHIS Select Agent program officer plus 31 volunteer working group members from Universities, Industry, U.S. and European Plant Protection organization national leaders. The Convening Committee (CC) meets twice monthly and has had 22+ zoom sessions, planning and coming to an agreement on how to proceed. Plenary session number 1- Oct. 01, 2020, had 31 participants plus CC. Objectives were to 'socialize' the ideas concerning diagnostic assay validation and to establish 4 working groups: a. Assay Validation Research & Statistics, b. Diagnostic Assay Development, c. Reference Collections, and d. IT framework. Plenary session number 2 - Dec. 10, 2020. Reports from the four worked to compile what currently exists and envision how to coordinate into a national strategy to harmonize diagnostic assay development, validation. Ouputs: Validation working group met 4 times in 2020. Future vision: International harmonization, defining the tiers of validation and research standards. There is diversity in the terms used, so DALN will impose some structure on the language and terminology to be used in the diagnostic assay development and validation. I Will work with Am. Phytopath. Society to have a platform needed for it. Diagnostic assay development working group met 4 times in 2020 to deliver uniformity and standards to the members and partners, provide a set format of standards and guidelines for assay validation publications to the journal editors and reviewers. DALN will ensure that publications describing diagnostic assays (appropriate to each taxa) provide: strength and weaknesses of assays, protocols for various sample matrices, Internal experimental/diagnostic controls, sequence alignment algorithms used, databases and archived alignments, data from assay optimization experiments, andadaptability of assays to instrument platforms (e.g. different thermocycler models) for analysis or reporting. Reference collections working group met 4 times in 2020 and envisions building a framework to connect reference collections nationally and internationally. DALN will have standardized fields for data collection and sharing. We have the knowledge of what already exists and where the gaps are. IT working group, charged with determining what types of tools could help coordinate and sustain a DALN. They met twice as a working group and then split up to participate in the other 3 working groups to identify needs and resources for communications and information technology. IT tools needed for DALN project portal: project management and reporting, reference collections catalog/directory, expertise directory, validation calculators, communications tools, messaging, reporting, outreach.
Publications
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