Source: OKLAHOMA STATE UNIVERSITY submitted to NRP
DIAGNOSTIC ASSAY VALIDATION NETWORK (DAVN) TO COORDINATE AND HARMONIZE DIAGNOSTIC ASSAY DEVELOPMENT AND VALIDATION FOR PLANT DISEASES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1028220
Grant No.
2022-68013-36537
Cumulative Award Amt.
$985,739.00
Proposal No.
2021-11306
Multistate No.
(N/A)
Project Start Date
Mar 1, 2022
Project End Date
Feb 28, 2026
Grant Year
2022
Program Code
[A1181]- Tactical Sciences for Agricultural Biosecurity
Recipient Organization
OKLAHOMA STATE UNIVERSITY
(N/A)
STILLWATER,OK 74078
Performing Department
IBMF
Non Technical Summary
Plant biosecurity depends heavily on early and accurate detection and diagnosis, feeding communication chains that allow for effective mitigation. In the U.S., most land-grant universities and some state/private diagnostic labs are successfully networked via the National Plant Diagnostic Network (npdn.org), with access to training, shared protocols, and standardized communications. However, the ecosystem for plant disease diagnostic assay development, validation, and selection is siloed and detached, a critical gap in our biosecurity infrastructure, especially for new or emerging pathogens. In essence, every assay is developed independently in a research program and then chosen independently by the end-use laboratory. This ecosystem needs to be connected, integrated, and standardized to ensure a consensus on the standards of method validation for each taxon, harmonization with our neighbors and trade partners, and availability of validated protocols and essential controls for use in emergencies as well as day-to-day detection. Extensive collaboration in the tactical sciences of plant disease diagnostic assay development and validation, reference standards, and communications platforms does not currently exist and is acutely needed. 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. This proposal outlines a project to standardize the reference standards, terminology, and statistics used in diagnostic assay development and validation via a portal of tools to be made widely available to the research and extension community. The project summary is limited to 250 words.
Animal Health Component
50%
Research Effort Categories
Basic
20%
Applied
50%
Developmental
30%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2112299116080%
2127299104020%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants; 211 - Insects, Mites, and Other Arthropods Affecting Plants;

Subject Of Investigation
2299 - Miscellaneous and new crops, general/other; 7299 - Research equipment and methods, general/other;

Field Of Science
1040 - Molecular biology; 1160 - Pathology;
Goals / Objectives
DAVN Coordination through dynamic web-portal design: The Diagnostic Assay Validation Information System (DAVIS) - With APS, we will design dynamic architecture for a graphic user interface with linkages that coordinate DAVN assets and support multilevel communication. The main goal of the project is to build and test a sustainable model for multidirectional communication, validation tools, and libraries of validated protocols, controls, and collections for researchers and assay end-users. If successful, we envision it would be implemented within an expanded private-public partnership to ensure sustainable and long-term effectiveness.Diagnostic Assay Development Research (researchable elements): Conduct transformational research to overcome technical challenges across the array of molecular diagnostic tools. Universal internal controls for molecular and HTS diagnostic assays will be developed and tested in three expert labs across the country: Brown at UAZ, Cardwell at OSU, and Martin at ARS, Salinas CA. Bioinformatic processes will be used to identify informative sequences at the family/genus for specific viruses, bacteria, fungi, and oomycetes to serve as basis for assay (primer/probe) design and validation. Initial assembly of existing nucleic acid extraction protocols will provide content for objective 1. Outreach and Extension: Develop/adapt and communicate language and standards for diagnostic method development and validation within the plant science community. We will communicate, educate, and train the plant pathology community (assay developers, validators, and users, reference collection managers, taxonomic subject matter experts, publisher editors and reviewers, and stakeholders) on standards, language, and terminology. We will convene a working group to develop guidance/training for validation publications to the reviewers and editors for a home journal (Phytofrontiers). Develop and conduct outreach about an interactive workspace for assay developers, validators, and users, subject matter experts, publisher editors and reviewers, and stakeholders. Together with the APS, we will create liaisons with the impacted communities (industries, exporters, importers, etc.); and be sure to align our efforts with international partners, the International Plant Protection Convention, and the European and Mediterranean Plant Protection Organization.
Project Methods
Objective 1. DAVN Coordination through dynamic web-portal design: Diagnostic Assay Validation Information Systems (DAVIS)With APS, design dynamic architecture for graphic user interface with linkages that coordinate DAVN assets. Assets can be broken into three categories: existing resources, resources to be developed during this proposed project, and resources that will be assembled in the future. The goal of this element of the proposal is the development of an Information and Communications Technology (ICT) dashboard prototype (see Figure 2). We will develop a committee to work with the APS programming staff to lay out the storyboard of features for an interactive DAVN graphic user interface.Objective 2: Diagnostic Assay Development Research (researchable elements): Develop a standardized set of universal internal and positive controls for assay development by an extensive desk study, bioinformatics tools - to be conducted by Post Doc in 3 labsObjective 3:Communicate, educate, train the plant pathology community; Guidance/training for validation publications;Develop and conduct outreach of an interactive workspace;Conduct outreach to the impacted communities; Conduct outreach and collaboration with IPPC/EPPO and other international partners to engage them in harmonization discussion

Progress 03/01/23 to 02/29/24

Outputs
Target Audience:The DAVN is a framework to coordinate and standardize plant disease diagnostic assay development and validation research and develop and deploy a series of tools and resources to the plant pathology community. Extension and outreach efforts engage the plant protection community, solicit feedback from participants, users, and engage industry stakeholdersto raise awareness of diagnostic method development and validation resources available in the DAVN web portal. DAVN Communications and Outreach products housed in the DAVN portal publicize news, events, and products of DAVN. More than 80 scientists have opted in to receive news about DAVN and get involved in the network. Outreach and communications efforts are essential to engaging the widest possible cohort of scientists to the DAVN effort. Objectives: Engage scientists within these agencies/associations: Industry (seed, horticulture, vegetable, support services, and private labs) Agdia, Driscoll's, BallHort, etc) US Culture Collection Network National Plant Diagnostic Network National Clean Plant Network National Seed Health Testing Association National Plant Board USDA-APHIS-Plant Protection and Quarantine North American Plant Protection Organization Changes/Problems:No major changes have been encountered. Milestones for the objectives are being met. What opportunities for training and professional development has the project provided?In the summer of 2024, an APS-DAVN workshop will be held at the Plant Health meeting in Memphis. The event is being advertised by APS to the Early Career Professionals and Graduate Student committees. The project is waiving registration fees for the first 30 registrants from these committees. An additional workshop will be held on-line later in 2024. The DAVN webinar series was free to all APS members, and are available recordings for everyone in the DAVN webportal. Many professors told us that they dedicated lecture periods to air these webinars to their students to expose them to the prinicples of diagnostic assay development and validation. How have the results been disseminated to communities of interest?DAVN Communications and Outreach products housed in the DAVN portal publicize news, events, and products of DAVN. More than 80 scientists have opted in to receive news about DAVN and get involved in the network. Publications - A DAVN based focus issue was published in 2023 in PhytoFrontiers. It had recommended diagnostic assay validation guidelines for the authors and reviewers. The focus issue attracted >30 articles/perspectives/reviews. In total, 26 articles were accepted including the 6 foundational perspective articles on DAVN. We also had publications from international researchers. The whole issue has been downloaded close to 400 times, the independent articles have been downloaded more than 34,000 times. The articles in this issue have received 84 citations according to Google Scholar. The success of that issue indicated a demand for a publication outlet for diagnostic assay development and validation research. So a new focus issue has been announced (Call for Papers: Diagnostic Assay Development and Validation: The Science of Getting It Right II (apsnet.org) In addition, publication guidelines were proposed to APS Press Editorial Board and these guidelines are live in the Information to Authors page under the section Instructions to Authors of Diagnostic Assay Validation Papers (https://apsjournals.apsnet.org/page/authorinformation) DAVN webinar series highlighted new and upcoming molecular techniques that can be applied to diagnostics (recordings available in DAVN web portal). Five webinars drew 746 registrants and averaged nearly 100 participants each; remarkably, dozens of non-APS members paid to participate, an indication of the value of the DAVN resources and a possible contribution towards the sustainability conversation. Additional assets include tools for collaboration such as directories and participant registries, standard assay validation terminology and workflow for different tiers of validation, validation statistical calculators, and guidelines for publication of diagnostic assay development and validation research. What do you plan to do during the next reporting period to accomplish the goals? The success of the initial PhytoFrontiers focus issue indicated a demand for a publication outlet for diagnostic assay development and validation research. So a new focus issue has been announced (Call for Papers: Diagnostic Assay Development and Validation: The Science of Getting It Right II (apsnet.org), with a submission deadline of the end of August 2024 and on-ine publication in Reb 2025. At the 2024 APS meeting (July, 27 2024) in Memphis Tennessee, DAVN is presenting a day-long workshop on the network products, and opportunities. An industry focus group will be hosted to participate in this workshop. Set up Manucscript Central template to convert diagnostic assay development and validation research journal articles into Work Instructions for diagnostic assay users. The authors will recieve a second publication DOI for the research, once the Work Instruction protocol has cleared review.

Impacts
What was accomplished under these goals? The DAVN web-portal, being developed in partnership with the American Phytopathological Society (APS), provides access to diagnostic sciences assets, integrating validation research data, providing workflow, calculators, and community. These features are currently available: The nucleic acid extraction techniques database is searchable and includes information based on 115 peer reviewed publications since 2011 on NA extraction and assay mix kits, and equipment used depending upon the host, matrix and the purpose of the study. The searchable assay controls database presents definitions and data on controls available from an extensive literature search from the past decade. Additionally, a proposal to further develop the database of validated and published exogenous and endogenous controls was submitted by DAVN research committee members to PPA 7721. It has been approved. This new information will be integrated into the controls database. Framework, workflow and a glossary of assay development terminology are presented to promote research in tiers of validation related to fitness of purpose of an assay (Validation Tools (apsnet.org). Assay performance metric validation calculators with information about the statistical algorithms behind each calculator, links to the calculators and how to report the performance metric in published protocols are published and beta tested. DAVN Communications and Outreach products housed in the DAVN portal publicize news, events, and products of DAVN. More than 80 scientists have opted in to receive news about DAVN and get involved in the network. Publications - A DAVN based focus issue was published in 2023 in PhytoFrontiers. It had recommended diagnostic assay validation guidelines for the authors and reviewers. The focus issue attracted >30 articles/perspectives/reviews. In total, 26 articles were accepted including the 6 foundational perspective articles on DAVN. We also had publications from international researchers. The whole issue has been downloaded close to 400 times, the independent articles have been downloaded more than 34,000 times. The articles in this issue have received 84 citations according to Google Scholar. The success of that issue indicated a demand for a publication outlet for diagnostic assay development and validation research. So a new focus issue has been announced (Call for Papers: Diagnostic Assay Development and Validation: The Science of Getting It Right II (apsnet.org) In addition, publication guidelines were proposed to APS Press Editorial Board and these guidelines are live in the Information to Authors page under the section Instructions to Authors of Diagnostic Assay Validation Papers (https://apsjournals.apsnet.org/page/authorinformation) DAVN webinar series (see Other Products in this report) highlighted new and upcoming molecular techniques that can be applied to diagnostics (recordings available in DAVN web portal). Five webinars drew 746 registrants and averaged nearly 100 participants each; remarkably, dozens of non-APS members paid to participate, an indication of the value of the DAVN resources and a possible contribution towards the sustainability conversation. Additional assets include tools for collaboration such as directories and participant registries, standard assay validation terminology and workflow for different tiers of validation, validation statistical calculators, and guidelines for publication of diagnostic assay development and validation research.

Publications


    Progress 03/01/22 to 02/28/23

    Outputs
    Target Audience: To build a community of diagnostic researchers, regulators, industry members, and diagnostic professionals across silos of government, industry, and academia Achievements - Below is the list of work that has been done so far: A DAVN mailbox DAVN@scisoc.com and Twitter account (https://twitter.com/the_davn) has been set up and is actively publishing updates. We have also a link for the community to receive DAVN updates - https://forms.scisoc.org/davn-info/ DAVN was presented in the NPDN webinar (March 1, 2023), the recording has been posted in the DAVN portal - https://learnerresources.s3.eu-west-1.amazonaws.com/102661/learner_resource_uploads/108ee1cb1658c7f0cffc0f0b46/GPDN%20Webinar%20Series_03-01-2023.mp4?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAQZVLRHER6MLZQEAI%2F20230717%2Feu-west-1%2Fs3%2Faws4_request&X-Amz-Date=20230717T220857Z&X-Amz-Expires=30&X-Amz-SignedHeaders=host&X-Amz-Signature=0769105fd477b40a819f37ed63acd840630b39248b325da9bd4252a3aed5d2d2 Publication guidelines proposed to APS Press Editorial Board and these guidelines are already live in the Information to Authors page under the section Instructions to Authors of Diagnostic Assay Validation Papers (https://apsjournals.apsnet.org/page/authorinformation) DAVN was featured on the Plantopia podcast episode titled "Collecting Samples, Bridging Silos: Plant Diagnostics and the NPDN," which was broadcasted on April 27th, 2023 - https://aphid.fireside.fm/d/1437767933/43a22cf8-a632-4de5-8c29-0a5c6de955d8/459e9acc-25fa-478f-ba7f-922e9573756b.mp3 On May 9th, 2023, DAVN was showcased during the Western Extension Research Activity WERA 20 meeting, which took place from May 9-11, 2023. Changes/Problems:Dr Frank Martin, USDA ARS Salinas, requested to withdraw from the project to be replaced by his previous Post Doc, Timothy Miles at Michigan State University, Dr Martin continues to advise the reserach group. Dr Judy Brown, U AZ, did not have time to dedicate to the DAVN project. She was replaced by Dr Ozgur Batuman at U FL. Dr Batuman is in the process of recruiting a Post Doctoral Fellow. What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Outreach committee - To build a community of diagnostic researchers, regulators, industry members, and diagnostic professionals across silos of government, industry, and academia Achievements - Below is the list of work that has been done so far: A DAVN mailbox DAVN@scisoc.com and Twitter account (https://twitter.com/the_davn) has been set up and is actively publishing updates. We have also a link for the community to receive DAVN updates - https://forms.scisoc.org/davn-info/ DAVN was presented in the NPDN webinar (March 1, 2023), the recording has been posted in the DAVN portal - https://learnerresources.s3.eu-west-1.amazonaws.com/102661/learner_resource_uploads/108ee1cb1658c7f0cffc0f0b46/GPDN%20Webinar%20Series_03-01-2023.mp4?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAQZVLRHER6MLZQEAI%2F20230717%2Feu-west-1%2Fs3%2Faws4_request&X-Amz-Date=20230717T220857Z&X-Amz-Expires=30&X-Amz-SignedHeaders=host&X-Amz-Signature=0769105fd477b40a819f37ed63acd840630b39248b325da9bd4252a3aed5d2d2 Publication guidelines proposed to APS Press Editorial Board and these guidelines are already live in the Information to Authors page under the section Instructions to Authors of Diagnostic Assay Validation Papers (https://apsjournals.apsnet.org/page/authorinformation) DAVN was featured on the Plantopia podcast episode titled "Collecting Samples, Bridging Silos: Plant Diagnostics and the NPDN," which was broadcasted on April 27th, 2023 - https://aphid.fireside.fm/d/1437767933/43a22cf8-a632-4de5-8c29-0a5c6de955d8/459e9acc-25fa-478f-ba7f-922e9573756b.mp3 On May 9th, 2023, DAVN was showcased during the Western Extension Research Activity WERA 20 meeting, which took place from May 9-11, 2023. What do you plan to do during the next reporting period to accomplish the goals?Next step actions: 1. DAVN poster to be presented in the upcoming APS conference (Aug-12-16, 2023 Denver, CO) 2. APS to present DAVN in International Conference on Plant Pathology (ICPP) conference in (Aug-20-25, 2023 Lyon, France) 3. Schedule list of webinars on DAVN Fall/Winter 2023-2024 3. Plug-in the validation statistical calculators in the DAVN webpage 4. Plug-in the extraction techniques database in the DAVN portal 5. Develop Pitch Decks for Researchers, Assay Developers and Validation Researchers; Industry and Government Stakeholders

    Impacts
    What was accomplished under these goals? DAVN WEBportal Site Map Home Page - Welcome the audience to the DAVN homepage. You can access more information by visiting DAVN.org or following us on Twitter. 1. What DAVN Does - This section addresses what DAVN is about and what does it consist of and all of its activities. 2. DAVN Assets - Explore the information DAVN has to offer in the form of databases for diagnostic assay development (extraction techniques, universal internal controls, positive controls, primers, probes, and genomic markers); tools for collaboration such as directories and participant registries; validation tools and standards; and a repository for validated techniques, methods, and work instructions. 3. Research sandbox - Discover DAVN-relevant research by checking on the Research sandbox which will also have project management Gantt charts. We will be happy to hear your feedback, and everyone is welcome to interact with the research team. 4. Communications and Outreach - This section emphasizes the outreach, the importance of staying connected with DAVN and be informed about the latest developments in DAVN by following us on DAVN.org, and @the.davn in Twitter. It provides links to publications, training, essays, and webinars. In addition, please explore our network through DAVN directories and registries. ?

    Publications

    • Type: Journal Articles Status: Published Year Published: 2023 Citation: The Need and a Vision for a Diagnostic Assay Validation Network. Kitty F. Cardwell, Carrie L. Harmon, Douglas G. Luster, James P. Stack, Aimee M. Hyten, Poonam Sharma, and Mark K. Nakhla PhytoFrontiers" 2023 3:1, 9-17 https://doi.org/10.1094/PHYTOFR-05-22-0056-FI Downloaded 729 times
    • Type: Journal Articles Status: Published Year Published: 2023 Citation: State of the Field of Plant Pathogen Diagnostic Assay Development and Validation Poonam Sharma and Douglas G. Luster PhytoFrontiers" 2023 3:1, 18-22 https://doi.org/10.1094/PHYTOFR-05-22-0054-FI Downloaded 306 times
    • Type: Journal Articles Status: Published Year Published: 2023 Citation: Terminology and Guidelines for Diagnostic Assay Development and Validation: Best Practices for Molecular Tests Deborah Groth-Helms, Yazm�n Rivera, Frank N. Martin, Mohammad Arif, Poonam Sharma, and Lisa A. Castlebury PhytoFrontiers" 2023 3:1, 23-35 https://doi.org/10.1094/PHYTOFR-05-22-0059-FI Downloaded 459 times
    • Type: Journal Articles Status: Published Year Published: 2023 Citation: Knowledge Gaps, Research Needs, and Opportunities in Plant Disease Diagnostic Assay Development and Validation David M. Geiser, Frank N. Martin, Andres S. Espindola, Judith K. Brown, Terrence H. Bell, Yinong Yang, and Seogchan Kang PhytoFrontiers" 2023 3:1, 51-63 https://doi.org/10.1094/PHYTOFR-05-22-0057-FI Downloaded 556 times
    • Type: Journal Articles Status: Published Year Published: 2023 Citation: 5. Communications Ecosystem to Support the Assay Validation Community: A Concept James P. Stack and Kitty F. Cardwell PhytoFrontiers" 2023 3:1, 36-42 https://doi.org/10.1094/PHYTOFR-05-22-0055-FI Downloaded 204 times
    • Type: Journal Articles Status: Published Year Published: 2023 Citation: Standards of Diagnostic Validation: Recommendations for Reference Collections Carrie L. Harmon, Lisa A. Castlebury, Kyria Boundy-Mills, Kirk D. Broders, Aimee M. Hyten, Jonathan L. Jacobs, Victoria K. Knight-Connoni, Dimitre Mollov, Marco A. Riojas, and Poonam Sharma PhytoFrontiers" 2023 3:1, 43-50 https://doi.org/10.1094/PHYTOFR-05-22-0050-FI Downloaded 490 times
    • Type: Books Status: Published Year Published: 2023 Citation: Carwell, Harmon, Stack, and Sharma, eds. Special Focus Issue - Diagnostic Assay Development and Validation: The Science of Getting It Right. Phytofrontiers Vol3, No. 1. https://doi.org/10.1094/PHYTOFR-3-1