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Validation of diagnostic tests to support plant health

Periodic Reporting for period 2 - VALITEST (Validation of diagnostic tests to support plant health)

Période du rapport: 2019-11-01 au 2021-10-31

Plant pests (bacteria, virus, fungi, nematodes, arthropods or weeds) are responsible for major crop losses. Accurate and reliable detection and identification of these pests are essential to avoid or reduce economical costs and trade disruptions and to support surveillance activities and crop monitoring. Validation is essential to provide information on the performance of the tests. However, since most detection and identification tests are usually validated on an intra-laboratory basis or through limited Test Performance Studies (TPS), a need to further harmonise practices has been identified. The VALITEST project aimed to improve diagnostic by producing validation data, harmonising processes and enlarging/triggering enlargement of the commercial offer for reliable detection and identification tests.
VALITEST has prepared and organised two rounds of test performance studies. The first round has included combinations of pest/test/matrix, prioritised based on the expertise of the project consortium partners for the following pests: Erwinia amylovora, Pantoea stewartii subsp. stewartii, citrus tristeza virus, plum pox virus, Fusarium circinatum and Bursaphelenchus xylophilus. The second round has included six pests selected based on the results of the survey organised in the framework of WP4. This prioritisation process has been implemented in such a way that the project's validation actions are in line with the needs of the stakeholders and of the market. The selected pests were: tomato brown rugose fruit virus, tomato spotted wilt virus, plum pox virus (on site testing), Xanthomonas citri pv. citri, Xylophilus ampelinus and Cryphonectria parasitica.
To maximise the impact of the project, calls of interest have been organised in order to include in the TPS programme, kits from suppliers outside of the consortium and to allow participation in the TPS of interested proficient laboratories. In total the performance of 83 tests covering 11 pests and including about 10,000 samples were analyzed during the two rounds of TPS. The framework and associated documentation for the selection of tests, the selection of laboratories, the organisation of TPS and the analysis of the results has been created. The experience gained by TPS organisers will be shared in a book to be published in Springer.

An improved framework, proposing new statistical tools to be used for the analysis of validation data and guidelines to ensure the reliability of the results obtained with high-throughput sequencing have been prepared and will be used to revise relevant EPPO Standards (PM 7/98 and PM 7/122) or draft new Standards.

A list of general minimum criteria for the production of reference material to be used in interlaboratory studies (including validations through TPS) has been developed as well as a general standard operating procedure for the production of reference material for use in plant health diagnostics. These results have been used to draft a new EPPO Standard on the production of reference material.

In order to assess the demand for current and future tests, two surveys were organised. The analysis of the data has allowed the prioritisation of pests and their selection for the organisation of the second round of TPS. Collected data will be further used to assess the impact of validation.

In order to optimize proficiency evaluation for a horizontal assessment, the needs and views of laboratories on possible horizontal proficiency tests have been identified through a survey sent to laboratories registered in the EPPO database on diagnostic expertise. Discussions with accreditation bodies have started on a possible plant health approach regarding the level and frequency of proficiency testing in laboratories.

Three series of webinars and training activities have been organised in the framework of VALITEST: one on the concept of test validation in Plant Health, one on the organisation of TPS and one on the guidelines for the development, validation and routine use of High Throughput Sequencing (HTS) tests for diagnostics of plant pests. Moreover, the validation section from the EPPO Database on diagnostic expertise (a key dissemination tool for the outputs of the project) was improved to a more searchable and user-friendly database.

An EU Association of the Plant Health Diagnostic Industry (EPDIA) has been established to ensure the market sustainability of the SMEs by facilitating dialogue with stakeholders and decision makers. In parallel to the establishment of EPDIA, an EU Plant Health Diagnostics Charter describing the quality procedures for the production and the validation of commercial tests produced by EU manufacturers has been developed. This Charter will contribute to guarantee the quality and the reliability of the products to the end-users worldwide. Manufacturers’ adhesion to EPDIA and to the Charter will permit SMEs to increase their competitiveness.
The aim of VALITEST was to complement existing data or produce new validation data for the detection and identification of plant pests that are of interest for various stakeholders in the region. This goal has been achieved through the organization of two rounds of Test Performance Studies (TPS).

Current harmonized procedures for validation and organisation of TPS have been improved based on the experience gained from the project, by including appropriate statistical approaches, by adapting the process for new promising technologies (e.g. high-throughput sequencing) and by providing new guidelines for the production of reference materials for validation studies. It also tackled the need for proficient users by evaluating the possibility to develop a horizontal approach for the evaluation of laboratories’ proficiency and by organising training activities. The outcomes of the project stimulate, optimize and strengthen the interactions between stakeholders in Plant Health for better diagnostics and lay the foundations for structuring the quality and the commercial offers for plant health diagnostics tools thanks to a dedicated association and a quality charter.

In a near future, more companies will join the EU Association of the Plant Health Diagnostic Industry which will become a major stakeholder of the plant health sector. Concerning the official control, the recently appointed EURLs will continue to structure the plant health sector and will be able to build on the project outputs. As mentioned above, the results of the project will be used to improve existing EPPO Standards or draft new ones ensuring the use and dissemination of the results to a large part of the plant health diagnostic community.
Preparation of samples for a Test Performance Study