Ensuring validation in diagnostic testing is fit for purpose: a view from the plant virology laboratory

Abstract

Plant diagnostic laboratories are facing increasing demands for accreditation of their testing activities from both private and public organizations. For diagnostics, validating tests for the intended use is one of the key elements of accreditation. Thus far, validation has mainly focused on tests with a fixed scope, i.e. a test for organism X in matrix Y by method Z, suitable for the analysis of targeted samples. In many laboratories, however, targeted samples only form a minority of the samples. The majority consists of symptomatic (non‐targeted) samples including a huge variety of pest, host and matrix combinations. Since it is impossible to validate all tests used for the analysis of these non‐targeted samples, ensuring the reliability of the final results needs a different approach. This paper describes such an approach for diagnostic testing in plant virology, where the extent of validation of a test is determined based on the risks of a false result within the context of the diagnostic process. Examples illustrate how this risk‐based system approach relies on a tight inter‐relationship of validation, expertise and quality assurance within the diagnostic laboratory.

Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges

“…Alongside the appropriate use of controls, expertise in bioinformatics and plant virology has been identified as critical for the effective interpretation of diagnostic data (Roenhorst et al, 2018). The proficiency test performed in the frame of COST Action FA1407 (Massart et al, 2018) highlights significant variability in pipeline performance/expertise of users and shows that only a fraction of the laboratories were able to detect all the agents tested, while each of them was confirmed by classical RT-PCR assays.…”

Using high‐throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae)

“…As testing was primarily for confirmation of the presence of viruses inferred from sequence data, and in each case real-time PCR tests were also verified by subsequent PCR and Sanger sequencing, these primers were considered to be fit for the intended purpose. Further validation would be required to apply these in routine use (Roenhorst et al, 2018). The results of this testing are shown in Table 3.…”

“…However, with reference to this particular case study, the framework does not consider the point at which HTS analysis sits within the overarching diagnostic workflow. When used in a diagnostic support role (as in this case), HTS will form part of a broader diagnostic process, with multiple different tests applied to a sample as a cascading set of validated tests (Roenhorst et al, 2018). These complementary data can be considered holistically, alongside metadata from samples, to aid in the initial assessment of risk during the preliminary taxonomic assignment of the novel virus.…”

Implementation of an ISO 17025 flexible scope in the phytosanitary field at the National Reference Centre in the Netherlands

“…In this situation, analytical sensitivity is less critical as long as further testing is considered in the case of negative results. Meanwhile, analytical specificity is very important because cross‐reaction(s) with other species should be prevented since the target organism must be identified correctly (Roenhorst et al ., 2018).…”