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SCHUMPP Olivier

  • Plant protection, Agroscope, Nyon, Switzerland
  • Diagnosis, Phytopathology, Plant diseases, Resistance/Virulence/Tolerance, Taxonomy of hosts, infectious agents, or vectors, Viruses
  • recommender

Recommendation:  1

Reviews:  0

Areas of expertise
Development of molecular diagnostic assays for highthroughput and strain specific virus detection in cultivated plants. Epidemiology and prevention of plant virus infections. Virus interactions: influence of asymptomatic persistent plant virus on viral disease incidence. Molecular mechanisms of crop resistance to viral diseases and viral disease emergence.

Recommendation:  1

07 Oct 2022
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Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests

High-throughput sequencing for the diagnostic of plant pathologies and identification of pests: recommendations and challenges

Recommended by based on reviews by Denise Altenbach and David Roquis

High-throughput sequencing (HTS) has revealed an incredible diversity of microorganisms in ecosystems and is also changing the monitoring of macroorganism biodiversity (Deiner et al. 2017; Piper et al. 2019).  

The diagnostic of plant pathogens and the identification of pests is gradually integrating the use of these techniques, but there are still obstacles. Most of them are related to the reliability of these analyses, which have long been considered insufficient because of their dependence on a succession of sophisticated operations involving parameters that are sometimes difficult to adapt to complex matrices or certain diagnostic contexts. The need to validate HTS approaches is gradually being highlighted in recent work but remains poorly documented (Bester et al. 2022).

In this paper, a large community of experts presents and discusses the key steps for optimal control of HTS performance and reliability in a diagnostic context (Massart et al. 2022). It also addresses the issue of costs. The article provides recommendations that closely combine the quality control requirements commonly used in conventional diagnostics with newer or HTS-specific control elements and concepts that are not yet widely used. It discusses the value of these for the use of the various techniques currently covered by the terms "High Throughput Sequencing" in diagnostic activities. The elements presented are intended to limit false positive or false negative results but will also optimise the interpretation of contentious results close to the limits of analytical sensitivity or unexpected results, both of which appear to be frequent when using HTS.

Furthermore, the need for risk analysis, verification and validation of methods is well illustrated with numerous examples for each of the steps considered crucial to ensure reliable use of HTS. The clear contextualisation of the proposals made by the authors complements and clarifies the need for user expertise according to the experimental objectives. Some unanswered questions that will require further development and validation are also presented.

This article should benefit a large audience including researchers with some level of expertise in HTS but unfamiliar with the recent concepts of controls common in the diagnostic world as well as scientists with strong diagnostic expertise but less at ease with the numerous and complex procedures associated with HTS.

References

Bester R, Steyn C, Breytenbach JHJ, de Bruyn R, Cook G, Maree HJ (2022) Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids. Plants, 11, 1939. https://doi.org/10.3390/plants11151939

Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L (2017) Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26, 5872–5895. https://doi.org/10.1111/mec.14350

Massart, S et al. (2022) Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests. Zenodo, 6637519, ver. 3  peer-reviewed and recommended by Peer Community in Infections. https://doi.org/10.5281/zenodo.6637519

Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ (2019) Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. GigaScience, 8, giz092. https://doi.org/10.1093/gigascience/giz092

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SCHUMPP Olivier

  • Plant protection, Agroscope, Nyon, Switzerland
  • Diagnosis, Phytopathology, Plant diseases, Resistance/Virulence/Tolerance, Taxonomy of hosts, infectious agents, or vectors, Viruses
  • recommender

Recommendation:  1

Reviews:  0

Areas of expertise
Development of molecular diagnostic assays for highthroughput and strain specific virus detection in cultivated plants. Epidemiology and prevention of plant virus infections. Virus interactions: influence of asymptomatic persistent plant virus on viral disease incidence. Molecular mechanisms of crop resistance to viral diseases and viral disease emergence.