High-Throughput Sequencing for the Detection of Viruses in Grapevine: Performance Analysis and Best Practices
Kristian A Stevens1,2,3, Maher Al Rwahnih3,4,5
1Department of Computer Science, University of California-Davis, Davis, CA 95616, USA.
Viruses
|January 8, 2025
Summary
High-throughput sequencing (HTS) is a powerful tool for diagnosing grapevine viruses. This study evaluates HTS performance, offering recommendations for its use in detecting known and novel grapevine pathogens.
Area of Science:
- Plant pathology
- Virology
- Genomics
Background:
- Grapevines host numerous viruses, necessitating accurate pathogen identification for disease management.
- Next-generation high-throughput sequencing (HTS) offers rapid and broad molecular characterization of potential pathogens.
Purpose of the Study:
- To empirically analyze the diagnostic performance of HTS for grapevine viruses.
- To compare different HTS data analysis modalities in a phytosanitary context.
- To provide recommendations for deploying HTS in grapevine virus detection.
Main Methods:
- Evaluation of HTS performance using standard diagnostic criteria: sensitivity, specificity, and analytical sensitivity.
- Comparison of three popular HTS data analysis modalities.
- Testing with grapevine samples to assess detection of known and novel viruses.
Main Results:
- HTS demonstrates significant potential as a diagnostic tool for grapevine viruses.
- Performance varied across different HTS data analysis modalities.
- Sensitivity and specificity were key metrics for evaluating diagnostic accuracy.
Conclusions:
- HTS is a valuable technology for identifying infected vines and characterizing new grapevine pathogens.
- Careful selection of HTS data analysis methods is crucial for optimal diagnostic performance.
- Recommendations are provided for the effective deployment of HTS in grapevine phytosanitary surveillance.
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