Viroscope™: a universal solution for plant virus and viroid diagnostics using HTS and cloud-based analysis

Area of Science:

• Plant pathology
• Genomics
• Biosecurity

Background:

• International plant trade increases the global risk of plant virus spread, threatening food security.
• High-throughput sequencing (HTS) offers advanced virus diagnostics but faces data analysis and implementation hurdles.
• Viroscope™ is a cloud service designed to overcome HTS limitations for reliable virus and viroid identification.

Purpose of the Study:

• To evaluate the Viroscope™ algorithm for phytosanitary diagnostics of plant viruses and viroids in post-entry quarantine settings.
• To assess the performance of Viroscope™ in detecting regulated and emergent viral pathogens.
• To compare Viroscope™'s diagnostic capabilities against conventional methods like RT-qPCR.

Main Methods:

• Deep sequencing of 144 plant tissue samples from post-entry quarantine using the Illumina® platform.
• Parallel analysis of samples using the Viroscope™ algorithm and conventional RT-qPCR methods.
• Evaluation of Viroscope™'s detection capabilities, including for low viral abundance and emergent viruses.

Main Results:

• 28.5% of quarantined plants harbored regulated and/or emergent viruses and viroids.
• Viroscope™ detected emergent viruses in 25% of plants, highlighting risks missed by traditional methods.
• Viroscope™ showed high correlation with RT-qPCR and detected viruses in samples negative by RT-qPCR.

Conclusions:

• Viroscope™ enhances virus and viroid detection accuracy and provides valuable biological insights for phytosanitary diagnostics.
• The cloud-based platform facilitates global adoption of HTS technology by making diagnostics user-friendly and efficient.
• Viroscope™ improves biosecurity by identifying potential risks, including emergent viruses, that traditional methods may overlook.