Ppoc-ia: plant point-of-care genetic assessment using isothermal amplification and long-read sequencing

Overview

This project delivers a novel point-of-care genetic assessment tool for plant health diagnostics. By combining nucleic acid isothermal amplification with high-throughput long-read sequencing, the platform enables rapid, reliable, and massively multiplexed testing of plant pathogens outside traditional laboratory environments. The approach supports simultaneous detection of multiple targets across several hundred samples within a few hours, making it well suited for large-scale plant health screening, agricultural biosecurity, and crop management programs.

Technical specifications

Key features:

• Isothermal nucleic acid amplification compatible with rapid, non-laboratory sample processing
• High-throughput long-read sequencing as the read-out for comprehensive target identification
• Multiplexing capability for multiple nucleic acid targets and internal controls in a single assay
• Detection of single nucleotide polymorphisms for variant-level pathogen identification
• Pooling strategy enabling analysis of several hundred samples within hours
• Reduced susceptibility to inhibitors compared to other amplification methods, supporting robust plant diagnostics
• Automated bioinformatics workflow that demultiplexes samples and targets and generates concise result reports
• Flexible assay design accommodating diverse crops and targets of interest

Technology readiness level

The combination of isothermal amplification and long-read sequencing has been validated in human diagnostics contexts, including COVID-19 mass testing and ultra-rapid cancer mutation detection. The team has already demonstrated successful application of this combined approach to plant RNA virus diagnostics, representing the first proof-of-concept in plant health. Ongoing and future validation will focus on designing and testing target-specific oligonucleotides across the partner's crops of interest, validating assays with rapidly extracted nucleic acids, and confirming multiplexed assay performance under point-of-care conditions.