High Throughput Sequencing (HTS) enables comprehensive detection of plant pathogens by analyzing their DNA or RNA directly from citrus fruits and leaves. In EmergeNOW, portable Nanopore devices are being optimized to rapidly identify both fungal and bacterial agents responsible for Citrus Black Spot (P. citricarpa) and Huanglongbing (Candidatus Liberibacter spp.). Unlike conventional HTS workflows requiring laboratory instruments and long processing times, the new approach focuses on fast nucleic-acid extraction and rapid library preparation that can be performed at import control facilities by trained inspectors. This allows complex samples containing diverse microbes to be analyzed efficiently without culturing or lengthy amplification steps.
The system integrates automated bioinformatics pipelines that run in real time, guiding users through data interpretation and reducing the need for advanced computational expertise. This approach not only differentiates between closely related Liberibacter species but also detects new strains or variants, supporting improved surveillance of emerging threats. By delivering highly informative genetic data directly at EU borders, HTS complements other on-site diagnostic tools in EmergeNOW, such as RPA kits, and strengthens early decision-making for import controls while helping prevent the introduction of regulated citrus diseases.
