Detection of Emerging Viral Pathogens in Chilean Zucchini, Capsicum pubescens and Tomato Samples Using High-Throughput Sequencing and Viroscope™ Analysis

Accurate and early detection of plant viral pathogens is crucial for safeguarding agricultural production and food security. High-throughput sequencing (HTS) has emerged as a powerful tool for broad-spectrum pathogen diagnosis, enabling the identification of known and emerging viruses and viroids without prior sequence knowledge. This study reports the detection of three economically significant, emerging viral pathogens in symptomatic foliar plant samples collected in Chile, utilizing HTS combined with the robust Viroscope™ bioinformatic algorithm (Valenzuela et al., 2022). Out of five foliar samples analyzed, two tested positive for viral pathogens. Detailed HTS analysis of sample Uarica-A1 yielded 7,325,159 plant reads (97.8%), 163,125 unassigned reads (2.18%), and 175 viral/viroid reads (0.00234%), revealing the presence of Southern tomato virus (STV) with 60% genomic completeness. Sample Uarica-D showed 14,336,556 plant reads (85.5%), 2,235,984 unassigned reads (13.3%), and 191,108 viral/viroid reads (1.14%), with positive detections of Cucumber yellows virus (CuYV) and Beet pseudoyellows virus (BPYV), showing 62% and 59% genomic completeness, respectively. Significantly, functional evidence of viral replicase was detected for both CuYV and BPYV in sample Uarica-D, indicating active viral replication and high diagnostic certainty. The detection of STV, CuYV, and BPYV in these Chilean plant samples highlights the ongoing threat posed by emerging viral pathogens to economically important crops. The integration of HTS with the Viroscope™ algorithm, particularly its capacity to confirm active infection via replicase identification, provides a robust and comprehensive diagnostic approach vital for timely intervention and underscores the continuous need for vigilant phytosanitary surveillance in Chile.