First Comprehensive Characterization and Highly Sensitive Detection of Hop Stunt Viroid in Chinese Sweet Cherry

Hop stunt viroid (HSVd) is an emerging threat to sweet cherry production in China, yet its geographic distribution and genomic characteristics remain poorly understood. Here, we report the first occurrence of HSVd in cherry in Hebei Province and the complete genome sequences of three local isolates: YT-HSVd‑1 (PQ580329), YT-HSVd‑14 (PQ580330), and YT-HSVd‑15 (PQ580350). Phylogenetic analysis placed them within a distinct Plum‑type clade alongside isolates SC‑17, SC‑13 (Shandong sweet cherry), FP2 (Japanese plum; AB098502.1), HSVd.apr9, and HSVd.apr10 (Moroccan apricot), sharing 91.45-97.01% nucleotide identity with other known HSVd variants. Additionally, we developed a cherry‑adapted SYBR Green I‑based RT‑qPCR assay using optimized primer sets (HSVd‑q117F/R and HSVd‑q168F/R) at 10 μmol·L⁻¹ with annealing temperatures of 55.0 ℃ and 56.9 ℃, respectively. The assay demonstrated high sensitivity, with detection limits of 12.9 and 1.29 copies·µL-1 and excellent reproducibility (Ct value CV < 5%). When applied to field samples, HSVd was reliably detected (100% detection rate) across all tested tissues, showing the highest viral titer in branch bark, followed by leaves and fruit stalks, and the lowest in fruit peels. This study provides the first complete HSVd genomes from Hebei Province and establishes a rapid, sensitive detection tool to support future surveillance and etiological research.