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

Area of Science:

• Plant Pathology
• Virology
• Genomics

Background:

• Hop stunt viroid (HSVd) poses an emerging threat to sweet cherry production in China.
• The geographic distribution and genomic characteristics of HSVd in China are poorly understood.

Purpose of the Study:

• To report the first occurrence and complete genome sequences of HSVd in cherry from Hebei Province, China.
• To develop and validate a sensitive and rapid detection assay for HSVd in cherry.
• To investigate the distribution of HSVd in different cherry tissues.

Main Methods:

• Whole-genome sequencing of three HSVd isolates from Hebei Province.
• Phylogenetic analysis to determine the relationship of local isolates with known HSVd variants.
• Development and optimization of a cherry-adapted SYBR Green I-based RT-qPCR assay.
• Application of the RT-qPCR assay to detect HSVd in various cherry tissues.

Main Results:

• The first complete HSVd genomes from Hebei Province were obtained (accession numbers PQ580329, PQ580330, PQ580350).
• Phylogenetic analysis revealed that the Hebei isolates belong to a distinct Plum-type clade, sharing 91.45-97.01% nucleotide identity with other HSVd variants.
• A highly sensitive RT-qPCR assay with detection limits of 12.9 and 1.29 copies·µL⁻¹ and excellent reproducibility was developed.
• HSVd was detected in all tested cherry tissues, with the highest viral titer in branch bark, followed by leaves and fruit stalks, and the lowest in fruit peels.

Conclusions:

• This study provides crucial genomic data for HSVd in China and establishes a reliable detection tool.
• The developed RT-qPCR assay is effective for rapid and sensitive HSVd diagnosis in sweet cherry.
• Findings will aid in future surveillance, etiological research, and management strategies for HSVd in Chinese cherry production.