Prevalence, genetic diversity, and molecular detection of the apple hammerhead viroid in Germany

Kerstin Zikeli¹Constanze Berwarth¹Ute Born²Thomas Leible¹Wilhelm Jelkmann¹Michael Helmut Hagemann^2*

• ¹Julius Kühn-Institut, Institute for Plant Protection in Fruit Crops and Viticulture, Dossenheim, Germany
• ²University of Hohenheim, Stuttgart, Germany

Impacts, Detection, and Management in a Changing World by addressing the genetic diversity, epidemiology, and diagnostic challenges of Apple Hammerhead Viroid (AHVd), an emerging pathogen affecting apple production. Utilizing RT real-time PCR, Sanger sequencing, and next-generation sequencing (NGS), we provide a comprehensive analysis of AHVd prevalence in German orchards, its phylogenetic relationships, and intra-sample variability. Our findings contribute to understanding viroid evolution, adaptation, and detection in a changing agricultural landscape. The high genetic variability of AHVd complicates molecular diagnostics and requires improved detection strategies, which are critical for effective disease management. This study directly supports the application of high-throughput sequencing for viroid detection, epidemiological studies, and the development of new diagnostic approaches, as outlined in the Research Topic. By integrating bioinformatics and molecular techniques, our study provides insights into the ecology and transmission of plant viroids, addressing key challenges posed by climate change, global trade, and intensive agriculture. This work is highly relevant to researchers in plant virology, bioinformatics, and integrated pest management, contributing to the broader goal of protecting global food security from emerging viroid threats.