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Hop stunt viroid (HSVd) infects a variety of natural hosts, including fruit trees, leading to significant economic losses worldwide. This survey aimed to assess the incidence of HSVd in fruit trees in southern Kazakhstan. Out of 482 fruit trees examined, 28 (5.81%) were found to be infected with HSVd. The incidence was significantly higher in stone fruit trees (8.15%; 22/270) compared to pome fruit trees (2.82%; 6/212; p = 0.0133). Apricots had the highest infection rate at 12.66% (10/79), while pears had the lowest rate at 2.08% (1/48). Fifteen of the identified viroids were cloned for full-genome sequencing. Sequence analysis revealed a high percentage of nucleotide sequence similarity (99–100%) among the Kazakhstani HSVd isolates, suggesting a possible unique origin for the infection. We also identified several SNPs of HSVd that have not been previously documented. A phylogenetic analysis indicated that the Kazakhstani HSVd variants clustered together in a separate group, distinct from the five known groups of HSVd. This potentially new group displayed differences in its predicted secondary structure compared to other viroid groups. These findings emphasize the need for the development of effective control measures for HSVd and other viroids affecting fruit trees.
