Identification of cachexia-inducible Hop stunt viroid variants in citrus orchards in Japan using biological indexing and improved reverse transcription polymerase chain reaction

The distribution of Hop stunt viroid (HSVd) variants related to cachexia disease in Japan was investigated using reverse transcription polymerase chain reaction (RT-PCR) to specifically detect the five nucleotide differences in the “cachexia motif.” With RT-PCR, HSVd variants having the cachexia motif were detected in samples from 10 of 43 citrus trees in experimental orchards and from only 3 of 530 in commercial orchards. Although the trees were symptomless cachexia carriers, biological indexing using “Parson's Special” mandarin (Citrus reticulata Blanco) verified the presence of the cachexia agent. RT-PCR with the primer pair CCV-M1 and CCV-P1 will be useful in preventing the spread of cachexia HSVd variants.