Sequence and structure of defective interfering RNAs associated with cucumber necrosis virus infections.

The presence of symptom-attenuating defective interfering (DI) RNAs in a laboratory culture of cucumber necrosis tombusvirus (CNV) was confirmed. Sequencing of cDNA clones of these DI RNAs revealed that CNV DI RNAs retained sequences from the CNV 5'-untranslated and 3'-terminal regions as well as a portion of the coding region for the 92K protein. Similar sequence arrangements were also observed in symptom-attenuating DI RNAs generated de novo from synthetic wild-type CNV transcripts. A comparison of the sequences and biological activities of these CNV DI RNAs is presented. In co-infections of synthetic wild-type CNV and CNV DI RNAs, prominent RNA species of a higher M(r) than the DI RNA used in the co-infection were found. The possible nature of these RNA species is discussed.