Characterization of defective interfering RNAs of Berne virus

1 Department of Virology, Institute of Medical Microbiology, Faculty of Medicine, Leiden University, Postbus 320, 2300 AH Leiden and 2 Institute of Virology, Veterinary Faculty, State University of Utrecht, Yalelaan 1, 3584 CL Utrecht, The Netherlands Defective interfering (DI) RNAs of Berne virus (BEV) were generated by serial undiluted passaging of the virus in embryonic mule skin cells. Two DI RNAs of 1.0 and 1.4 kb (designated DI1000 and DI1400) were characterized in more detail. Isokinetic sucrose gradient analysis showed that these DI RNAs are specifically packaged into particles with smaller S values than standard virions. Both DI RNAs were cloned and sequenced. Three genomic cDNA clones were identified using probes complementary to the 5' end of a DI RNA, which are thought to be derived from the 5'-terminal region of the BEV genome. A non-translated region of about 700 nt and the 5' end of the putative BEV replicase gene were identified in the consensus nucleotide sequence. Both DI RNAs were shown to contain sequences from the 5' and 3' ends of the BEV genome. A conserved sequence motif, which has been postulated to be involved in sub-genomic RNA transcription, was also identified just downstream of the extreme 5' ends of DI1000 and DI1400. Received 26 November 1990; accepted 4 March 1991.