The discrepancy between published sequences of the 5′ non-coding regions of RNA of a Scottish (S) and that of Dutch (D), Australian and Canadian isolates of potato leafroll virus (PLRV) was investigated. Reverse transcription followed by amplification by polymerase chain reaction showed that RNA from three distinct Scottish isolates of PLRV contained molecules with 5′ ends like that of the original Scottish isolate. However, determination of the 5′-terminal sequences of RNA in two of these preparations showed that most RNA molecules had 5′ termini like those of the Dutch and other non-Scottish sequences. Northern blot analysis confirmed that only a small fraction of PLRV RNA contained sequences homologous to the 5′-terminal 119 nucleotides of the PLRV-S sequence. Most PLRV-S RNA molecules therefore have termini like that reported for PLRV-D. The 5′-terminal 119 nucleotides of the minor species of PLRV-SRNA were very similar (109/119 nucleotides were identical) in sequence to an exon of tobacco chloroplast DNA open reading frame 196. The results therefore suggest that recombination has occurred between virus RNA and host RNA.


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