Structure and variability of the 3' end of RNA 3 of Beet soil-borne pomovirus--a virus with uncertain pathogenic effects.

PCR products representing c. 550 3' terminal bases of Beet soil-borne pomovirus (BSBV) RNA 3 were compared for sources of this virus from all major sugarbeet-growing areas in Germany. In none of these areas conspicious symptoms could be attributed to the presence of BSBV. Single strand conformation polymorphism analyses suggested that the BSBV genome may be very variable. This was confirmed by nucleotide sequence analysis. Each PCR product which was analysed showed sequence differences to others. Even the PCR products obtained from plants grown in the same soil sample were different. The highly variable nature of the BSBV genome is in contrast to the much more conserved nature of the Beet necrotic yellow vein virus genome. By means of the STAR programme a secondary structure was predicted for the 3' end of BSBV RNA 3, in which some areas are highly conserved, whereas others are characterized by a clustering of nucleotide exchanges.