Analysis of the 5′ and 3′ Non-Coding Regions of Cherry Leaf Roll Virus

Genetic variability of Cherry leaf roll virus (CLRV) isolates depends largely upon original host plants species. However, this is not a strict principle and an exception may be a highly virulent CLRV strain originating from raspberry. Sequence analyses of different genome regions of the raspberry strain indicate towards genetic recombination, which may be responsible for the clustering of the isolate in different phylogenetic groups. This should be investigated by recombination analyses as well as by investigation of sequence variability within the RNA population of the CLRV isolate and comparison of this strain with CLRV isolates from other host plant species.

The bipartite CLRV genome consists of short 5´ non-coding regions (NCRs) and long polyadenylated 3´ NCRs flanking a large open reading frame on each RNA segment. Translation of virus polyproteins is initiated in a cap-independent manner, but regulation of the translation of the CLRV genome is still unknown. Both, the 5´ as well as the 3´ NCRs are thought to be involved in the process by formation of secondary structures and intramolecular basepairing as described for other nepoviruses. Therefore, the CLRV 5´ and 3´NCRs will be screened for putative translation-associated sequence-motifs in order to develop a translation model for this virus species.