Comparative Analysis of Cherry leaf roll virus strains Identifies Common Genetic Characteristics of the isolates infecting Cherry and Birch. CLRV-E327 and CLRV-E51448

Cherry leaf roll virus (CLRV) is a bipartite ss(+)RNA virus with a genome of approx. 14.5 kb. CLRV encoded proteins are expressed as polyproteins P1 (from RNA1) and P2 (RNA2) that is processed into mature proteins by the viral proteinase (Pro). Strains are defined based on their biology, serology and partial sequence analysis of the genome. Here, we report the first complete genome sequence of a birch and a cherry isolate of CLRV from Germany, and compare them with eight other full length genomes of the virus representing different strains originating from diverse hosts. Analyses revealed Pro sequences specific for cherry and birch isolates assumed to cleave the P1 between the proteinase cofactor (PCo) and the nucleotide-binding protein (NTB) domain at a Q528/G site instead of a Q520/S site. The high-variability 2B region in P2 is also characteristic of isolates infecting cherry and birch. In vitro studies demonstrated that translation of polyproteins is exclusively initiated at the first AUG encoded, independent of the presence of a second intact putative start codon in both genome segments typical for cherry and birch isolates. This work provides first insights into genetic determinants differentiating isolates from cherry and birch from other strains.