Characterization, epidemiology, and ecology of a virus associated with black raspberry decline Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/js956j691

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  • The objective of this study was to characterize an unknown agent associated with decline in black raspberry (Rubus occidentalis) in Oregon. A virus was found consistently associated with decline symptoms of black raspberries and was named Black raspberry decline associated virus (BRDaV). Double stranded RNA extraction from BRDaV-infected black raspberry revealed the presence of two bands of approximately 8.5 and 7 kilobase pairs, which were cloned and sequenced. The complete nucleotide sequences of RNA 1 and RNA 2 are 7581 nt and 6364 nt, respectively, excluding the 3' poly(A) tails. The genome structure was identical to that of Strawberry mottle virus (SMoV), with the putative polyproteins being less than 50% identical to that of SMoV and other related sequenced viruses. The final 189 amino acids of the RNA-dependent- RNA-polymerase (RdRp) reveal an unusual indel with homology to AlkB-like protein domains, suggesting a role in repair of alkylation damage. This is the first report of a virus outside the Flexiviridae and ampeloviruses of the Closteroviridae to contain these domains. An RT-PCR test was designed for the detection of BRDaV from Rubus tissue. BRDaV is vectored non-persistently by the large raspberry aphid Amphorophora agathonica, the green peach aphid Myzus persicae, and likely nonspecifically by other aphid species. Phylogenetic analysis of conserved motifs of the RdRp, helicase, and protease regions indicate that BRDaV belongs to the Sadwavirus genus. To assess the rate of spread BRDaV, four newly planted fields of black raspberries (Rubus occidentalis) in Oregon were studied for three years. In an effort to characterize the suspected complexity of synergistic interactions between BRDaV and other Rubus-infecting viruses, the prevalence of ten additional Rubus viruses was also monitored in the study fields. The timing of BRDaV infection as it relates to aphid populations and flights was also determined. Testing of nearby vegetation identified several symptomless Rubus hosts of BRDaV, as well as detection in multiple cultivars of black raspberry and several non-Rubus weeds. It was determined that BRDaV spreads rapidly with a low aphid threshold and consistently is associated with decline of black raspberries in Oregon.
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