Identification, Characterization, and Detection of Black raspberry necrosis virus

Abstract

A serious disease was observed in black raspberry (Rubus occidentalis) in Oregon in the last decade. Plants showing mosaic symptoms declined rapidly and, in many cases, died after several years. Double-stranded RNA extraction from symptomatic black raspberry revealed the presence of two high molecular weight bands which were cloned and sequenced. Sequence analysis disclosed the presence of a novel virus that was tentatively named Black raspberry decline-associated virus (BRDaV). The complete sequences of the two genomic RNAs, excluding the 3' poly-adenosine tails, were 7,581 and 6,364 nucleotides, respectively. The genome organization was identical to that of Strawberry mottle virus, a member of the genus Sadwavirus. The C terminus of the RNA 1 poly-protein is unique within the genus Sadwavirus, with homology to AlkB-like domains, suggesting a role in repair of alkylation damage. A reverse-transcriptase polymerase chain reaction test was designed for the detection of BRDaV from Rubus tissue, and tests revealed that BRDaV was associated consistently with the observed decline symptoms. While this publication was under review, it came to our attention that scientists at the Scottish Crop Research Institute had molecular data on Black raspberry necrosis virus (BRNV), a virus that shared many biological properties with BRDaV. After exchange of data, we concluded that BRDaV is a strain of BRNV, a previously described yet unsequenced virus. The North American strain was vectored nonpersistently by the large raspberry aphid and the green peach aphid. Phylogenetic analysis indicates that BRNV belongs to the genus Sadwavirus.

Cheravirus and Sadwavirus: two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae)

“…the structural genes excluding VP4) from human poliovirus (PV, family Picornaviridae) was used as outgroup. ( Ã ) the StPV CP sequence is probably not complete but lacks 10-40 amino-acids at its N-terminus [3]; ( ÃÃ ) the SMoV and BRNV CP cleavage sites are unknown [12,34] and were therefore approximated to produce the alignment from the best homologous portion of the polyprotein (SMoV: GLPED . .…”

“…The number of CP subunits is one of the distinctive features of the ''atypical nepoviruses'' discussed here: LASV, RCSV, SDV, SLRSV have 2 CP subunits, a large one and a small one as in comoviruses and fabaviruses, while ALSV, AVB, CRLV and StPV have 3 CP subunits of similar sizes, like sequiviruses and picornaviruses [3,12,23,24]. The number of CP subunits has not been experimentally determined for SMoV and BRNV [12,34].…”

“…However, the observed patterns of spread in the field suggest soil transmission [3,14]. Black raspberry necrosis virus (BRNV) and strawberry mottle virus (SMoV) are transmitted by aphids [12,34]. Arracacha virus B (AVB) is pollen-borne.…”

Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers

“…Today, growers in Oregon, the leading production region, typically see a decline in production after the second harvest and remove fields after only three or four seasons because of decreased profitability (Halgren et al 2007). At the same time, demand for black raspberry fruit has increased in recent years in large part because of studies outlining the potential health benefits of black raspberry consumption (Kresty et al 2001;Seeram et al 2006;Seeram 2008;Stoner et al 2005Stoner et al , 2008.…”

In vitro elimination of Black raspberry necrosis virus from black raspberry (Rubus occidentalis) - Short Communication

“…It is a member of the genus Sadwavirus in the family Secoviridae. The host range of the virus is restricted to Rubus species where it causes chlorosis along the leaf veins (Jones et al 2002;Martin 2002;Halgren et al 2007).…”