Identification and molecular characterization of a marafivirus in Rubus spp.

An undescribed virus with isometric particles and a diameter of ca. 30 nm was identified in diseased samples of wild and cultivated Rubus species and molecularly characterized. Its genome was 6,463 nt, excluding the 3'-terminal poly(A) tail, and contained a single open reading frame coding for a 2,035-amino-acid-long precursor polypeptide (p223). The amino terminal portion of p223, identified as a replication-associated polyprotein, contained conserved motifs of methyltransferase, endopeptidase/protease, helicase and RNA-dependent RNA polymerase. The carboxy terminus of the large polypeptide is involved in the formation of two viral coat protein subunits with deduced molecular masses of 23 and 21 kDa. Pairwise comparisons and phylogenetic analyses showed closest relationships of this virus with oat blue dwarf virus and citrus sudden death-associated virus, sharing levels of genome sequence conservation far below the species demarcation level established for tymovirids. Our data indicate that this virus, for which the name blackberry virus S (BlVS) is proposed, is a hitherto undescribed species of the genus Marafivirus, family Tymoviridae. A survey conducted in Mississippi, USA, has shown that BlVS is also present in cultivated Rubus germplasm. This work represents the first report of a marafivirus infecting small fruits.