Complete sequence and genetic characterization of Raspberry latent virus, a novel member of the family Reoviridae

Authors: QUITO, D - Oregon State University; JELKMANN, W - Julius Kuhn Institute; TZANETAKIS, I - University Of Arkansas; Keller, Karen; Martin, Robert

Submitted to: Virus Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/19/2010
Publication Date: 2/2/2011
Citation: Quito, D.F., Jelkmann, W., Tzanetakis, I.E., Keller, K.E., Martin, R.R. 2011. Complete sequence and genetic characterization of Raspberry latent virus, a novel member of the family Reoviridae. Virus Research. 155:397-405..

Interpretive Summary: In studies to compare 'Meeker' red raspberry plants with severe versus mild or lack of crumbly fruit, it was observed that plants with severe crumbly fruit symptoms had mixed virus infections. Efforts to identify the viruses that were present in addition to Raspberry bushy dwarf virus led the discovery of two new viruses. The virus reported here is a member of the Reovirus family and does not cause symptoms when present in by itself; thus, we have named it Raspbery latent virus. It contains 10 genomic segments and appears to have several unique features that distinguish it from other known viruses in this family. One of the genomic segments is very diverse and was not identified as viral sequence in computer searches against all known virus sequences. As a result, this fragment was difficult to identify as part of the viral genome. Since most plant reoviruses infect monocots and are transmitted by leafhoppers, it is possible that this very divergent gene is involved in host range (raspberries are dicots) or vector interactions. Preliminary studies suggest this virus is aphid transmitted, which would be unique for viruses in the family. Experiments have been established to understand the role of this virus in crumbly fruit when it occurs in mixed infections with Raspberry bushy dwarf virus and/or Raspberry leaf mottle virus.

Technical Abstract: A new virus isolated from red raspberry plants and detected in the main production areas in northern Washington State, the United States and British Columbia, Canada was fully sequenced and found to be a novel member of the family Reoviridae. The virus was designated as Raspberry latent virus (RpLV) based on the fact that it doesn't cause symptoms when present in single infections in several Rubus virus indicators and commercial raspberry cultivars. RpLV genome contains 26,128 nucleotides (nt) divided into 10 dsRNA segments. The length of the genomic segments (S) were similar to those of other reoviruses ranging from 3948nt (S1) to 1141nt (S10). All of the segments, except S8, have the conserved terminal sequences 5'-AGUU----GAAUAC-3'. A point mutation at each terminus of S8 resulted in the sequences 5'-AGUA----GAUUAC-3'. Inverted repeats, 6-11 nt in length, were identified adjacent to each conserved terminus. Stem loops and extended pan handles were identified by the analysis of secondary structures of the non-coding sequences. All segments, except S3 and S10, contained a single open reading frame (ORF) on the positive sense RNAs. Two out-of-frame overlapping ORFs were identified in segments S3 (ORF S3a and S3b) and S10 (ORF S10a and S10b). Amino acid (aa) alignments of the putative proteins encoded by the main ORF in each segment revealed a high homology to several proteins encoded by reoviruses from different genera including Oryzavirus, Cypovirus, and Dinovernavirus. The analysis of the putative proteins encoded by ORFs S3b and S10b failed to identify any conserved domains or similarity with other known sequences in databases. Alignments of the polymerase, the most conserved protein among reoviruses, revealed a 36% aa identity between RpLV and Rice ragged stunt virus (RRSV), the type member of the genus Oryzavirus, indicating that these two viruses are very closely related. Phylogenetic analyses showed that RpLV clusters with members of the genera Oryzavirus, Cypovirus, Dinovernavirus and Fijivirus.