Molecular detection and characterisation of black raspberry necrosis virus and raspberry bushy dwarf virus isolates in wild raspberries

Abstract

Virus-derived small interfering RNAs (siRNAs) were extracted from leaves of wild raspberries (Rubus idaeus) sampled from three different regions in Finland and subjected to deep sequencing. Assembly of the siRNA reads to contigs and their comparison to sequences in databases revealed the presence of the bipartite positive-sense single-stranded RNA viruses, raspberry bushy dwarf virus (RBDV, genus Idaeovirus), and black raspberry necrosis virus (BRNV, family Secoviridae) in 19 and 26 samples, respectively, including 15 plants coinfected with both viruses. Coverage with siRNA reads [21 and 22 nucleotides (nt)] was higher in BRNV-FI (Finland) RNA1 (79%) than RNA2 (45%). In RBDV, the coverage of siRNA reads was 89% and 90% for RNA1 and RNA2, respectively. Average depth of coverage was 1.6-4.9 for BRNV and 16.5-36.5 for RBDV. PCR primers designed for RBDV and BRNV based on the contigs were used for screening wild raspberry and a few cultivated raspberry samples from different regions. Furthermore, the sequences of BRNV RNA1 and RNA2 were determined by amplification and sequencing of overlapping contigs (length 1000-1200 nt) except for the 3 ′ and 5 ′ ends of RNA1 and RNA2 covered by primers. RNA1 of the Finnish BRNV isolate (BRNV-FI) was 80% and 86% identical to BRNV-NA (USA) and BRNV-Alyth (UK), respectively, whereas the identity of NA and Alyth was 79%. RNA2 of BRNV-FI was 84% and 80% identical to BRNV-NA and BRNV-Alyth, respectively, whereas NA and Alyth were 82% identical. Hence, the strains detected in Finland differ from those reported in the UK and USA. Our results reveal the presence of BRNV in Finland for the first time. The virus is common in wild raspberries and nearly identical isolates are found in cultivated raspberries as well. The results show that wild raspberries in Finland are commonly infected with RBDV or BRNV or both viruses and thus are likely to serve as reservoirs of RBDV and BRNV for cultivated Rubus spp.Rosaceae), which is native to Europe and northern Asia. Hybrids of R. idaeus and the closely related wild North American form known as Rubus idaeus var. strigosus or Rubus strigosus are cultivated as well (Dale et al., 1993).The perennial nature of raspberries and the fact that they propagate vegetatively and produce berries only by the shoots of the second year make the crop prone to Ann Appl Biol 173 (2018) 97-111 97

Incidence of aphid-transmitted viruses in raspberry and raspberry aphids in Norway and experiments on aphid transmission of black raspberry necrosis virus (BRNV)

“…idaei, and the same is the case for RVCV in A. idaei (McMenemy et al, 2009;Stace-Smith, 1955a;Stace-Smith, 1961). The high incidence of BRNV in raspberry growing area in Norway is corresponding to the previous survey in Finland (Susi et al, 2018).…”

“…The proliferation of viral infections in "wild" raspberry is a point of concern. These plants may act as viral reservoirs for both pollen-transmitted raspberry viruses like raspberry bushy dwarf virus (not included in this study) and aphid-borne viruses like BRNV (Susi et al, 2018).…”

Strawberry Mottle Virus (Family Secoviridae , Order Picornavirales ) Encodes a Novel Glutamic Protease To Process the RNA2 Polyprotein at Two Cleavage Sites

“…Multiple sequence alignments and structure modeling. Multiple amino acid sequence alignments were produced using the full-length sequences of SMoV, BRNV, and LSV1 isolates (14,16,17,21,53,54) and Clustal Omega (55). Secondary structure predictions were performed by PSIPRED as implemented in the Phyre2 platform (27).…”