Partial sequence and RT‐PCR diagnostic test for the plant rhabdovirus Raspberry vein chlorosis virus

Abstract

A partial (c. 3 kb) nucleotide sequence of the genome of Raspberry vein chlorosis virus (RVCV) has been obtained, confirming that it is a plant rhabdovirus. Sequence data were obtained using two approaches, conventional reverse transcriptase polymerase chain reaction (RT‐PCR) of single‐strand RNA using degenerate primers designed from rhabdovirus L gene sequences, and mass (454) sequencing of randomly‐amplified double‐stranded RNA. Amplification using the degenerate primers of RNA extracted from virus‐infected raspberry plants was unsuccessful, whereas amplification of rhabdovirus sequences from RNA extracts of the RVCV vector aphid, Aphis idaei, was successful. From these sequences, RVCV‐specific primers were designed which could be used to direct amplification of fragments of the viral genome both from infected aphids and from infected raspberry plants. Phylogenetic analysis of available rhabdovirus sequences shows that RVCV is most closely related to Strawberry crinkle virus.