Sequence similarities between Raspberry leaf mottle virus, Raspberry leaf spot virus and the closterovirus Raspberry mottle virus

Abstract

A sequencing study was performed to determine the relationship between Raspberry mottle virus (RMoV), a newly identified tentative closterovirus found in the United States, and Raspberry leaf mottle virus (RLMV) and Raspberry leaf spot virus (RLSV), which have been known for many years to be components of Raspberry mosaic disease (RMD) in the UK and Europe but which have not been characterised at the molecular level. Cloning and sequencing of cDNAs amplified by reverse transcription‐PCR revealed the presence of closteroviruses with high sequence similarity to RMoV in infected plants from the SCRI Rubus virus collection, as well as in a number of samples collected from RMD‐symptomatic raspberry plants located at different farms in Scotland and England. These results suggest that RMoV, RLMV and RLSV are isolates of the same virus and we propose that they all should be referred to as RLMV, which was the first of these viruses to be described. Many of the field samples were also infected with a second closterovirus isolate, parts of which could be amplified using RLMV‐derived primers. The coat protein amino acid sequences of RLMV and the second virus (PM1) were only 78% identical, even though helicase domain and RNA‐dependent RNA polymerase (RDRP) domain sequences were more than 97% identical between RLMV and PM1.