The detection and variation of Strawberry mottle virus

Strawberry mottle virus (SMoV) is probably the most important virus to infect strawberry (Fragaria spp.). All species of strawberry are susceptible to SMoV, resulting in severe losses both in fruit and runner yield. However, due to the absence of definitive symptoms in commercial varieties, the only effective means of detecting SMoV is by transmission to susceptible indicator plants. In this study, we describe a reverse transcription-polymerase chain reaction (RT-PCR) method for the detection of SMoV in Fragaria spp. with the use of primers specific for the noncoding regions (NCR) of both RNA1 and RNA2 of the virus. Using this method, all of 16 isolates from various geographical origins were positive for SMoV. Partial sequences of a 327-nt long coding region were obtained for the putative large coat protein of all isolates by RT-PCR using degenerate primers. Nucleotide identities between isolates ranged from 72.8 to 99.7%. A 546-nt sequence of the putative polymerase gene of nine isolates was obtained by RT-PCR and compared. Nucleotide identities ranged from 73.4 to 100%. There was a clear tendency for isolates to group according to their geographical origin. Sequence data obtained of the NCR show four completely conserved regions of 20 or more bases.