Soybean blotchy mosaic virus (SbBMV), a plant virus of the genus Cytorhabdovirus is an economically important virus of soybean reported only from the warmer, lower-lying soybean production areas in South Africa. The virus consistently appears in soybean crops annually in spite of the absence of soybean plants in winter. One possible reason for this may be that the virus replicates and hence persists in the SbBMV vector, a leafhopper, Peragallia caboverdensis. RNA viruses with antisense genomes as inferred for SbBMV produce positive sense RNAs as intermediate replicative forms during replication in their hosts, and detection of the positive strand in the plant host or vector is evidence of virus replication. In this study, a positive-strand specific RT-PCR (pss-RT-PCR) was developed to detect the positive RNA strand of SbBMV and validated on nine SbBMV isolates from soybean. The effect of tagged reverse transcription (RT) primers for cDNA synthesis, coupled with PCR using a tag-specific primer, as well as removal of unincorporated RT primers following cDNA synthesis was assessed. The positive RNA strand of SbBMV in infected plants was successfully detected following this protocol. Reverse transcription with forward and unmodified reverse primers confirmed that the assay was not able to detect the genomic sense RNA or self-primed cDNAs, lacking the non-viral tag, respectively. However, Exonuclease I (ExoI) treatment of cDNA was required to eliminate false-positive results during PCR amplification.

Soybean blotchy mosaic virus (SbBMV) is an important virus of soybean in the warmer regions of South Africa. The presence of the virus is associated with blotchy mosaic symptoms on soybean leaves and significant annual yield losses. The virus is a member of the genus Cytorhabdovirus and persists between soybean growing seasons. In this study, multiple specimens of indigenous tree species, other crops and herbaceous weeds surrounding soybean fields with high disease incidences of SbBMV were tested for the presence of SbBMV by RT-PCR in order to determine whether the presence of alternative hosts facilitates the seasonal carry-over of the virus.Commercial soybean cultivars commonly grown in the region were also evaluated for seed transmissibility of the virus. A total of 487 accessions representing 27 different species were screened and one accession each of Flaveria bidentis, Lamium amplexicaule and Gymnosporia buxifolia tested positive for the presence of SbBMV and may serve as possible alternative hosts of SbBMV, allowing over-wintering of the virus when soybean is absent. Symptoms associated with SbBMV infection were not present in any of the 2, 829 seedlings collected from naturally infected SbBMV plants, and none of the 21 seedlings showing various abnormalities and tested by RT-PCR were positive. SbBMV does not appear to be seed transmissible in soybean at an incidence above that which numbers screened would have detected. It was concluded that the presence of alternative plant hosts, functioning as viral reservoirs during the soybean off-season might allow for the re-emergence of the disease early in the soybean production season each year. Future work will investigate the role of Peragallia caboverdensis, the leafhopper vector of SbBMV, and specifically the possible propagative transmission of the virus in the persistence of the disease.

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Infection of soybean by the plant cytorhabdovirus soybean blotchy mosaic virus (SbBMV) results in significant yield losses in the temperate, lower-lying soybean production regions of South Africa. A 277 bp portion of the RNA-dependent RNA polymerase gene of 66 SbBMV isolates from different: hosts, geographical locations in South Africa, and times of collection (spanning 16 years) were amplified by RT-PCR and sequenced to investigate the genetic diversity of isolates. Phylogenetic reconstruction revealed three main lineages, designated Groups A, B and C, with isolates grouping primarily according to geographic origin. Pairwise nucleotide identities ranged between 85.7% and 100% among all isolates, with isolates in Group A exhibiting the highest degree of sequence identity, and isolates of Groups A and B being more closely related to each other than to those in Group C. This is the first study investigating the genetic diversity of SbBMV.