Limited studies have been undertaken with regard to virus complexes contributing to the aetiology of sweet potato virus disease (SPVD) in South Africa (SA). In this study, a metagenomic approach was adopted to reveal the genetic diversity of viruses infecting sweet potato. In order to undertake a comprehensive analysis of viral sequences, total RNA was isolated from 17 asymptomatic and symptomatic sweet potato plants that were collected from the Eastern (EC) and Western Cape (WC) provinces of SA. DNase-treated total RNA was depleted of ribosomal RNA (rRNA) and deep-sequenced using the Illumina MiSeq platform. Genomic DNA, isolated from the same plants, underwent rolling circle amplification (RCA) and deep sequencing. Sequence reads were analysed with the CLC Bio Genomics Workbench. Both de novo and reference-guided assemblies were performed resulting in four near full-length RNA virus genomes. BLAST searches using de novo assembled sequences against published virus genomes confirmed the presence of previously detected begomoviruses in the Western Cape (WC) province, namely Sweet potato mosaic virus (SPMaV) and Sweet potato leaf curl Sao Paulo virus (SPLCSPV). The begomoviruses were detected in mixed infections with two major disease-causing RNA viruses, Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV). The sequence data further demonstrated mixed infections of RNA and DNA viruses from 11 of the 17 sequenced samples. Metagenomics is a reliable diagnostic tool for virus diversity detection, in particular virus-complexes and synergies affecting disease aetiology.
The tuber necrotic strain of Potato virus Y (PVY NTN ) causes widespread disease and has severe negative effects on the growth and yields of plants, especially those of the Solanaceae family. The consequences of residual toxicity and non-biodegradation of synthetic chemicals and pollution of the environment has led to investigations into new non-toxic and biological treatments to control plant viral diseases. Ethanolic extracts of Bowiea volubilis (bulbs), Cotyledon orbiculata (leaves), Gomphocarpus fruticosus (leaves), Merwilla plumbea (dry and fresh bulbs), Nerium oleander (leaves), and the fruits and leaves of Strophanthus speciosus, were evaluated against PVY NTN in vivo and in vitro. At a concentration of 20 mg • ml −1 , ethanolic extracts of Strophanthus speciosus (leaves) and fruits (50 mg • ml −1 ) significantly reduced the expression of PVY NTN symptoms on tobacco plants in vitro without affecting the normal growth and development of the plant. Similarly, at 50 mg • ml −1 , N. oleander, C. orbiculata and B. volubilis (fresh bulbs) and S. speciousus leaves at 20 mg • ml −1 extracts showed significant differences in PVY NTN symptoms in the in vivo experiment. Strophanthus speciosus leaf and fruit extracts showed significant inhibition in the in vitro and in vivo assays and demonstrated that S. speciosus has potential to be used as an antiphytoviral treatment.
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