The Status of Sweetpotato Viruses in South Africa: Using Viral Metagenomics for the Detection and Characterisation of Potyviruses, Criniviruses, Geminiviruses and Badnaviruses

To date, limited studies have been undertaken with regard to the etiology of Sweetpotato virus disease (SPVD) in South Africa. A metagenomic approach was adopted to establish the genetic diversity of viruses infecting sweetpotato. Total RNA was isolated from asymptomatic and symptomatic plants collected from the Eastern and Western Cape provinces, and depleted of ribosomal RNA (rRNA) using the Ribo-Zero Magnetic Kit. Sequencing was done on the Illumina MiSeq Benchtop platform. Sequence assembly and analysis were done using the CLC Bio Genomics Workbench, Velvet and PRICE. De novo and reference-guided assemblies generated near full-length virus genomes at high sequence depth. Sweet potato feathery mottle virus and Sweet potato virus C were detected in the Western and Eastern Cape symptomatic samples, while Sweet potato chlorotic stunt virus and Sweet potato virus G were detected in symptomatic plants from the Western Cape province only. Reads aligning to geminiviruses (Sweet potato mosaic virus and Sweet potato leaf curl Sao Paulo virus) were detected in symptomatic plants from the Western Cape; while badnaviruses (Sweet potato badnavirus A and Sweet potato badnavirus B) were detected in symptomatic and asymptomatic plants from both provinces. This is the first report of sweetpotato badnaviruses in South Africa. Virus presence was validated by PCR and RT-PCR. The sequence data demonstrates the presence of multiple RNA and DNA viruses in individual plants. We recommend the use of deep sequencing of nucleic acids as a reliable diagnostic tool for virus detection as well as for differentiating between diverse viral strains.