Viral Metagenomic Analysis of Sweet Potato Using High-Throughput Deep Sequencing

To date, limited studies have been undertaken with regard to the etiology of Sweet potato virus disease (SPVD) in South Africa. In this study, a non-enrichment metagenomic approach was adopted to establish the genetic diversity of RNA viruses infecting sweet potato. 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^TM Magnetic Kit. Sequencing was done on the Illumina MiSeq Benchtop platform. Sequence assembly and analysis were done using the CLC Bio Genomics Workbench, Metavir2 and ShoRAH. 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 only. Reads aligning to geminiviruses (Sweet potato mosaic-associated virus and Sweet potato leaf curl Sao Paulo virus) were detected in symptomatic plants from the Western Cape and two badnaviruses (Sweet badnavirus A and Sweet potato badnavirus B) were detected in symptomatic and asymptomatic plants from both provinces. This is the first report of sweet potato badnaviruses in South Africa. The sequence data gives evidence of mixed infections of multiple RNA and DNA viruses in individual plant samples. rRNA depletion and deep sequencing of nucleic acids can be used as a diagnostic tool, which detects viruses and differentiates between diverse viral strains.