Viral metagenomics reveals sweet potato virus diversity in the Eastern and Western Cape provinces of South Africa

Nhlapo, T F and Rees, D J G and Odeny, D A and Mulabisana, J M and Rey, M E C (2018) Viral metagenomics reveals sweet potato virus diversity in the Eastern and Western Cape provinces of South Africa. South African Journal of Botany (TSI), 117. pp. 256-267. ISSN 02546299

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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.

Item Type: Article
Divisions: Research Program : East & Southern Africa
Uncontrolled Keywords: Viral metagenomics, Ipomoea batatas, Virus detection, Next generation sequencing (NGS), Mixed infections, Sweet potato
Subjects: Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 27 Jul 2018 08:54
Last Modified: 27 Jul 2018 08:54
Official URL:
Funders: National Research Foundation of South Africa
Acknowledgement: This work is based on the research support in part by the National Research Foundation of South Africa (Grant reference number UID 79983). The authors would like to acknowledge our colleagues Sidwell Tjale, Thakhani Ramathavhatha, Sunette Laurie, for assistancewith sample collection; Molemi Rauwane and Mr. Thobejane for assistance with glasshouse trials; Jonathan Featherston, Marija Kvas, and Kerry-Anne Pillay for assistance with library preparation.
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