title: Next-generation sequencing for virus detection: covering all the bases.
abstract: BACKGROUND
  The use of next-generation sequencing has become an established method for virus detection. Efficient study design for accurate detection relies on the optimal amount of data representing a significant portion of a virus genome.
  
  
  RESULTS
  In this study, genome coverage at different sequencing depths was determined for a number of viruses, viroids, hosts and sequencing library types, using both read-mapping and de novo assembly-based approaches. The results highlighted the strength of ribo-depleted RNA and sRNA in obtaining saturated genome coverage with the least amount of data, while even though the poly(A)-selected RNA yielded virus-derived reads, it was insufficient to cover the complete genome of a non-polyadenylated virus. The ribo-depleted RNA data also outperformed the sRNA data in terms of the percentage of coverage that could be obtained particularly with the de novo assembled contigs.
  
  
  CONCLUSIONS
  Our results suggest the use of ribo-depleted RNA in a de novo assembly-based approach for the detection of single-stranded RNA viruses. Furthermore, we suggest that sequencing one million reads will provide sufficient genome coverage specifically for closterovirus detection.
authors.affiliation: Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa.|Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
authors.forename: Marike
authors.initials: M
authors.lastname: Visser
authors.affiliation: Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
authors.forename: Rachelle
authors.initials: R
authors.lastname: Bester
authors.affiliation: Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
authors.forename: Johan T
authors.initials: JT
authors.lastname: Burger
authors.affiliation: Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa. hjmaree@sun.ac.za.|Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. hjmaree@sun.ac.za.
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Maree
mesh_terms: D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012328:RNA Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014772:Viroids / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*
keywords: CTV; Closterovirus; GLRaV-3; Genome coverage; Next-generation sequencing; Sequencing depth; Virus detection