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Next-generation sequencing for virus detection: covering all the bases
Marike Visser1,2, Rachelle Bester2, Johan T Burger2
1Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa.
Virology Journal
|June 3, 2016
Summary
For accurate virus detection using next-generation sequencing, ribo-depleted RNA offers superior genome coverage. One million reads are sufficient for closterovirus detection with de novo assembly.
Area of Science:
- Virology
- Genomics
- Bioinformatics
Background:
- Next-generation sequencing (NGS) is a standard technique for virus detection.
- Optimal study design requires sufficient data for comprehensive viral genome coverage.
Purpose of the Study:
- To evaluate genome coverage at various sequencing depths for diverse viruses and library types.
- To compare read-mapping and de novo assembly approaches for viral genome detection.
Main Methods:
- Assessed genome coverage across different sequencing depths and library types (ribo-depleted RNA, sRNA, poly(A)-selected RNA).
- Utilized both read-mapping and de novo assembly methodologies.
- Analyzed data for various viruses, viroids, and host organisms.
Main Results:
- Ribo-depleted RNA and small RNA (sRNA) libraries achieved saturated genome coverage with minimal data.
- Poly(A)-selected RNA provided insufficient coverage for non-polyadenylated viruses.
- Ribo-depleted RNA outperformed sRNA in achieving higher genome coverage, especially with de novo assembly.
Conclusions:
- Ribo-depleted RNA combined with de novo assembly is recommended for single-stranded RNA virus detection.
- Sequencing approximately one million reads ensures adequate genome coverage for closterovirus detection.
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