Next-generation sequencing for virus detection : covering all the bases

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dc.contributor.authorVisser, Marikeen_ZA
dc.contributor.authorBester, Rachelleen_ZA
dc.contributor.authorBurger, Johan T.en_ZA
dc.contributor.authorMaree, Hans J.en_ZA
dc.date.accessioned2016-06-15T12:09:24Z
dc.date.available2016-06-15T12:09:24Z
dc.date.issued2016-06
dc.descriptionCITATION: Visser, M., et al. 2016. Next-generation sequencing for virus detection : covering all the base. Virology Journal, 13(1): 85, doi: 10.1186/s12985-016-0539-x.
dc.descriptionThe original publication is available at http://bmcmusculoskeletdisord.biomedcentral.com
dc.descriptionPublication of this article was funded by the Stellenbosch University Open Access Fund.
dc.description.abstractBackground: 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. Findings: 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. Conclusion: 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.en_ZA
dc.description.versionPublisher's version
dc.format.extent6 pages
dc.identifier.citationVisser, M., et al. 2016. Next-generation sequencing for virus detection : covering all the base. Virology Journal, 13(1): 85, doi: 10.1186/s12985-016-0539-x
dc.identifier.issn1743-422X (online)
dc.identifier.issn1743-422X (print)
dc.identifier.otherdoi: 10.1186/s12985-016-0539-x
dc.identifier.urihttp://hdl.handle.net/10019.1/99041
dc.language.isoen_ZAen_ZA
dc.publisherBioMed Central
dc.rights.holderAuthors retain copyright
dc.subjectClosterovirusen_ZA
dc.subjectGenome coverageen_ZA
dc.subjectGLRaV-3en_ZA
dc.subjectNext-generation sequencingen_ZA
dc.subjectSequencing depthen_ZA
dc.subjectVirus detectionen_ZA
dc.titleNext-generation sequencing for virus detection : covering all the basesen_ZA
dc.typeArticleen_ZA
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