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

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. FINDINGS: In this study, genome coverage at different seque...

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Autores principales: Visser, Marike, Bester, Rachelle, Burger, Johan T., Maree, Hans J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890495/
https://www.ncbi.nlm.nih.gov/pubmed/27250973
http://dx.doi.org/10.1186/s12985-016-0539-x
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author Visser, Marike
Bester, Rachelle
Burger, Johan T.
Maree, Hans J.
author_facet Visser, Marike
Bester, Rachelle
Burger, Johan T.
Maree, Hans J.
author_sort Visser, Marike
collection PubMed
description 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. 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-016-0539-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-48904952016-06-03 Next-generation sequencing for virus detection: covering all the bases Visser, Marike Bester, Rachelle Burger, Johan T. Maree, Hans J. Virol J Short Report 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. 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-016-0539-x) contains supplementary material, which is available to authorized users. BioMed Central 2016-06-02 /pmc/articles/PMC4890495/ /pubmed/27250973 http://dx.doi.org/10.1186/s12985-016-0539-x Text en © Visser et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Short Report
Visser, Marike
Bester, Rachelle
Burger, Johan T.
Maree, Hans J.
Next-generation sequencing for virus detection: covering all the bases
title Next-generation sequencing for virus detection: covering all the bases
title_full Next-generation sequencing for virus detection: covering all the bases
title_fullStr Next-generation sequencing for virus detection: covering all the bases
title_full_unstemmed Next-generation sequencing for virus detection: covering all the bases
title_short Next-generation sequencing for virus detection: covering all the bases
title_sort next-generation sequencing for virus detection: covering all the bases
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890495/
https://www.ncbi.nlm.nih.gov/pubmed/27250973
http://dx.doi.org/10.1186/s12985-016-0539-x
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