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Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples

Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity,...

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Autores principales: Schuele, Leonard, Cassidy, Hayley, Lizarazo, Erley, Strutzberg-Minder, Katrin, Schuetze, Sabine, Loebert, Sandra, Lambrecht, Claudia, Harlizius, Juergen, Friedrich, Alex W., Peter, Silke, Niesters, Hubert G. M., Rossen, John W. A., Couto, Natacha
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759923/
https://www.ncbi.nlm.nih.gov/pubmed/33260903
http://dx.doi.org/10.3390/v12121358
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author Schuele, Leonard
Cassidy, Hayley
Lizarazo, Erley
Strutzberg-Minder, Katrin
Schuetze, Sabine
Loebert, Sandra
Lambrecht, Claudia
Harlizius, Juergen
Friedrich, Alex W.
Peter, Silke
Niesters, Hubert G. M.
Rossen, John W. A.
Couto, Natacha
author_facet Schuele, Leonard
Cassidy, Hayley
Lizarazo, Erley
Strutzberg-Minder, Katrin
Schuetze, Sabine
Loebert, Sandra
Lambrecht, Claudia
Harlizius, Juergen
Friedrich, Alex W.
Peter, Silke
Niesters, Hubert G. M.
Rossen, John W. A.
Couto, Natacha
author_sort Schuele, Leonard
collection PubMed
description Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.
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spelling pubmed-77599232020-12-26 Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples Schuele, Leonard Cassidy, Hayley Lizarazo, Erley Strutzberg-Minder, Katrin Schuetze, Sabine Loebert, Sandra Lambrecht, Claudia Harlizius, Juergen Friedrich, Alex W. Peter, Silke Niesters, Hubert G. M. Rossen, John W. A. Couto, Natacha Viruses Article Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative. MDPI 2020-11-27 /pmc/articles/PMC7759923/ /pubmed/33260903 http://dx.doi.org/10.3390/v12121358 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Schuele, Leonard
Cassidy, Hayley
Lizarazo, Erley
Strutzberg-Minder, Katrin
Schuetze, Sabine
Loebert, Sandra
Lambrecht, Claudia
Harlizius, Juergen
Friedrich, Alex W.
Peter, Silke
Niesters, Hubert G. M.
Rossen, John W. A.
Couto, Natacha
Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
title Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
title_full Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
title_fullStr Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
title_full_unstemmed Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
title_short Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples
title_sort assessment of viral targeted sequence capture using nanopore sequencing directly from clinical samples
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759923/
https://www.ncbi.nlm.nih.gov/pubmed/33260903
http://dx.doi.org/10.3390/v12121358
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