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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,...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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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. |
format | Online Article Text |
id | pubmed-7759923 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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