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Article

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

1
Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The Netherlands
2
Institute of Medical Microbiology and Hygiene, University of Tübingen, 72076 Tübingen, Germany
3
IVD Innovative Veterinary Diagnostics (IVD GmbH), 30926 Seelze, Germany
4
Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, Germany
5
Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
6
Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
These authors contributed equally to this work.
Academic Editor: Arvind Varsani
Viruses 2020, 12(12), 1358; https://doi.org/10.3390/v12121358
Received: 10 November 2020 / Revised: 23 November 2020 / Accepted: 25 November 2020 / Published: 27 November 2020
(This article belongs to the Special Issue Viral Genomics: Elucidating Virology in a Metagenomic World)
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. View Full-Text
Keywords: next-generation sequencing; one health; shotgun metagenomic sequencing; porcine viruses; targeted sequence capture; viral metagenomics; virome next-generation sequencing; one health; shotgun metagenomic sequencing; porcine viruses; targeted sequence capture; viral metagenomics; virome
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MDPI and ACS Style

Schuele, L.; Cassidy, H.; Lizarazo, E.; Strutzberg-Minder, K.; Schuetze, S.; Loebert, S.; Lambrecht, C.; Harlizius, J.; Friedrich, A.W.; Peter, S.; Niesters, H.G.M.; Rossen, J.W.A.; Couto, N. Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples. Viruses 2020, 12, 1358. https://doi.org/10.3390/v12121358

AMA Style

Schuele L, Cassidy H, Lizarazo E, Strutzberg-Minder K, Schuetze S, Loebert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Niesters HGM, Rossen JWA, Couto N. Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples. Viruses. 2020; 12(12):1358. https://doi.org/10.3390/v12121358

Chicago/Turabian Style

Schuele, Leonard, Hayley Cassidy, Erley Lizarazo, Katrin Strutzberg-Minder, Sabine Schuetze, Sandra Loebert, Claudia Lambrecht, Juergen Harlizius, Alex W. Friedrich, Silke Peter, Hubert G. M. Niesters, John W. A. Rossen, and Natacha Couto. 2020. "Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples" Viruses 12, no. 12: 1358. https://doi.org/10.3390/v12121358

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