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,...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-11-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/12/1358 |
| _version_ | 1827701335312564224 |
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| author | Leonard Schuele 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 Natacha Couto |
| author_facet | Leonard Schuele 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 Natacha Couto |
| author_sort | Leonard Schuele |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T14:31:08Z |
| format | Article |
| id | doaj.art-7c0ded7201be45e6a8699120c177d9df |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T14:31:08Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-7c0ded7201be45e6a8699120c177d9df2023-11-20T22:34:04ZengMDPI AGViruses1999-49152020-11-011212135810.3390/v12121358Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical SamplesLeonard Schuele0Hayley Cassidy1Erley Lizarazo2Katrin Strutzberg-Minder3Sabine Schuetze4Sandra Loebert5Claudia Lambrecht6Juergen Harlizius7Alex W. Friedrich8Silke Peter9Hubert G. M. Niesters10John W. A. Rossen11Natacha Couto12Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The NetherlandsDepartment of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The NetherlandsDepartment of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The NetherlandsIVD Innovative Veterinary Diagnostics (IVD GmbH), 30926 Seelze, GermanyAnimal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, GermanyAnimal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, GermanyAnimal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, GermanyAnimal Health Services, Chamber of Agriculture of North Rhine-Westphalia, 59505 Bad Sassendorf, GermanyDepartment of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The NetherlandsInstitute of Medical Microbiology and Hygiene, University of Tübingen, 72076 Tübingen, GermanyDepartment of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The NetherlandsDepartment of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The NetherlandsDepartment of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 RC Groningen, The NetherlandsShotgun 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.https://www.mdpi.com/1999-4915/12/12/1358next-generation sequencingone healthshotgun metagenomic sequencingporcine virusestargeted sequence captureviral metagenomics |
| spellingShingle | Leonard Schuele 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 Natacha Couto Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples Viruses next-generation sequencing one health shotgun metagenomic sequencing porcine viruses targeted sequence capture viral metagenomics |
| 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 | next-generation sequencing one health shotgun metagenomic sequencing porcine viruses targeted sequence capture viral metagenomics |
| url | https://www.mdpi.com/1999-4915/12/12/1358 |
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