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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Bibliographic Details
Published in:Viruses 2020-11, Vol.12 (12), p.1358
Main Authors: 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
Format: Article
Language:English
Subjects:
Acids
Animals
Computational Biology - methods
Data acquisition
Genome, Viral
Genomes
Hogs
Humans
Hybridization
Influenza A
Metagenomics
Metagenomics - methods
Nanopore Sequencing - methods
next-generation sequencing
Nucleic Acid Hybridization
one health
Pathogens
porcine viruses
Sequence Analysis, DNA
Severe acute respiratory syndrome coronavirus 2
shotgun metagenomic sequencing
targeted sequence capture
viral metagenomics
Virus Diseases - diagnosis
Virus Diseases - virology
Viruses
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Summary: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.
ISSN:1999-4915
1999-4915
DOI:10.3390/v12121358