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

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

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article number1358
JournalViruses
Volume12
Issue number12
Early online date27 Nov 2020
DOIs
Publication statusPublished - 31 Dec 2020

Keywords

  • next-generation sequencing
  • one health
  • porcine viruses
  • shotgun metagenomic sequencing
  • targeted sequence capture
  • viral metagenomics
  • virome

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

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