Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses

Daniel Wüthrich; Daniela Lang; Nicola F Müller; Richard A Neher; Tanja Stadler; Adrian Egli

doi:10.1016/j.jviromet.2019.01.009

Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses

J Virol Methods. 2019 Apr:266:30-33. doi: 10.1016/j.jviromet.2019.01.009. Epub 2019 Jan 21.

Authors

Daniel Wüthrich¹, Daniela Lang², Nicola F Müller³, Richard A Neher⁴, Tanja Stadler³, Adrian Egli⁵

Affiliations

¹ Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland.
² Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
³ Swiss Institute of Bioinformatics, Basel, Switzerland; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
⁴ Swiss Institute of Bioinformatics, Basel, Switzerland; Biozentrum, University of Basel, Basel, Switzerland.
⁵ Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland. Electronic address: adrian.egli@usb.ch.

PMID: 30677464
DOI: 10.1016/j.jviromet.2019.01.009

Abstract

We compared two sample preparation protocols for whole genome sequencing of influenza A viruses. Each protocol was assessed using cDNA quantity and quality and the resulting mean genome coverage after sequencing. Both protocols produced acceptable result for samples with high viral load, whereas one protocol performed slightly better with limited virus count.

Keywords: Influenza A; Method; Typing; Virus; Whole genome sequencing.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't

MeSH terms

DNA, Viral / genetics
Genome, Viral
High-Throughput Nucleotide Sequencing / methods
Humans
Influenza A virus / classification*
Influenza A virus / genetics*
Influenza, Human / virology
Specimen Handling / methods*
Whole Genome Sequencing / methods*
Workflow*

Substances

DNA, Viral