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Article

Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells

1
Institute for Infectious Diseases, University of Bern, CH-3012 Bern, Switzerland
2
Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
*
Author to whom correspondence should be addressed.
Genes 2019, 10(9), 659; https://doi.org/10.3390/genes10090659
Received: 31 July 2019 / Revised: 21 August 2019 / Accepted: 26 August 2019 / Published: 29 August 2019
(This article belongs to the Special Issue Viral Diagnostics Using Next-Generation Sequencing)
Enteroviruses affect millions of people worldwide and are of significant clinical importance. The standard method for enterovirus identification and genotyping still relies on Sanger sequencing of short diagnostic amplicons. In this study, we assessed the feasibility of nanopore sequencing using the new flow cell “Flongle” for fast, cost-effective, and accurate genotyping of human enteroviruses from clinical samples. PCR amplification of partial VP1 gene was performed from multiple patient samples, which were multiplexed together after barcoding PCR and sequenced multiple times on Flongle flow cells. The nanopore consensus sequences obtained from mapping reads to a reference database were compared to their Sanger sequence counterparts. Using clinical specimens sampled over different years, we were able to correctly identify enterovirus species and genotypes for all tested samples, even when doubling the number of barcoded samples on one flow cell. Average sequence identity across sequencing runs was >99.7%. Phylogenetic analysis showed that the consensus sequences achieved with Flongle delivered accurate genotyping. We conclude that the new Flongle-based assay with its fast turnover time, low cost investment, and low cost per sample represents an accurate, reproducible, and cost-effective platform for enterovirus identification and genotyping. View Full-Text
Keywords: enterovirus; NGS; nanopore sequencing; diagnostics enterovirus; NGS; nanopore sequencing; diagnostics
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MDPI and ACS Style

Grädel, C.; Terrazos Miani, M.A.; Barbani, M.T.; Leib, S.L.; Suter-Riniker, F.; Ramette, A. Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells. Genes 2019, 10, 659. https://doi.org/10.3390/genes10090659

AMA Style

Grädel C, Terrazos Miani MA, Barbani MT, Leib SL, Suter-Riniker F, Ramette A. Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells. Genes. 2019; 10(9):659. https://doi.org/10.3390/genes10090659

Chicago/Turabian Style

Grädel, Carole, Miguel A. Terrazos Miani, Maria T. Barbani, Stephen L. Leib, Franziska Suter-Riniker, and Alban Ramette. 2019. "Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells" Genes 10, no. 9: 659. https://doi.org/10.3390/genes10090659

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