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

Grädel, Carole; Terrazos Miani, Miguel Angel; Barbani, Maria Teresa; Leib, Stephen L.; Suter-Riniker, Franziska; Ramette, Alban (2019). Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells. Genes, 10(9) MDPI, Molecular Diversity Preservation International 10.3390/genes10090659

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Research
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Infection Serology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Clinical Microbiology

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Grädel, Carole Salome; Terrazos Miani, Miguel Angel; Barbani, Maria Teresa; Leib, Stephen; Suter, Franziska Marta and Ramette, Alban Nicolas

Subjects:

500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

ISSN:

2073-4425

Publisher:

MDPI, Molecular Diversity Preservation International

Language:

English

Submitter:

Stephen Leib

Date Deposited:

20 Sep 2019 10:34

Last Modified:

23 Oct 2019 10:06

Publisher DOI:

10.3390/genes10090659

PubMed ID:

31470607

Uncontrolled Keywords:

NGS diagnostics enterovirus nanopore sequencing

BORIS DOI:

10.7892/boris.133329

URI:

https://boris.unibe.ch/id/eprint/133329

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