Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing.

Grädel, Carole; Terrazos Miani, Miguel A.; Baumann, Christian; Barbani, Maria Teresa; Neuenschwander, Stefan; Leib, Stephen L.; Suter-Riniker, Franziska; Ramette, Alban (2020). Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing. Viruses, 12(8) Molecular Diversity Preservation International MDPI 10.3390/v12080841

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Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains.

Item Type:

Journal Article (Original Article)

Division/Institute:

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

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

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

Subjects:

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

ISSN:

1999-4915

Publisher:

Molecular Diversity Preservation International MDPI

Language:

English

Submitter:

Alban Ramette

Date Deposited:

12 Nov 2020 12:27

Last Modified:

12 Nov 2020 12:27

Publisher DOI:

10.3390/v12080841

PubMed ID:

32752120

Uncontrolled Keywords:

direct RNA sequencing enterovirus nanopore

BORIS DOI:

10.7892/boris.147598

URI:

https://boris.unibe.ch/id/eprint/147598

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