About: Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission

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About: Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission
Creator	Vipond, Richard Carroll, Miles Foster, Dona Jeffery, Katie Kavanagh, James Lewandowski, Kuiama Morgan, Marcus Sanderson, Nicholas Xu, Yifei Lumley, Sheila Matthews, Philippa Walker, A Crook, Derrick Peto, Timothy Pullan, Steven Downs, Louise Hender, Thomas Vaughan, Ali
Source	MedRxiv
abstract	Background: Influenza virus presents a significant challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid diagnosis of infection, rationalising antimicrobial therapy, and supporting interventions for infection control. This study aimed to evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings. Methods: We conducted Nanopore metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic testing. We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data. Results: Metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses compared with the diagnostic standard (Cepheid Xpress/BioFire FilmArray Respiratory Panel). We identified a H3N2 genome with the oseltamivir resistant S331R mutation in the NA protein, potentially associated with the emergence of a distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in the infectious diseases ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant strain circulating in the community. We also detected a range of other potentially pathogenic viruses and bacteria from the metagenome. Conclusion: Nanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Generation of full genomes can contribute to the investigation and management of nosocomial outbreaks.
has issue date	2020-04-22(xsd:dateTime)
bibo:doi	10.1101/2020.04.21.20073072
has license	medrxiv
sha1sum (hex)	dfaf345802b4c3dac0aac96c7df4cc66785bfef5
schema:url	https://doi.org/10.1101/2020.04.21.20073072
resource representing a document's title	Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission
resource representing a document's body	covid:dfaf345802b4c3dac0aac96c7df4cc66785bfef5#body_text
is schema:about of	named entity 'applicability' named entity 'influenza' named entity 'viruses' named entity 'Title' named entity 'PROVIDING' named entity 'ROUTINE' named entity 'BACKGROUND' named entity 'infection' named entity 'Influenza virus' named entity 'infection control' named entity 'infection' named entity 'infection control' named entity 'metagenomic sequencing' named entity 'pandemics' named entity 'drug resistance' named entity 'influenza viruses' named entity 'influenza virus' named entity 'preprint' named entity 'preprint' named entity 'clade' named entity 'SNPs' named entity 'Nanopore' named entity 'IAV' named entity 'doi' named entity 'enveloped viruses' named entity 'medRxiv' named entity 'genome sequence' named entity 'mutation' named entity 'medRxiv' named entity 'IAV' named entity 'Nanopore' named entity 'turnaround time' named entity 'peer review' named entity 'RNA' named entity 'medRxiv' named entity 'genome' named entity 'Influenza A viruses' named entity 'reassortment' named entity 'genomes' named entity 'drug resistance' named entity 'M2 protein' named entity 'influenza' named entity 'Nanopore sequencing' named entity 'H3N2' named entity 'genome' named entity 'medRxiv' named entity 'genome' named entity 'medRxiv' named entity 'Nanopore' named entity 'pH1N1' named entity 'H3N2' named entity 'genome' named entity 'genetically diverse' named entity 'epidemics' named entity 'medRxiv' named entity 'HMPV' named entity 'H3 subtype' named entity 'medRxiv' named entity 'clinical diagnostic' named entity 'preprint' named entity 'influenza season' named entity 'sequence data' named entity 'parainfluenza' named entity 'genome' named entity 'nosocomial' named entity 'viruses' named entity 'ONT' named entity 'preprint'

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