ArticleEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin2021
Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season.
Article in Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 32 citations in OpenAlex.
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- Nanopore sequencing for precise detection ofJournal of clinical microbiology · 2025Article
- Validation of an Automated, End-to-End Metagenomic Sequencing Assay for Agnostic Detection of Respiratory Viruses.The Journal of infectious diseases · 2024Article
- Cancer liquid biopsies by Oxford Nanopore Technologies sequencing of cell-free DNA: from basic research to clinical applications.Molecular cancer · 2024Review
- Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23.The Journal of infection · 2024Article
- The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research.Viruses · 2024Review
- An amplicon-based nanopore sequencing workflow for rapid tracking of avian influenza outbreaks, France, 2020-2022.Frontiers in cellular and infection microbiology · 2024Article
- Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana.Nature microbiology · 2023Article
- Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections.Molecular diagnosis & therapy · 2023Review
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Detection of Biological Molecules Using Nanopore Sensing Techniques.Biomedicines · 2023Review
- Review
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- Strategies and tools in illumina and nanopore-integrated metagenomic analysis of microbiome data.iMeta · 2023Review
- Investigating Epidemiologic and Molecular Links Between Patients With Community- and Hospital-Acquired Influenza A: 2017-2018 and 2019-2020, Michigan.Open forum infectious diseases · 2023Article
- Building a nomogram plot based on the nanopore targeted sequencing for predicting urinary tract pathogens and differentiating from colonizing bacteria.Frontiers in cellular and infection microbiology · 2023Article
- Metagenomic Sequencing for the Diagnosis ofInternational journal of molecular sciences · 2022Article
- A general approach to identify low-frequency variants within influenza samples collected during routine surveillance.Microbial genomics · 2022Article
- Metagenomic next-generation sequencing identified psittacosis among poultry processing workers in Shandong Province, China.Infectious medicine · 2022Article
- Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing.Frontiers in microbiology · 2022Article
Corrections and comments
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Authors and funding
18 authors at 4 institutions in 1 country.
Funding
Abstract
BackgroundInfluenza virus presents a considerable 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 infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.