دورية أكاديمية
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Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23.

التفاصيل البيبلوغرافية
العنوان: Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23.
المؤلفون: Cane J; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom., Sanderson N; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom., Barnett S; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom., Vaughan A; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom., Pott M; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom., Kapel N; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom., Morgan M; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom., Jesuthasan G; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom., Samuel R; Berkshire and Surrey Pathology Services, Camberley, United Kingdom., Ehsaan M; Berkshire and Surrey Pathology Services, Camberley, United Kingdom., Boothe H; Berkshire and Surrey Pathology Services, Camberley, United Kingdom., Haduli E; Berkshire and Surrey Pathology Services, Camberley, United Kingdom., Studley R; Office for National Statistics, Newport, United Kingdom., Rourke E; Office for National Statistics, Newport, United Kingdom., Diamond I; Office for National Statistics, Newport, United Kingdom., Fowler T; UK Health Security Agency, United Kingdom; William Harvey Research Institute, Queen Mary University of London, London, United Kingdom., Watson C; UK Health Security Agency, United Kingdom., Stoesser N; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom., Walker AS; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom., Street T; NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom., Eyre DW; Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom; Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom. Electronic address: david.eyre@bdi.ox.ac.uk.
المصدر: The Journal of infection [J Infect] 2024 Jun; Vol. 88 (6), pp. 106164. Date of Electronic Publication: 2024 Apr 29.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: W.B. Saunders Country of Publication: England NLM ID: 7908424 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1532-2742 (Electronic) Linking ISSN: 01634453 NLM ISO Abbreviation: J Infect Subsets: MEDLINE
أسماء مطبوعة: Publication: Kent, UK : W.B. Saunders
Original Publication: London, New York, Academic Press.
مواضيع طبية MeSH: Influenza, Human*/epidemiology , Influenza, Human*/virology , Nanopore Sequencing*/methods , Influenza B virus*/genetics , Influenza B virus*/isolation & purification , Influenza B virus*/classification, Humans ; United Kingdom/epidemiology ; Female ; Male ; Influenza A virus/genetics ; Influenza A virus/classification ; Influenza A virus/isolation & purification ; Adult ; Middle Aged ; Adolescent ; Aged ; Young Adult ; Child ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A Virus, H1N1 Subtype/isolation & purification ; Influenza A Virus, H3N2 Subtype/genetics ; Influenza A Virus, H3N2 Subtype/isolation & purification ; Influenza A Virus, H3N2 Subtype/classification
مستخلص: Objectives: We evaluated Nanopore sequencing for influenza surveillance.
Methods: Influenza A and B PCR-positive samples from hospital patients in Oxfordshire, UK, and a UK-wide population survey from winter 2022-23 underwent Nanopore sequencing following targeted rt-PCR amplification.
Results: From 941 infections, successful sequencing was achieved in 292/388 (75 %) available Oxfordshire samples: 231 (79 %) A/H3N2, 53 (18 %) A/H1N1, and 8 (3 %) B/Victoria and in 53/113 (47 %) UK-wide samples. Sequencing was more successful at lower Ct values. Most same-sample replicate sequences had identical haemagglutinin segments (124/141, 88 %); 36/39 (92 %) Illumina vs. Nanopore comparisons were identical, and 3 (8 %) differed by 1 variant. Comparison of Oxfordshire and UK-wide sequences showed frequent inter-regional transmission. Infections were closely-related to 2022-23 vaccine strains. Only one sample had a neuraminidase inhibitor resistance mutation. 849/941 (90 %) Oxfordshire infections were community-acquired. 63/88 (72 %) potentially healthcare-associated cases shared a hospital ward with ≥ 1 known infectious case. 33 epidemiologically-plausible transmission links had sequencing data for both source and recipient: 8 were within ≤ 5 SNPs, of these, 5 (63 %) involved potential sources that were also hospital-acquired.
Conclusions: Nanopore influenza sequencing was reproducible and antiviral resistance rare. Inter-regional transmission was common; most infections were genomically similar. Hospital-acquired infections are likely an important source of nosocomial transmission and should be prioritised for infection prevention and control.
Competing Interests: Declaration of Competing Interest No author has a conflict of interest to declare.
(Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
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فهرسة مساهمة: Keywords: Epidemiology; Influenza; Respiratory virus; Sequencing
تواريخ الأحداث: Date Created: 20240501 Date Completed: 20240519 Latest Revision: 20240603
رمز التحديث: 20240603
مُعرف محوري في PubMed: PMC11101610
DOI: 10.1016/j.jinf.2024.106164
PMID: 38692359
قاعدة البيانات: MEDLINE
الوصف
تدمد:1532-2742
DOI:10.1016/j.jinf.2024.106164