دورية أكاديمية
Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23.
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.) |
References: | J Infect Dis. 2018 Sep 22;218(9):1485-1489. (PMID: 29873767) J Infect. 2021 Oct;83(4):473-482. (PMID: 34332019) Nat Methods. 2022 Jul;19(7):823-826. (PMID: 35789207) J Virol. 2009 Oct;83(19):10309-13. (PMID: 19605485) Nature. 2021 Dec;600(7889):506-511. (PMID: 34649268) Nature. 2023 Nov;623(7985):132-138. (PMID: 37853126) Front Microbiol. 2018 Nov 13;9:2748. (PMID: 30483243) Lancet Infect Dis. 2009 May;9(5):291-300. (PMID: 19393959) Influenza Other Respir Viruses. 2017 Sep;11(5):367-371. (PMID: 28646615) BMC Infect Dis. 2020 Sep 3;20(1):648. (PMID: 32883215) Emerg Infect Dis. 2018 Mar;24(3):492-497. (PMID: 29460729) Influenza Other Respir Viruses. 2019 Nov;13(6):556-563. (PMID: 31536169) Nat Biotechnol. 2017 Apr 11;35(4):316-319. (PMID: 28398311) Nature. 2016 Feb 11;530(7589):228-232. (PMID: 26840485) Am J Epidemiol. 2008 Apr 1;167(7):775-85. (PMID: 18230677) Microb Genom. 2023 Aug;9(8):. (PMID: 37590039) J Clin Microbiol. 2019 Dec 23;58(1):. (PMID: 31666364) BMC Med. 2024 Mar 26;22(1):143. (PMID: 38532381) Euro Surveill. 2021 Jul;26(27):. (PMID: 34240696) J Clin Microbiol. 2023 Jul 20;61(7):e0044823. (PMID: 37338345) |
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 |
تدمد: | 1532-2742 |
---|---|
DOI: | 10.1016/j.jinf.2024.106164 |