Nanopore metagenomic sequencing of full length human metapneumovirus (HMPV) within a unique sub-lineage
Nanopore metagenomic sequencing of full length human metapneumovirus (HMPV) within a unique sub-lineage
Abstract Human metapneumovirus (HMPV) has been recognized as an important pathogen which can cause a spectrum of respiratory tract disease. Here, we report Nanopore metagenomic sequencing of the first full length HMPV genome directly from a throat swab from a UK patient with complex lung disease and immunocompromise. We found a predominance (26.4%) of HMPV reads in the metagenomic sequencing data and consequently assembled the full genome at a high depth of coverage (mean 4,786). Through phylogenetic analyses, we identified this HMPV strain to originate from a unique genetic group in A2b, showing the presence of this group in the UK. Our study demonstrated the effectiveness of Nanopore metagenomic sequencing for diagnosing infectious diseases and recovering complete sequences for genomic characterization, highlighting the applicability of Nanopore sequencing in clinical settings. ImportanceNanopore metagenomic sequencing has the potential to evolve as a point-of-care test for a range of infectious diseases. Here, we report the first full length human metapneumovirus (HMPV) genome in the UK sequenced by Nanopore from a non-invasive sample from an immunocompromised patient. We demonstrate the presence of HMPV from a unique genetic group not previously reported from the UK. Our study demonstrates the effectiveness of Nanopore sequencing for diagnosing an infection that was not detected by routine first-line tests in the clinical microbiology laboratory. We report sufficient genomic data to provide insight into the epidemiology of infection and with the potential to inform treatment decisions.
Vipond Richard、Lewandowski Kuiama、Jeffery Katie、Walker A Sarah、Peto Timothy、Crook Derrick、Matthews Philippa C、Vaughan Ali、Pullan Steven T、Sanderson Nicholas、Xu Yifei、Lumley Sheila、Foster Dona、Carroll Miles
Public Health England, National Infection ServicePublic Health England, National Infection ServiceDepartment of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalNuffield Department of Medicine, University of Oxford||NIHR Oxford Biomedical Research Centre, University of OxfordNuffield Department of Medicine, University of Oxford||NIHR Oxford Biomedical Research Centre, University of OxfordNuffield Department of Medicine, University of Oxford||NIHR Oxford Biomedical Research Centre, University of OxfordNIHR Oxford Biomedical Research Centre, University of Oxford||Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford||Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalNuffield Department of Medicine, University of Oxford||NIHR Oxford Biomedical Research Centre, University of OxfordPublic Health England, National Infection ServiceNuffield Department of Medicine, University of Oxford||NIHR Oxford Biomedical Research Centre, University of OxfordNuffield Department of Medicine, University of Oxford||NIHR Oxford Biomedical Research Centre, University of OxfordNuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford||Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalNuffield Department of Medicine, University of Oxford||NIHR Oxford Biomedical Research Centre, University of OxfordPublic Health England, National Infection Service
医学研究方法微生物学分子生物学
Human metapneumovirusHMPVnanopore sequencingmetagenomicsthroat swabunique genetic grouprespiratory tract infectioncystic fibrosislung transplantmicrobiome
Vipond Richard,Lewandowski Kuiama,Jeffery Katie,Walker A Sarah,Peto Timothy,Crook Derrick,Matthews Philippa C,Vaughan Ali,Pullan Steven T,Sanderson Nicholas,Xu Yifei,Lumley Sheila,Foster Dona,Carroll Miles.Nanopore metagenomic sequencing of full length human metapneumovirus (HMPV) within a unique sub-lineage[EB/OL].(2025-03-28)[2025-06-28].https://www.biorxiv.org/content/10.1101/496687.点此复制
评论