Next generation sequencing approaches for the detection and characterization of enteroviruses in clinical, public health, and research settings: Expert view of the European non-polio enterovirus network (ENPEN)
Journal of Clinical Virology, vol. 184, pp. 105940
Abstract
Enteroviruses (EVs) are a common cause of a wide spectrum of infectious diseases, ranging from mild respiratory illnesses to severe neurological conditions, particularly affecting children. Current molecular methods, such as 5'UTR-based PCR for detection and (partial) VP1 gene sequencing for typing, are widely utilized. However, Next-Generation Sequencing (NGS), and bioinformatics offer a comprehensive alternative, enabling full-genome analyses for improved virus characterization, genomic epidemiological surveillance, and outbreak investigation. Despite its advantages, implementation of NGS poses challenges, particularly in standardizing and optimizing laboratory workflows (wet-lab) and bioinformatics analyses (dry-lab), methods that are not often readily accessible in many laboratories. Here, we discuss the potential of NGS as a tool for EV detection/characterization in clinical virology, public health, and research settings. We provide practical options for actions for implementing NGS to advance the understanding and management of enterovirus infections. These recommendations are based on expert discussions during the recent European non-polio enterovirus network (ENPEN) workshop held in Corfu, Greece, on 23-24 May 2024, aiming to guide harmonization of NGS practices across clinical, public health, and research settings.
Authors 77
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National Institute for Public Health and the Environment
Affiliation as printed
Centre for Infectious Disease Control (CIb), Centre for Infectious Disease Research, Diagnostics and laboratory Surveillance (IDS) Dutch National Institute for Public Health and the Environment, Bilthoven, the Netherlands. Electronic address: kim.benschop@rivm.nl
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National Institute for Public Health and the Environment
Affiliation as printed
Centre for Infectious Disease Control (CIb), Centre for Infectious Disease Research, Diagnostics and laboratory Surveillance (IDS) Dutch National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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Affiliation as printed
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden
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Vall d'Hebron Institut de Recerca · Vall d'Hebron Hospital Universitari
Affiliation as printed
Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Spain
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Vall d'Hebron Institut de Recerca · Vall d'Hebron Hospital Universitari
Affiliation as printed
Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Spain
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Universitat Autònoma de Barcelona · Hospital de Sant Pau
Affiliation as printed
Microbiology Department. Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
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National Laboratory of Health, Environment and Food
Affiliation as printed
National Laboratory of Health, Environment and Food, Laboratory for Public Health Virology, Ljubljana, Slovenia
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Centre National de la Recherche Scientifique · Institut Pasteur · Université Paris Cité · Department of Virology
Affiliation as printed
Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus sensing & signaling Unit, Paris, France
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Centre Hospitalier Universitaire de Clermont-Ferrand
Affiliation as printed
CHU Clermont-Ferrand, 3 IHP, National Reference Centre for enteroviruses and parechoviruses, Clermont-Ferrand, France
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Medicines and Healthcare products Regulatory Agency
Affiliation as printed
Division of Vaccines, Science and Research, Medicines and Healthcare products Regulatory Agency, South Mimms, (MHRA), Hertfordshire EN6 3QG, United Kingdom
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Nottingham University Hospitals NHS Trust
Affiliation as printed
Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, NG7 2UH, United Kingdom
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Lund University · Skåne University Hospital
Affiliation as printed
Department of Clinical microbiology, Lund University Hospital, Lund, Sweden
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Elisabeth-TweeSteden Ziekenhuis · ZorgSaam
Affiliation as printed
ElisabethTweesteden Hospital, Tilburg, the Netherlands; Zorgsaam, Terneuzen, the Netherlands
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European Centre for Disease Prevention and Control
Affiliation as printed
European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
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Affiliation as printed
Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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Ospedale Sacro Cuore Don Calabria
Affiliation as printed
Department of Infectious, Tropical Diseases and Microbiology - IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella (VR), Italy
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Affiliation as printed
Enteric Virus Unit, Virus Reference Department, UK Health Security Agency, London, United Kingdom
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Charles University · University Hospital in Motol
Affiliation as printed
Department of Microbiology, Second Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic
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Affiliation as printed
National Biosafety Laboratory, National Center for Public Health and Pharmacy, Budapest, Hungary
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Affiliation as printed
Institute of Virology, University Hospital Bonn, Germany
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Affiliation as printed
Laboratory for Medical Microbiology and Immunology, Dicoon, Elst, the Netherlands
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National Institute of Public Health
Affiliation as printed
National Reference Laboratory for Enteroviruses, National Institute of Public Health, Prague, Czech Republic
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Institutul National de Sanatate Publica
Affiliation as printed
National Institute of Public Health, Bucharest, Romania
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National Center of Infectious and Parasitic Diseases
Affiliation as printed
National Reference Laboratory for Enteroviruses, Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
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Affiliation as printed
Department of Clinical Surgical Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
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Vall d'Hebron Institut de Recerca · Vall d'Hebron Hospital Universitari
Affiliation as printed
Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Spain
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Guy's and St Thomas' NHS Foundation Trust
Affiliation as printed
Infectious Diseases and Microbiology Department, Guy's and St Thomas' NHS Foundation Trust, United Kingdom
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University Medical Center Groningen · University of Groningen
Affiliation as printed
Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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Affiliation as printed
Virology laboratory, Bristol, United Kingdom Health Security Agency, Bristol, United Kingdom
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Affiliation as printed
Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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Affiliation as printed
Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
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Affiliation as printed
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
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Children's Hospital Agia Sophia
Affiliation as printed
Microbiology Department, Agia Sofia Children's Hospital, Athens, Greece
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Affiliation as printed
Department of Clinical Research, Nordsjællands Hospital, Hilleroed, Denmark
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Affiliation as printed
Pathogen Sequencing Service, Specialist Virology Centre, Edinburgh, Royal Infirmary of Edinburgh, Edinbrugh, Scotland, United Kingdom
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Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
Laboratory Diagnostic Center, University Hospital RWTH Aachen, Aachen, Germany
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Hospital Universitario de Gran Canaria Doctor Negrín
Affiliation as printed
Microbiology Department, Doctor Negrin Gran Canaria's Universitary Hospital, Gran Canaria, Spain
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Oslo University Hospital · University of Oslo
Affiliation as printed
Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Affiliation as printed
Pharmaceutical Care Research Group, University College Cork, Cork, Ireland
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Universitat de València · Instituto de Salud Carlos III · Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana · Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública
Affiliation as printed
CIBERESP, Instituto de Salud Carlos III, Madrid, Spain; Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO - Public Health), Valencia, Spain; Department of Microbiology & Ecology, University of Valencia Medical School, Spain
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Affiliation as printed
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
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Affiliation as printed
Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
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Medicines and Healthcare products Regulatory Agency
Affiliation as printed
Division of Vaccines, Science and Research, Medicines and Healthcare products Regulatory Agency, South Mimms, (MHRA), Hertfordshire EN6 3QG, United Kingdom
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Medicines and Healthcare products Regulatory Agency
Affiliation as printed
Division of Vaccines, Science and Research, Medicines and Healthcare products Regulatory Agency, South Mimms, (MHRA), Hertfordshire EN6 3QG, United Kingdom
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Affiliation as printed
Wolfson Centre for Global Virus Research, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Universitat Internacional de Catalunya · Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública · Institut de Recerca Sant Joan de Déu
Affiliation as printed
Grupo de Investigación en Enfermedades Infecciosas y Microbioma, Institut de Recerca Sant Joan de Déu,Institut Recerca Sant Joan de Deu-Hospital Sant Joan de Deu, CIBER de Epidemiología y Salud Pública- CIBERESP, Medicine Department, Universitat Internacional de Catalunya, Spain
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Affiliation as printed
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
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Norwegian Institute of Public Health
Affiliation as printed
Department of Virology, Norwegian Institute of Public Health, Norway
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National Institute of Health Dr. Ricardo Jorge
Affiliation as printed
National Reference Laboratory for Influenza and Other Respiratory Viruses, National Institute of Health Dr Ricardo Jorge (INSA), Lisbon, Portugal
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Aristotle University of Thessaloniki
Affiliation as printed
Department of Microbiology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Affiliation as printed
Department of Biomedical Sciences for Health, University of Milan, Milano (MI), Italy
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Affiliation as printed
Department of Biomedical Sciences for Health, University of Milan, Milano (MI), Italy
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Affiliation as printed
Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
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Policlinico San Matteo Fondazione
Affiliation as printed
Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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Affiliation as printed
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
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Ospedale Sacro Cuore Don Calabria
Affiliation as printed
Department of Infectious, Tropical Diseases and Microbiology - IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella (VR), Italy
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Vall d'Hebron Institut de Recerca · Vall d'Hebron Hospital Universitari
Affiliation as printed
Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Spain
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Rega Institute for Medical Research · KU Leuven
Affiliation as printed
Department of Microbiology, immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Reference center for Enterovirus, KU Leuven, Rega Institute, Belgium
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Affiliation as printed
Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Hungary
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European Centre for Disease Prevention and Control
Affiliation as printed
European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
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Carol Davila University of Medicine and Pharmacy
Affiliation as printed
Carol Davila University of Medicine and Pharmacy, Bucharest, Romania; Stefan S Nicolau Institute of Virology, Bucharest, Romania
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University of Geneva · University Hospital of Geneva
Affiliation as printed
Laboratory of Virology, Division of Laboratory Medicine, Division of Infectious Diseases, Geneva University Hospitals, Switzerland
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Affiliation as printed
Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Norway
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Affiliation as printed
Nuttfield Department for Medicine, University of Oxford, Oxford, United Kingdom
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Affiliation as printed
Laboratory of Clinical Virology, Medical School, University of Crete, Crete, Greece
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Affiliation as printed
National WHO Poliovirus Reference Laboratory, National Center for Public Health and Pharmacy, Budapest, Hungary
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Affiliation as printed
Institute of Biomedicine, University of Turku, Finland
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Hrvatski zavod za javno zdravstvo
Affiliation as printed
Microbiology Division, Croatian Institute of Public Health, Zagreb, Croatia
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Affiliation as printed
Microbiology and Virology Unit, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchestar, United Kingdom
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Affiliation as printed
Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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Sheba Medical Center · Israel Ministry of Health
Affiliation as printed
Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
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Narodowy Instytut Zdrowia Publicznego PZH – Państwowy Instytut Badawczy
Affiliation as printed
Department of Virology, National Institute of Public Health NIH - National Institute of Research, Warsaw, Poland
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Rega Institute for Medical Research · KU Leuven
Affiliation as printed
Department of Microbiology, immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Reference center for Enterovirus, KU Leuven, Rega Institute, Belgium
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Amsterdam UMC Location University of Amsterdam · Amsterdam University Medical Centers
Affiliation as printed
OrganoVIR Labs, Dept of Medical Microbiology and Infection prevention, Amsterdam UMC location AMC, Amsterdam, the Netherlands
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Sheba Medical Center · Israel Ministry of Health
Affiliation as printed
Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
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Roskilde University · University of Copenhagen · Nordsjællands Hospital
Affiliation as printed
Department of Clinical Research, Nordsjællands Hospital, Hilleroed, Denmark; Department of Public Health, University of Copenhagen, Copenhagen, Denmark; Pandemix Center for Excellence (DNRF 170), Roskilde University, Roskilde, Denmark
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NHS Blood and Transplant · University of Turku · Turku University Hospital · University of Oxford
Affiliation as printed
Nuttfield Department for Medicine, University of Oxford, Oxford, United Kingdom; NHS Blood and Transplant, Microbiology Services, Colindale, United Kingdom; Clinical Microbiology, Turku University Hospital and Institute of Biomedicine, University of Turku, Turku, Finland
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