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)
Por:
Benschop KSM, Zwagemaker F, Andersson-Li L, Andrés C, Antón A, Berengua C, Berginc N, Bessaud M, Bisseux M, Bujaki E, Canning B, Christiansen CB, Couderé K, Broberg EK, Cassidy H, Castilletti C, Celma C, Cinek O, Deézsi-Magyar N, Eis-Hübinger AM, Flipse J, Jirincová H, Gatej R, Georgieva I, Giardina F, González-Sánchez A, Hack B, Helfferich J, Hutchings S, Hietanen E, Hönemann M, Virant MJ, Kalogera E, Johannesen CK, Kenicer J, Kleines M, Lagarejos E, Landaas ET, Kandulu CC, Xavier López Labrador F, Lunar MM, Maier M, Majumdar M, Martin J, McClure CP, Munoz-Almagro C, Ošep A, Øverbø J, Palminha P, Papa A, Pariani E, Pellegrinelli L, Pietsch C, Piralla A, Poljak M, Pomari E, Prats-Méndez I, Rector A, Reuter G, Riess M, Ruta S, Schibler M, Nilsen HS, Simmonds P, Sourvinos G, Szomor K, Susi P, Tabain I, Vallely P, von Eije KJ, Weil M, Wieczorek M, Wollants E, Wolthers KC, Zuckerman NS, Fischer TK and Harvala H
Publicada:
1 jun 2026
Ahead of Print:
24 mar 2026
Resumen:
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.
Filiaciones:
Benschop KSM:
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
Zwagemaker F:
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
Andersson-Li L:
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden
Andrés C:
Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Spain
Antón A:
Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Spain
Berengua C:
Microbiology Department. Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
Berginc N:
National Laboratory of Health, Environment and Food, Laboratory for Public Health Virology, Ljubljana, Slovenia
Bessaud M:
Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus sensing & signaling Unit, Paris, France
Bisseux M:
CHU Clermont-Ferrand, 3 IHP, National Reference Centre for enteroviruses and parechoviruses, Clermont-Ferrand, France
Bujaki E:
Division of Vaccines, Science and Research, Medicines and Healthcare products Regulatory Agency, South Mimms, (MHRA), Hertfordshire EN6 3QG, United Kingdom
Canning B:
Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, NG7 2UH, United Kingdom
Christiansen CB:
Department of Clinical microbiology, Lund University Hospital, Lund, Sweden
Couderé K:
ElisabethTweesteden Hospital, Tilburg, the Netherlands
Zorgsaam, Terneuzen, the Netherlands
Broberg EK:
European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
Cassidy H:
Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
Castilletti C:
Department of Infectious, Tropical Diseases and Microbiology - IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella (VR), Italy
Celma C:
Enteric Virus Unit, Virus Reference Department, UK Health Security Agency, London, United Kingdom
Cinek O:
Department of Microbiology, Second Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic
Deézsi-Magyar N:
National Biosafety Laboratory, National Center for Public Health and Pharmacy, Budapest, Hungary
Eis-Hübinger AM:
Institute of Virology, University Hospital Bonn, Germany
Flipse J:
Laboratory for Medical Microbiology and Immunology, Dicoon, Elst, the Netherlands
Jirincová H:
National Reference Laboratory for Enteroviruses, National Institute of Public Health, Prague, Czech Republic
Gatej R:
National Institute of Public Health, Bucharest, Romania
Georgieva I:
National Reference Laboratory for Enteroviruses, Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
Giardina F:
Department of Clinical Surgical Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
González-Sánchez A:
Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Spain
Hack B:
Infectious Diseases and Microbiology Department, Guy's and St Thomas' NHS Foundation Trust, United Kingdom
Helfferich J:
Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
Hutchings S:
Virology laboratory, Bristol, United Kingdom Health Security Agency, Bristol, United Kingdom
Hietanen E:
Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
Hönemann M:
Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
Virant MJ:
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
Kalogera E:
Microbiology Department, Agia Sofia Children's Hospital, Athens, Greece
Johannesen CK:
Department of Clinical Research, Nordsjællands Hospital, Hilleroed, Denmark
Kenicer J:
Pathogen Sequencing Service, Specialist Virology Centre, Edinburgh, Royal Infirmary of Edinburgh, Edinbrugh, Scotland, United Kingdom
Kleines M:
Laboratory Diagnostic Center, University Hospital RWTH Aachen, Aachen, Germany
Lagarejos E:
Microbiology Department, Doctor Negrin Gran Canaria's Universitary Hospital, Gran Canaria, Spain
Landaas ET:
Department of Microbiology, Oslo University Hospital, Oslo, Norway
Institute of Clinical Medicine, University of Oslo, Oslo, Norway
Kandulu CC:
Pharmaceutical Care Research Group, University College Cork, Cork, Ireland
Xavier López Labrador F:
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
Lunar MM:
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
Maier M:
Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
Majumdar M:
Division of Vaccines, Science and Research, Medicines and Healthcare products Regulatory Agency, South Mimms, (MHRA), Hertfordshire EN6 3QG, United Kingdom
Martin J:
Division of Vaccines, Science and Research, Medicines and Healthcare products Regulatory Agency, South Mimms, (MHRA), Hertfordshire EN6 3QG, United Kingdom
McClure CP:
Wolfson Centre for Global Virus Research, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
Munoz-Almagro C:
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
Ošep A:
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
Øverbø J:
Department of Virology, Norwegian Institute of Public Health, Norway
Palminha P:
National Reference Laboratory for Influenza and Other Respiratory Viruses, National Institute of Health Dr Ricardo Jorge (INSA), Lisbon, Portugal
Papa A:
Department of Microbiology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
Pariani E:
Department of Biomedical Sciences for Health, University of Milan, Milano (MI), Italy
Pellegrinelli L:
Department of Biomedical Sciences for Health, University of Milan, Milano (MI), Italy
Pietsch C:
Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
Piralla A:
Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
Poljak M:
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
Pomari E:
Department of Infectious, Tropical Diseases and Microbiology - IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella (VR), Italy
Prats-Méndez I:
Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Spain
Rector A:
Department of Microbiology, immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Reference center for Enterovirus, KU Leuven, Rega Institute, Belgium
Reuter G:
Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Hungary
Riess M:
European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
Ruta S:
Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
Stefan S Nicolau Institute of Virology, Bucharest, Romania
Schibler M:
Laboratory of Virology, Division of Laboratory Medicine, Division of Infectious Diseases, Geneva University Hospitals, Switzerland
Nilsen HS:
Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Norway
Simmonds P:
Nuttfield Department for Medicine, University of Oxford, Oxford, United Kingdom
Sourvinos G:
Laboratory of Clinical Virology, Medical School, University of Crete, Crete, Greece
Szomor K:
National WHO Poliovirus Reference Laboratory, National Center for Public Health and Pharmacy, Budapest, Hungary
Susi P:
Institute of Biomedicine, University of Turku, Finland
Tabain I:
Microbiology Division, Croatian Institute of Public Health, Zagreb, Croatia
Vallely P:
Microbiology and Virology Unit, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchestar, United Kingdom
von Eije KJ:
Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
Weil M:
Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
Wieczorek M:
Department of Virology, National Institute of Public Health NIH - National Institute of Research, Warsaw, Poland
Wollants E:
Department of Microbiology, immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Reference center for Enterovirus, KU Leuven, Rega Institute, Belgium
Wolthers KC:
OrganoVIR Labs, Dept of Medical Microbiology and Infection prevention, Amsterdam UMC location AMC, Amsterdam, the Netherlands
Zuckerman NS:
Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
Fischer TK:
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
Harvala H:
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
Green Submitted, Green Published, hybrid
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