A1 Refereed original research article in a scientific journal
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)
Authors: Benschop, Kimberley S. M.; Zwagemaker, Florian; Andersson-Li, Lili; Andrés, Cristina; Antón, Andrés; Berengua, Carla; Berginc, Natasa; Bessaud, Maël; Bisseux, Maxime; Bujaki, Erika; Canning, Benjamin; Christiansen, Claus Bohn; Couderé, Karen; Broberg, Eeva K.; Cassidy, Hayley; Castilletti, Concetta; Celma, Cristina; Cinek, Ondrej; Deézsi-Magyar, Nóra; Eis-Hübinger, Anna M.; Flipse, Jacky; Jiřincová, Helena; Gatej, Raluca; Georgieva, Irina; Giardina, Federica; González-Sánchez, Alejandra; Hack, Berkin; Helfferich, Jelte; Hutchings, Stephanie; Hietanen, Eero; Hönemann, Mario; Jevšnik Virant, Monika; Kalogera, Eleni; Klint Johannesen, Caroline; Kenicer, Juliet; Kleines, Michael; Lagarejos, Eduardo; Landaas, Elisabeth Toverud; Kandulu, Chikondi C.; Xavier López, Labrador F.; Lunar, Maja M.; Maier, Melanie; Majumdar, Manasi; Martin, Javier; McClure, C. Patrick; Muñoz-Almagro, Carmen; Ošep, Anja; Øverbø, Joakim; Palminha, Paula; Papa, Anna; Pariani, Elena; Pellegrinelli, Laura; Pietsch, Corinna; Piralla, Antonio; Poljak, Mario; Pomari, Elena; Prats-Méndez, Ignasi; Rector, Annabel; Reuter, Gábor; Riess, Maximilian; Ruta, Simona; Schibler, Manuel; Nilsen, Hans-Johnny Schjelderup; Simmonds, Peter; Sourvinos, George; Szomor, Katalin; Susi, Petri; Tabain, Irena; Vallely, Pamela; von Eije, Karin J.; Weil, Merav; Wieczorek, Magdalena; Wollants, Elke; Wolthers, Katja C.; Zuckerman, Neta S.; Fischer, Thea K.; Harvala, Heli
Publication year: 2026
Journal: Journal of Clinical Virology
Article number: 105940
Volume: 184
ISSN: 1386-6532
eISSN: 1873-5967
DOI: https://doi.org/10.1016/j.jcv.2026.105940
Publication's open availability at the time of reporting: Open Access
Publication channel's open availability : Partially Open Access publication channel
Web address : https://doi.org/10.1016/j.jcv.2026.105940
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/522896619
Self-archived copy's licence: CC BY NC
Self-archived copy's version: Publisher`s PDF
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.
Downloadable publication This is an electronic reprint of the original article. |  |
Funding information in the publication:
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
