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)

Kimberley S.M. Benschop; Florian Zwagemaker; Lili Andersson-Li; Cristina Andrés; Andrés Antón; Carla Berengua; Natasa Berginc; Maël Bessaud; Maxime Bisseux; Erika Bujaki; Benjamin Canning; Claus Bohn Christiansen; Karen Couderé; Eeva K. Broberg; Hayley Cassidy; Concetta Castilletti; Cristina Celma; Ondrej Cinek; Nóra Deézsi-Magyar; Anna M. Eis-Hübinger; Jacky Flipse; Helena Jiřincová; Raluca Gatej; Irina Georgieva; Federica Giardina; Alejandra González-Sánchez; Berkin Hack; Jelte Helfferich; Stephanie Hutchings; Eero Hietanen; Mario Hönemann; Monika Jevšnik Virant; Eleni Kalogera; Caroline Klint Johannesen; Juliet Kenicer; Michael Kleines; Eduardo Lagarejos; Elisabeth Toverud Landaas; Chikondi C. Kandulu; F. Xavier López Labrador; Maja M. Lunar; Melanie Maier; Manasi Majumdar; Javier Martin; C. Patrick McClure; Carmen Muñoz-Almagro; Anja Ošep; Joakim Øverbø; Paula Palminha; Anna Papa; Elena Pariani; Laura Pellegrinelli; Corinna Pietsch; Antonio Piralla; Mario Poljak; Elena Pomari; Ignasi Prats-Méndez; Annabel Rector; Gábor Reuter; Maximilian Riess; Simona Ruta; Manuel Schibler; Hans Johnny Schjelderup Nilsen; Peter Simmonds; George Sourvinos; Katalin Szomor; Petri Susi; Irena Tabain; Pamela Vallely; Karin J. von Eije; Merav Weil; Magdalena Wieczorek; Elke Wollants; Katja C. Wolthers; Neta S. Zuckerman; Thea K. Fischer; Heli Harvala; ENPEN study collaborators

doi:10.1016/j.jcv.2026.105940

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)

Kimberley S.M. Benschop^*, Florian Zwagemaker, Lili Andersson-Li, Cristina Andrés, Andrés Antón, Carla Berengua, Natasa Berginc, Maël Bessaud, Maxime Bisseux, Erika Bujaki, Benjamin Canning, Claus Bohn Christiansen, Karen Couderé, Eeva K. Broberg, Hayley Cassidy, Concetta Castilletti, Cristina Celma, Ondrej Cinek, Nóra Deézsi-Magyar, Anna M. Eis-HübingerJacky Flipse, Helena Jiřincová, Raluca Gatej, Irina Georgieva, Federica Giardina, Alejandra González-Sánchez, Berkin Hack, Jelte Helfferich, Stephanie Hutchings, Eero Hietanen, Mario Hönemann, Monika Jevšnik Virant, Eleni Kalogera, Caroline Klint Johannesen, Juliet Kenicer, Michael Kleines, Eduardo Lagarejos, Elisabeth Toverud Landaas, Chikondi C. Kandulu, F. Xavier López Labrador, Maja M. Lunar, Melanie Maier, Manasi Majumdar, Javier Martin, C. Patrick McClure, Carmen Muñoz-Almagro, Anja Ošep, Joakim Øverbø, Paula Palminha, Anna Papa, Elena Pariani, Laura Pellegrinelli, Corinna Pietsch, Antonio Piralla, Mario Poljak, Elena Pomari, Ignasi Prats-Méndez, Annabel Rector, Gábor Reuter, Maximilian Riess, Simona Ruta, Manuel Schibler, Hans Johnny Schjelderup Nilsen, Peter Simmonds, George Sourvinos, Katalin Szomor, Petri Susi, Irena Tabain, Pamela Vallely, Karin J. von Eije, Merav Weil, Magdalena Wieczorek, Elke Wollants, Katja C. Wolthers, Neta S. Zuckerman, Thea K. Fischer, Heli Harvala, ENPEN study collaborators

^*Corresponding author for this work

Department of Clinical Research

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.

Original language	English
Article number	105940
Journal	Journal of Clinical Virology
Volume	184
ISSN	1386-6532
DOIs	https://doi.org/10.1016/j.jcv.2026.105940
Publication status	Published - 2026

Keywords

Bioinformatics
Dry-lab
Enteroviruses
Next Generation Sequencing
Targeted PCR-based
Viral metagenomics
Wet-lab

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10.1016/j.jcv.2026.105940

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Benschop, K. S. M., Zwagemaker, F., Andersson-Li, L., Andrés, C., Antón, A., Berengua, C., Berginc, N., Bessaud, M., Bisseux, M., Bujaki, E., Canning, B., Christiansen, C. B., Couderé, K., Broberg, E. K., Cassidy, H., Castilletti, C., Celma, C., Cinek, O., Deézsi-Magyar, N., ... ENPEN study collaborators (2026). 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, 184, Article 105940. https://doi.org/10.1016/j.jcv.2026.105940

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). / Benschop, Kimberley S.M.; Zwagemaker, Florian; Andersson-Li, Lili et al.
In: Journal of Clinical Virology, Vol. 184, 105940, 2026.

Research output: Contribution to journal › Journal article › Research › peer-review

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, Jiřincová, 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, Muñoz-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, HJS, 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, Harvala, H & ENPEN study collaborators 2026, '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, 105940. https://doi.org/10.1016/j.jcv.2026.105940

Benschop KSM, Zwagemaker F, Andersson-Li L, Andrés C, Antón A, Berengua C et al. 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. 2026;184:105940. doi: 10.1016/j.jcv.2026.105940

@article{faaf5196959b42afbf678cdb5db8843a,

title = "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)",

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.",

keywords = "Bioinformatics, Dry-lab, Enteroviruses, Next Generation Sequencing, Targeted PCR-based, Viral metagenomics, Wet-lab",

author = "Benschop, \{Kimberley S.M.\} and Florian Zwagemaker and Lili Andersson-Li and Cristina Andr{\'e}s and Andr{\'e}s Ant{\'o}n and Carla Berengua and Natasa Berginc and Ma{\"e}l Bessaud and Maxime Bisseux and Erika Bujaki and Benjamin Canning and Christiansen, \{Claus Bohn\} and Karen Couder{\'e} and Broberg, \{Eeva K.\} and Hayley Cassidy and Concetta Castilletti and Cristina Celma and Ondrej Cinek and N{\'o}ra De{\'e}zsi-Magyar and Eis-H{\"u}binger, \{Anna M.\} and Jacky Flipse and Helena Ji{\v r}incov{\'a} and Raluca Gatej and Irina Georgieva and Federica Giardina and Alejandra Gonz{\'a}lez-S{\'a}nchez and Berkin Hack and Jelte Helfferich and Stephanie Hutchings and Eero Hietanen and Mario H{\"o}nemann and Virant, \{Monika Jev{\v s}nik\} and Eleni Kalogera and Johannesen, \{Caroline Klint\} and Juliet Kenicer and Michael Kleines and Eduardo Lagarejos and Landaas, \{Elisabeth Toverud\} and Kandulu, \{Chikondi C.\} and \{Xavier L{\'o}pez Labrador\}, F. and Lunar, \{Maja M.\} and Melanie Maier and Manasi Majumdar and Javier Martin and McClure, \{C. Patrick\} and Carmen Mu{\~n}oz-Almagro and Anja O{\v s}ep and Joakim {\O}verb{\o} and Paula Palminha and Anna Papa and Elena Pariani and Laura Pellegrinelli and Corinna Pietsch and Antonio Piralla and Mario Poljak and Elena Pomari and Ignasi Prats-M{\'e}ndez and Annabel Rector and G{\'a}bor Reuter and Maximilian Riess and Simona Ruta and Manuel Schibler and Nilsen, \{Hans Johnny Schjelderup\} and Peter Simmonds and George Sourvinos and Katalin Szomor and Petri Susi and Irena Tabain and Pamela Vallely and \{von Eije\}, \{Karin J.\} and Merav Weil and Magdalena Wieczorek and Elke Wollants and Wolthers, \{Katja C.\} and Zuckerman, \{Neta S.\} and Fischer, \{Thea K.\} and Heli Harvala and \{ENPEN study collaborators\}",

note = "Publisher Copyright: {\textcopyright} 2026 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC license. http://creativecommons.org/licenses/by-nc/4.0/",

year = "2026",

doi = "10.1016/j.jcv.2026.105940",

language = "English",

volume = "184",

journal = "Journal of Clinical Virology",

issn = "1386-6532",

publisher = "Elsevier BV",

}

TY - JOUR

T1 - Next generation sequencing approaches for the detection and characterization of enteroviruses in clinical, public health, and research settings

T2 - Expert view of the European non-polio enterovirus network (ENPEN)

AU - Benschop, Kimberley S.M.

AU - Zwagemaker, Florian

AU - Andersson-Li, Lili

AU - Andrés, Cristina

AU - Antón, Andrés

AU - Berengua, Carla

AU - Berginc, Natasa

AU - Bessaud, Maël

AU - Bisseux, Maxime

AU - Bujaki, Erika

AU - Canning, Benjamin

AU - Christiansen, Claus Bohn

AU - Couderé, Karen

AU - Broberg, Eeva K.

AU - Cassidy, Hayley

AU - Castilletti, Concetta

AU - Celma, Cristina

AU - Cinek, Ondrej

AU - Deézsi-Magyar, Nóra

AU - Eis-Hübinger, Anna M.

AU - Flipse, Jacky

AU - Jiřincová, Helena

AU - Gatej, Raluca

AU - Georgieva, Irina

AU - Giardina, Federica

AU - González-Sánchez, Alejandra

AU - Hack, Berkin

AU - Helfferich, Jelte

AU - Hutchings, Stephanie

AU - Hietanen, Eero

AU - Hönemann, Mario

AU - Virant, Monika Jevšnik

AU - Kalogera, Eleni

AU - Johannesen, Caroline Klint

AU - Kenicer, Juliet

AU - Kleines, Michael

AU - Lagarejos, Eduardo

AU - Landaas, Elisabeth Toverud

AU - Kandulu, Chikondi C.

AU - Xavier López Labrador, F.

AU - Lunar, Maja M.

AU - Maier, Melanie

AU - Majumdar, Manasi

AU - Martin, Javier

AU - McClure, C. Patrick

AU - Muñoz-Almagro, Carmen

AU - Ošep, Anja

AU - Øverbø, Joakim

AU - Palminha, Paula

AU - Papa, Anna

AU - Pariani, Elena

AU - Pellegrinelli, Laura

AU - Pietsch, Corinna

AU - Piralla, Antonio

AU - Poljak, Mario

AU - Pomari, Elena

AU - Prats-Méndez, Ignasi

AU - Rector, Annabel

AU - Reuter, Gábor

AU - Riess, Maximilian

AU - Ruta, Simona

AU - Schibler, Manuel

AU - Nilsen, Hans Johnny Schjelderup

AU - Simmonds, Peter

AU - Sourvinos, George

AU - Szomor, Katalin

AU - Susi, Petri

AU - Tabain, Irena

AU - Vallely, Pamela

AU - von Eije, Karin J.

AU - Weil, Merav

AU - Wieczorek, Magdalena

AU - Wollants, Elke

AU - Wolthers, Katja C.

AU - Zuckerman, Neta S.

AU - Fischer, Thea K.

AU - Harvala, Heli

AU - ENPEN study collaborators

PY - 2026

Y1 - 2026

N2 - 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.

AB - 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.

KW - Bioinformatics

KW - Dry-lab

KW - Enteroviruses

KW - Next Generation Sequencing

KW - Targeted PCR-based

KW - Viral metagenomics

KW - Wet-lab

UR - https://www.scopus.com/pages/publications/105034665174

U2 - 10.1016/j.jcv.2026.105940

DO - 10.1016/j.jcv.2026.105940

M3 - Journal article

C2 - 41905022

AN - SCOPUS:105034665174

SN - 1386-6532

VL - 184

JO - Journal of Clinical Virology

JF - Journal of Clinical Virology

M1 - 105940

ER -

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)

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Keywords

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