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 (author), Jevšnik Virant, Monika (author), Lunar, Maja M. (author), Ošep, Anja (author), Poljak, Mario (author)

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.

• Language: English
• Keywords: bioinformatics, dry-lab, enteroviruses, next generation sequencing, targeted PCR-based, viral metagenomics, wet-lab
• Work type: Article
• Typology: 1.02 - Review Article
• Organization: MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2026
• Number of pages: 10 str.
• Numbering: Vol. 184, iss. 2026, art. 105940
• PID: 20.500.12556/RUL-185870
• UDC: 61:578
• ISSN on article: 1386-6532
• DOI: 10.1016/j.jcv.2026.105940
• COBISS.SI-ID: 274121475
• Publication date in RUL: 21.08.2026

Record is a part of a journal

• Title: Journal of clinical virology
• Shortened title: J. clin. virol.
• Publisher: Elsevier
• ISSN: 1386-6532
• COBISS.SI-ID: 11769049

Licences

• License: CC BY-NC 4.0, Creative Commons Attribution-NonCommercial 4.0 International
• Link: http://creativecommons.org/licenses/by-nc/4.0/
• Description: A creative commons license that bans commercial use, but the users don’t have to license their derivative works on the same terms.

Secondary language

• Language: Slovenian
• Keywords: bioinformatika, laboratorij, enetrovirusi, sekvenciranje naslednje generacije, ciljno usmerjena PCR, virusna metagenomika