Next generation sequencing for enteroviruses: ENPEN recommendations for clinical and public health labs
Next generation sequencing approaches for enteroviruses: ENPEN expert view
The European non‑polio enterovirus network (ENPEN) presents a comprehensive expert review on how next generation sequencing (NGS) can be implemented for enterovirus detection and characterization in clinical, public health and research settings. Enteroviruses cause a broad spectrum of disease, and the paper discusses how NGS can move laboratories beyond partial VP1 sequencing towards full‑genome data that support more precise diagnosis, surveillance and outbreak investigation. For routine diagnostics and outbreak response, the authors emphasise targeted enterovirus NGS (EV‑tNGS) as a practical choice because it offers high sensitivity for known viruses and allows multiplexing of many samples at reasonable cost. In contrast, unbiased viral metagenomic NGS (VIR‑mNGS) is particularly valuable when standard assays remain negative or novel or unexpected viruses are suspected.
The paper provides concrete „options for action“ for laboratories planning to introduce EV NGS, including harmonised wet‑lab and dry‑lab workflows, robust quality control, and regularly updated reference databases. It also stresses the importance of external quality assessment and collaboration between clinical laboratories, public health institutes and networks such as ENPEN and ESCV to ensure comparable, high‑quality data across Europe.
The lead author of the project, Kimberley Benshop from the Dutch National Institute for Public Health and the Environment, stresses the collective effort leading to this publication: “Going into its 10th year, the European Non Polio Enterovirus Network (ENPEN), under the auspice of ESCV, has strived for advancing EV diagnostic, typing and surveillance in the clinical, public health and research setting through collaboration and team work. ENPEN has grown into a network encompassing now over 125 institutes in 36 European countries and a dozen more beyond Europe. Through collaboration, ENPEN has set up several projects, resulting in a total of 17 published articles and many more in the making.
The current review was initiated at the ENPEN workshop held in Corfu, Greece, on 23–24 May 2024, where expert discussions indicated a need for such a paper. One of the strengths is its pragmatic focus. Rather than simply advocating for NGS adoption, we provide detailed recommendations for both wet- and dry-lab workflows and address the technical complexity of NGS, the need for specialized personnel, and the validation hurdles posed by rapidly evolving platforms. We aimed to give a blueprint for overcoming these barriers, recognizing the transformative potential of NGS for EV surveillance, outbreak response, and research. We also underscore the importance of data sharing, collaborative analysis, and equitable access, especially in low-resource settings.”
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