Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

•A European Network on Next-Generation Sequencing (ENNGS) has been established.•Recommendations for the implementation of viral metagenomic high-throughput sequencing (mHTS) in diagnostic laboratories are provided, focusing on the wet lab (Part I).•Recommendations for implementation and validation of the bioinformatic procedure of viral mHTS warrants separate recommendations (Part II).•In the current manuscript, practical recommendations on facility requirements, extraction of nucleic acid, viral enrichment, library preparation, controls and assay validation are provided. Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.