Abstract
Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS 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 mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.
Highlights
Metagenomic next-generation sequencing is an untargeted technique for the determination of DNA/RNA sequences in a variety of clinical sample types from patients with infectious syndromes [1,2,3]. mNGS is suited for identification of any pathogen, including variants that have diverged at typical PCR amplification targets, pathogens not known to be associated with a specific clinical syndrome, and novel pathogens which may remain undetected by target-based methods [4,5]
Aim and scope This review aims to provide recommendations for the implementation and validation of bioinformatic analysis methods for viral mNGS, excluding the wet lab part of the process, which has been discussed previously (Part I) [13] and is outside the scope of the current review
We aim to provide practical recommendations for analysis and reporting steps to aid in the successful implementation of fit-for-purpose mNGS procedures in viral diagnostic laboratories
Summary
Metagenomic next-generation sequencing (mNGS) is an untargeted technique for the determination of DNA/RNA sequences in a variety of clinical sample types from patients with infectious syndromes [1,2,3]. mNGS is suited for identification of any pathogen, including variants that have diverged at typical PCR amplification targets, pathogens not known to be associated with a specific clinical syndrome, and novel pathogens which may remain undetected by target-based methods [4,5]. MNGS is suited for identification of any pathogen, including variants that have diverged at typical PCR amplification targets, pathogens not known to be associated with a specific clinical syndrome, and novel pathogens which may remain undetected by target-based methods [4,5]. Despite these clear advantages, mNGS is still in its early stages of translation into clinical application. The development of guidelines and recommendations on mNGS bioinformatic analysis methods and reporting will assist the implementation of mNGS in diagnostic laboratories, ensuring the validity of results and optimizing patient management
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