Discovery and diagnosis of new viral pathogens: proposal for a generic workflow based on next-generation sequencing and new integrated data analysis approaches

Diagnostic metagenomic analyses gained more impact for pathogen detection and discovery in recent years due to increasing opportunities for next-generation sequencing at simultaneously decreasing prices. However, as with all novel technologies, there is a lack of standardisation in this field. But, for day-to-day routine use in a diagnostic laboratory, standardisation is urgently required. This standardisation has to take into account all steps from sampling through library preparation to data evaluation. In this short outline, some examples of metagenomics-based pathogen identification are highlighted and the most critical steps of the whole procedure are discussed. Lastly, the reader is pointed to currently ongoing initiatives that aim to achieve these goals of standardisation to pave the way for broader use of next-generation sequencing in diagnosis.

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