Metagenomics enables the detection of all the genetic material of organisms present in a sample, making it a pathogen-agnostic approach for detecting common and rare or novel pathogens that are not included in conventional testing. Beforehand, a clinician does not need to have a hypothesis of what pathogen is expected, unlike traditional polymerase chain reaction (PCR) testing.This thesis is focusing on diagnostic yield, clinical findings, and enhancing technical opportunities in viral metagenomics. The identification, typing, and quantification of viruses by means of viral metagenomics as a diagnostic tool are evaluated. Technical aspects are appraised for improved sensitivity and specificity of the wet and dry (bioinformatic) lab components of viral metagenomics. The use of a metagenomic protocol for virus discovery directly in a patient sample is assessed, and the best methods and approaches for performing genetic analysis of the SARS-CoV-2 virus are investigated.Viral metagenomic testing results in the identification of more viruses, therefore it is a valuable addition to current diagnostic test protocols. Additionally, it is a useful test for virus discovery and monitoring during infectious disease outbreaks caused by novel viruses.LUMC / Geneeskund
