Exploring molecular diagnostic approaches in clinical virology: from point-of-care to next-generation sequencing

Following the SARS-CoV-2 pandemic and the re-emergence of monkeypox (mpox) virus, the need to monitor viral trends inside and outside the hospital has been made abundantly clear in recent years. Coincidentally, molecular virological methods have witnessed an unprecedented boost in this timeframe. While conventional Sanger sequencing provides a cheap and sturdy backbone, the emergence of point-of-care panels hints at a future in which dozens of viruses can be detected and quantified at the patient’s bedside. At the same time, next-generation sequencing approaches have the potential to sequence millions of nucleic acid fragments in parallel to screen all microbes and the host within an all-in-one assay. While this thesis focuses on the diagnostics of viral infections, with a special interest in enteroviruses, the molecular applications and recommendations presented here are highly applicable to emerging infectious diseases. Enterovirus infections are widespread within the community and responsible for thousands of hospital admissions every year, particularly in children. We investigated enterovirus D68 in particular due to several outbreaks reported worldwide, with accompanying severe respiratory and neurological presentation. In this thesis, we combined the available clinical and epidemiological data to provide several layers of information to help uncover the whole clinical picture. Our findings provide a groundwork for the early detection and higher resolution of viral infections which may prove crucial during outbreak scenarios.