Design and implementation of a next-generation sequencing test for the fast and cost-effective SARS-CoV-2 differantial diagnosis and variant detection

In the beginning of 2020 the WHO declared a pandemic that was initiated by the outbreak of a new virus named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that quickly spread globally, challenging our society and turning it upside down in ways we did not anticipate. The continuous emergence of new SARS-CoV-2 variants together with the compatibility of the coronavirus disease (COVID-19) symptomatology with other viral respiratory infections revealed the need of developing more specific tools than the methods that were widely implemented throughout the pandemic. This thesis presents a novel next generation sequencing (NGS) based testing strategy that aims to differentially diagnose SARS-CoV-2 virus and its variants, as well as other respiratory viruses in order to overcome the limitations of the existing testing methods.