Current surveillance of viral pathogens is mainly based on specific viruses and information from hospitalized patients. This gives a distorted picture of the situation, as most infections do not lead to hospitalization or a doctor’s visit. Therefore, a different approach is needed to gain better insight into viral pathogens circulating in the population. In this thesis, we studied a variety of approaches to map the genetic code of viruses by using sequencing to thereby get a better view of what is circulating among citizens. The most experimental, but promising method, is “metagenomic” sequencing, which can map all viruses in a sample at once. We demonstrated this approach by searching for viruses that may play a role in public health in sewage samples from around the globe. We also developed software to facilitate the visualization and interpretation of this type of complex data. Another approach to map the genetic code of a single specific virus is called “amplicon” sequencing. We extensively tested this method in this thesis on different viruses, virus concentrations, and sequencing machines. We then demonstrated the applicability of this method at the beginning of the COVID-19 pandemic and in hospital outbreak investigations by mapping the genetic code of the SARS-CoV-2 virus in a large number of citizens and patients in real time.