RNA viruses cause a wide range of diseases in humans, from the common cold to more severe illnesses such as gastroenteritis, influenza, Ebola virus disease, measles and COVID-19. The use of RNA (instead of DNA) by these viruses gives them unique properties since, unlike DNA, RNA can adopt specific shapes that allow the genome itself to carry out structural and enzymatic functions directly, even though it is not a protein or an enzyme in a conventional sense. All RNA viruses exploit this unique property of RNA in one way or another. This feature is exploited by all RNA viruses in one way or another. Coronaviruses, for example, use RNA structures to regulate their own genome replication, as well as to interact with host ribosomes. Influenza viruses use RNA structure to control splicing of viral genes and to drive reassortment of their eight genomic segments — the process that gives rise to new pandemic strains. Much of the details about how RNA structures act (and interact) during infection remains unknown. I will discuss our recent work on using high-throughput chemical probing coupled with high-throughput sequencing in order to map RNA structures in influenza A virus and in SARS-CoV-2.