Understanding the evolutionary history of viruses, particularly RNA viruses such as SARS-CoV-2, is critical to understanding them and developing effective treatments such as vaccinations. Most evolutionary methods rely on phylogenetic analyses based on the RNA sequences. Previous studies, however, have shown that incorporating the RNA secondary structures (S2s) can improve the resolution power of phylogenetic trees (Patiño-Galindo et al. 2018). In this research work, we aimed to develop a method which combined phylogenetic analysis with S2s to better understand how a virus is evolving. As a proof-of-concept, we analysed the SARS-CoV-2, Human Immunodeficiency Virus (HIV) and Hepatitis C Virus (HCV) phylogenies. The RNA structures from HIV and HCV were previously obtained experimentally from Siegfried et al. 2014 and Mauger et al. 2015, respectively. The RNA structures for SARS-CoV-2 were revealed by high-throughput studies from Huston et al. (2020) and Lan et al. (2020) (Reviewed in Manfredonia and Incarnato 2020). Incorporation of S2s allows us to identify regions of the genome under increased selection pressure to maintain both the encoded information and potentially functional secondary structures. These regions could potentially be ideal targets for intervention strategies such as vaccines, as the increased selection pressure on them makes it harder for the virus to develop an escape mutation. This approach based on RNA models and S2s will be fundamental for developing a new method for reconstructing phylogenetic studies of human viruses where molecular clock models and diversification rates are also implemented.