SARS-CoV-2 mutations and where to find them: an in silico perspective of structural changes and antigenicity of the spike protein

The recent emergence of a novel coronavirus (SARS-CoV-2) is causing a severe global health threat around the world characterized by severe acute respiratory syndrome (Covid-19). At the moment, there is no specific treatment for this disease and vaccines are still under development. The structural protein Spike is essential for virus infection and has been used as the main target for vaccine and serological diagnosis test development. We analysed 2363 sequences of the Spike protein from SARS-CoV-2 isolates and identified variability in 44 amino acid residues and their worldwide distribution in all continents. We use the three-dimensional structure of the homo-trimer model for epitope predictions of B-cell, T-Cytotoxic and T-Helper cells. A total of 45 epitopes with amino acids variation were identified. Finally, we showed the distribution of mutations within the epitopes. Our findings can help researches to identify more efficient strategies for the development of vaccines, therapies and serological diagnostic tests based on the Spike protein of Sars-Cov-2.