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

Gonçalves, Ricardo Lemes; Rodrigues Leite, Túlio César; de Paula Dias, Bruna; da Silva Caetano, Camila Carla; de Souza, Ana Clara Gomes; da Silva Batista, Ubiratan; Barbosa, Camila Cavadas; Reyes-Sandoval, Arturo; Leomil Coelho, Luiz Felipe; de Mello Silva, Breno

The recent emergence of a novel coronavirus (SARS-CoV-2) is causing a severe global health threat 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 used the three-dimensional structure of the homo-trimer model to predict conformational epitopes of B-cell, and sequence of Spike protein Wuhan-Hu-1 to predict linear epitopes of T-Cytotoxic and T-Helper cells. We identified 45 epitopes with amino acid variations. 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.