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

Abstract

SARS-CoV-2 mutations and where to find them: An in silico perspective of structural changes and antigenicity of the Spike proteinThe recent emergence of a novel coronavirus (SARS-CoV-2) is causing a severe global health threat characterized by severe acute respiratory syndrome . 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.

Update on Rapid Diagnostics for COVID-19: A Systematic Review

“…We believe next-generation tests should incorporate phylogenetic and structural analyses to select antigens used in their manufacturing process. For example, in the first semester of the pandemic, 45 epitopes with mutations in the main antigen of SARS-CoV-2 [99] were reported, denoting the need for the preemptive use of antigens with variants for the development of serological tests.…”