A Comparative Study between Spanish and British SARS-CoV-2 Variants.

The study of the interaction between the SARS-CoV-2 spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor is key to understanding binding affinity and stability. In the present report, we sought to investigate the differences between two already sequenced genome variants (Spanish and British) of SARS-CoV-2. Methods: In silico model evaluating the homology, identity and similarity in the genome sequence and the structure and alignment of the predictive spike by computational docking methods. Results: The identity results between the Spanish and British variants of the Spike protein were 28.67%. This close correspondence in the results between the Spanish and British SARS-CoV-2 variants shows that they are very similar (99.99%). The alignment obtained results in four deletions. There were 23 nucleotide substitutions also predicted which could affect the functionality of the proteins produced from this sequence. The interaction between the binding receptor domain from the spike protein and the ACE2 receptor produces some of the mutations found and, therefore, the energy of this ligand varies. However, the estimated antigenicity of the British variant is higher than its Spanish counterpart. Conclusions: Our results indicate that minimal mutations could interfere in the infectivity of the virus due to changes in the fitness between host cell recognition and interaction proteins. In particular, the N501Y substitution, situated in the RBD of the spike of the British variant, might be the reason for its extraordinary infective potential.

Spike protein of SARS-CoV-2 Omicron variant: An in-silico study evaluating spike interactions and immune evasion.

Background: The fundamentals of the infectivity and immune evasion of the SARS-CoV-2 Omicron variant are not yet fully understood. Here, we carried out an in-silico study analyzing the spike protein, the protein electrostatic potential, and the potential immune evasion. Methods: The analysis was based on the structure of the spike protein from two SARS-CoV-2 variants, the original Wuhan and the Botswana (Omicron). The full-length genome sequences and protein sequences were obtained from databanks. The interaction of the spike proteins with the human Angiotensin Converting Enzyme 2 (ACE2) receptor was evaluated through the open-source software. The Immune Epitope Database was used to analyze the potential immune evasion of the viruses. Results: Our data show that the Omicron spike protein resulted in 37 amino acid changes. The physicochemical properties of the spike had changed, and the electrostatic potentials differed between both variants. This resulted in a decrease in protein interactions, which does not establish a greater interaction with the ACE2 receptor. These changes compromise key receptor-binding motif residues in the SARS-CoV-2 spike protein that interact with neutralizing antibodies and ACE2. Conclusions: These mutations appear to confer enhanced properties of infectivity. The Omicron variant appears to be more effective at evading immune responses.