Binding Affinity in Theoretical SARS-CoV-2 S Protein Variants

SARS-CoV-2 first emerged in December 2019 and caused a worldwide pandemic that led to the infection of 776 million people with a reported mortality rate of 7.1.Over time, this virus has constantly mutated, leading to much more transmissible and immune-resistant strains.The appearance of these variants leads to the question of how a hypothetical variant containing all known mutations would look and function.This study analyzed all of the mutations of the Spike (S) protein data found in UniProt and selected all that had no known effect or increased transmissibility, among other things.Based on this, two experimental variants' genomes were created in SnapGene.Their 3D structure was predicted and modeled through Alpha Fold.Finally, their binding affinity to the hACE2 receptor was calculated using PRODIGY.It was found that a variant containing only mutations that are known to be beneficial to the virus resulted in a higher binding affinity to the hACE2 receptor compared to the original Wuhan strain and a theoretical strain with all mutations included.These findings suggest that some mutations counteract each other and limit the overall binding affinity of the S protein.