Spike selection in SARS-CoV-2 variants across different geographical regions reveals unique signature patterns and differential stability with drug interaction

03 March 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus since its emergence in 2019 has yielded several new viral variants with varied infectivity, disease severity, and antigenicity. Although most mutations are expected to be relatively neutral, mutations at the Spike region of the genome has shown to have a major impact on the viral transmission and infection in humans. Therefore, it is crucial to survey the structures of spike protein across the global virus population to contextualize the rate of therapeutic success against these variants. In this study, high-frequency mutational variants from different geographic regions were pooled in order to study the structural evolution of the spike protein through drug docking and MD simulations. We investigated the mutational burden in the spike sub regions and have observed that the different variants harbour unique signature patterns in the spike sub regions, with certain domains being highly prone to mutations. Further, the MD simulations and docking study revealed that different variants show differential stability when docked for the same set of drug targets. This work sheds light on the mutational burden and the stability landscape of the spike protein across the variants from different geographical regions.


Spike Protein
COVID 19 variants
Mutational frequency
Drug docking
MD simulation
Spike evolution
Geographical spike variants

Supplementary materials

Supplementary Files
Supplementary File 1: Acknowledgement of GISAID Supplementary File 2: Mutation Frequency


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