Identification of twenty-five mutations in surface glycoprotein (Spike) of SARS-CoV-2 among Indian isolates and their impact on protein dynamics

Abstract

SARS-CoV-2, the causative agent of the COVID-19 pandemic, is an RNA virus that has inherent high rate of mutation. Due to the mutations, the virus evolves at a rapid pace that helps them to survive better inside the host. One of the hotspots of pharmacological interventions is to inhibit binding of virus with the host cells, which is mediated by Spike glycoprotein of SARS-CoV-2 and ACE2 receptors present on the human cells. This study was conducted with an aim to identify and characterise the mutation (s) present in the Spike glycoprotein of the SARS-CoV-2. Towards this, an in silico methodology was used, and the mutations on Spike glycoprotein were identified by comparing the Spike glycoprotein of first reported sequence from Wuhan wet seafood market virus with the available sequences of SARS-CoV-2 from Indian isolates. Our analysis revealed the presence of twenty-five mutations in Spike glycoprotein among Indian SARS-CoV-2 isolates. These mutations spread all over the protein and can be clustered at least into four distinct positions. Further, mutations at eleven positions exhibited alterations in the secondary structure of the polypeptide chain. We also investigated the influence of these mutations on overall protein dynamics and have shown that they affect the dynamic stability of the Spike glycoprotein.