Mutations in structural proteins of SARS-CoV-2 and potential implications for the ongoing outbreak of infection in India

Abstract

SARS-CoV-2 has spread in India very quickly from its first reported case on 30 January 2020 in Thrissur, Kerala. With the drastic increasing number of positive cases around the world WHO raised the importance in the assessment of the risk of spread and understanding genetic modifications that could have occurred in the SARS-CoV-2. Using available genome sequence in NCBI repository from the samples of different locations in India, we identified the regions (hotspots) of the viral genome with high rates of mutation. We analysed four regions of the genome encoding structural proteins Spike (S), Nucleocapsid (N), envelop (E) and Membrane (M) proteins. Through computational biology approach, we identified multiple substitution mutations in S and N proteins whereas there is only one substitution in E protein and none in M protein.  We showed most of these amino acid residues are evolutionary conserved. The changes in the conserved residues may have significant implication on the stability of the proteins and subsequent interaction with other elements, which are essential for virus propagation. This provides a basis for a better understanding of the genetic variation in SARS-CoV-2 circulating in the India, which might provide important clues for identifying potential therapeutic targets, development of efficient vaccines, antiviral drugs and diagnostic assays for controlling COVID-19.