In Silico Characterisation of Severe Acute Respiratory SyndromeCoronavirus-2 (SARS-CoV-2) based on the Spike Protein Gene

Abstract

Objectives: The Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 has been the current global pandemicconcern. With a high transmission rate, especially through direct contact, this disease spreads from person to person,and this has in turn led to a huge number of infections on a global scale. Methods: In present study, comparative genomic analysis was performed using 151 gene sequences of the viral spikeprotein retrieved from NCBI and along with its translated nucleotide sequences using MEGAX software. Variation in thenucleotide and amino acid positions were identified. Results: Our analysis revealed that 22 nucleotide variations observed in positions 13, 141, 162, 233, 284, 328, 455, 459,716, 773, 784, 882, 1686, 1715, 1749, 1841, 2031, 2076, 2383, 2520, 2533, 3300 and 17 amino acid variations observedin position 5, 54, 78, 90, 95, 152, 153, 239, 258, 262, 572, 583, 614, 684, 677, 795 and 845. Further, phylogenetic analysiswas used to uncover the patterns of spread of the virus across the affected countries. Although, certain strains showedpatterns of transmission within communities, a vast majority revealed an evident mosaic pattern. Conclusion: The data obtained provides a clear understanding of variations in the nucleotide and translated nucleo tide sequences, which can be targeted towards drug designing and to study evolutionary analysis.