Phylogenetic Analysis of the Spike Region of SARS-CoV2

Since the novel coronavirus appeared in December 2019, it has brought global attention to

this new virus due to its high infectivity rate and increasing fatality rate to more than 7%. For

this purpose, in this study, we aimed to address the evolution and the genetic variation of the

spike region of the SARS-CoV2 extensively. In the current study, successive computational

work performed starting with multiple sequence alignment and phylogenetic tree construction

followed by alignment prediction with some cell receptors. The alignment analysis based on the

spike glycoprotein of SARS-CoV2 showed that this novel coronavirus is closer to Bat and

Pangolin coronavirus, and it is quite different from other human coronaviruses. Interestingly, the

sequence and structural alignments show that 23 amino acid residues are inserted in the S1

subunit of the five spike regions and most of them in the receptor-binding domain (RBD). None

of these proteins has been detected in any previously identified human coronaviruses, and some

of them are not shown in the sequence of Bat and Pangolin coronaviruses. They could be

considered unique for this novel coronavirus. Despite the need for more analysis, this study

revealed that the hypothetical binding between the novels inserted amino acid in the SARS-

CoV2 Spike RBD might be the right candidate for the development of antiviral treatment against COVID-19.