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Abstract

Since the novel coronavirus appeared in January 2020, 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, besides addressing some hypothetical binding with two cell receptors (CCR3 and ICAM-1) using computational tools, as the spike glycoproteins mediate the viral entry. The current study performed successive computational work, 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 the Bat and Pangolin coronavirus and quite different from other human coronaviruses. Interestingly, the sequence and structural alignments show that 23 amino acid (amino acid) residues are inserted in the S1 subunit of the five spike regions, most of which are 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. Some of these proteins are predicted to bind to 1IAM in the ICAM-1 receptor with a higher degree of affinity than binding to CCR3. The protein docking heuristic algorithms analysis revealed that some of the inserted amino acids in the spike region have a high affinity for binding to the ICAM-1 receptor through hydrophilic bonds and Beta-sheet bonding. 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 developing antiviral treatment against COVID-19. Moreover, the genomic region encoding these inserts only in the novel coronavirus represents an ideal candidate for distinguishing SARS-CoV2 from other coronavirus family members‎‎.