Molecular Modeling, Codon Usage, Rare Codon and Phylogenetic Relations Analysis of Spike Glycoprotein in SARS CoV-2 Virus

The 2019 novel coronavirus (2019-nCoV/SARS-CoV-2) initially appeared as part of an important prevalence of respiratory disease centered in Hubei province, China. Now, it is a pandemic globally and is a significant public health concern. Taxonomically, SARS-CoV-2 was revealed to be a Beta coronavirus (lineage B) related to SARS-CoV and SARS-related bat coronaviruses closely, and it has been stated to have a similar receptor with SARS-CoV (ACE-2). Here, we carried out the codon usage bias (CUB) by analyzing the codon bias index (CBI), codon adaptation index (CAI), and an effective number of codons (ENC) besides phylogenetic analysis of Coronaviridae and also structural modeling of the SARS-CoV-2 spike glycoprotein. We observed that 2019-nCoV has a rich composition of AT nucleotides that strongly affects its codon usage, which seems to be not optimized for the human hosts. Moreover, a close evolutionary phylogenetic relationship was detected between SARS-CoV-2/human/IRIN/ and SARS-CoV-2/human/CHN/WH-09/2020. By in silico modeling of spike glycoprotein, an I-TASSER server, the 3Dstructure of it was also evaluated. This type of analysis would be beneficial for exploring a virus adaptation to host, and evolution and is therefore of value to developing vaccine design and pharmaceutical agents.