Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes

Neha Jain; Uma Shankar; Prativa Majee; Amit Kumar

For the insertion of the vaccine construct into a plasmid vector, the 602 amino acid long protein sequence was reverse translated to cDNA of 1806 nucleotide length. The expression system of the expression host varies with each other and the cDNA needs to be adapted as per the host codon usage. For the optimal expression of the vaccine product in Escherichia coli K12 host, the resultant cDNA was codon optimized according using JCAT server. Also, during optimization, rho-independent transcription terminator and prokaryotic ribosomal binding sites were avoided in middle of the cDNA sequence so as to generate an optimal and complete protein expression. Further, for inserting the construct in the cloning vector, the cleavage sites of BamHI and HindIII were also avoided. The CAI value (codon adaptation index) of the cDNA before adaptation was observed to be 0.5379 and a GC content of 59.52 % ( Figure 9A ). After adaptation, the CAI score of the improved sequence was increased to 0.946 with 52.54 % GC content ( Figure 9B and Supplementary data S1). The enhanced CAI score depicts the presence of most abundant codons in Escherichia coli K12. The adapted cDNA sequence was used for In silico cloning purpose.