In silico codon optimization of the variant antigen-encoding genes of diverse strains of Zika Virus

Abstract

AbstractWith the recent emergence of the coronavirus pandemic, the scare for other viral pandemics is on the rise. Already having caused an epidemic in 2015-16, Zika virus (ZIKV) poses a threat for potential havoc. Thus, there is an urgent need to produce drugs and vaccines for the same as no approved vaccinations exist for the virus as of now. With the optimization of codon usage, the process of vaccine development can be accelerated and efficacy can be ensured. ZIKV genome has 3 structural genes (envelope, capsid and membrane which is obtained from pre membrane) and 7 nonstructural genes (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). We have used these 10 genes in 5 different strains of ZIKV for in silico DNA optimization in Escherichia coli. The mean CAI, GC% and AT% of wild-type DNA and optimized DNA of each were compared. It was observed that the CAI and GC% had increased in optimized DNA as compared to wild- type while the opposite was seen for AT%. The results show that codon optimization helps in efficient expression of proteins in the host. These could be used in the development of biotherapeutics. The ideal genes to be overexpressed in development of biotherapeutics are the membrane precursor (prM) and envelope (E) genes as the results have shown.