Analysis of the codon usage pattern in 2019-nCoV

Abstract

Upon a viral outbreak of novel coronavirus (2019-nCoV), it is very important to understand the molecular characteristics of the SARS-CoV-2 genome to detect the causative agent of the deadly viral infection. In the present study, we comprehensively analysed the codon usage pattern of SARS-CoV-2 to gain an insight into the viral pathogenesis as well as the evolutionary process of the newly emerging coronavirus. The correspondence analysis (CA), the effective number of codons versus GC3(NC-plot), and the relationship between GC12 versus GC3 show that a low codon usage bias exists in SARS-CoV-2. Both mutation and natural selection pressure have contributed to this low codon usage bias, with the former being the main determining factor. Lastly, the relationship of codon usage index (CUI), codon adaptation index (CAI), and the gene expression profile of SARS-CoV-2 genes have been discussed in reference to codon bias score (CBS) for further study on the virus-host relationship and their evolutionary phenomenon.