The characteristic of codon usage pattern and its evolution of hepatitis C virus

To give a new perspective on the codon usage of the hepatitis C virus (HCV) and the factors accounting for shaping the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, aromaticity and hydrophobicity of each polyprotein of the virus, effective number of codons (ENC) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution. The RSCU values of each codon of 144 HCV ORFs indicated that all abundant codons were C/G-ended codons. The plots of principal component analysis based on sub-genotype of HCV indicated that sub-genotype 1a and 1b separated clearly on the axis of f2 suggesting that the codon usage bias between sub-genotype 1a and 1b strains was different. By comparing the codon usage between HCV and human cells, we found that the synonymous codon usage pattern of HCV was a mixture of coincidence and antagonism to that of host cells. The characteristics of the synonymous codon usage patterns and nucleotide contents of HCV, and the correlation analysis between GC(3s), GC(1,2s), GC% (ORF), GC% (5'-UTR), GC% (3'-UTR), aromaticity, hydrophobicity and ENC value, respectively, indicated that mutational pressure was the dominant factor accounting for the codon usage variation and selection pressure also accounted for HCV codon usage pattern.