The ENC values calculated for HBV indicated that although a significantly lower bias of codon usage exists in HBV, the codon usage is not mainly affected by mutation pressure. As for some viruses, previous study reported that the major factor in shaping codon usage patterns appears to be mutation pressure rather than natural selection [19, 21, 24, 35]. However, the comparison of the synonymous codon usage between HBV and human cells suggested that the interaction of mutation pressure with translation selection exists in the process of HBV evolution, although ENC values for the whole HBV coding sequence to represent mutation pressure is one of the factors in influencing codon usage pattern. This characteristic of HBV confers adaptive advantages which result in a highly efficient dissemination of the virus through different ways of transmission.
The pattern of codon usage is a genetic characteristic of various organisms in Previous study [19, 20, 27, 31, 32, 35, 36]. Because C%, U%, U3% and C3% play roles in the formation of the different optimal codons with any nucleotide-ended, the codon usage pattern of HBV is likely influenced by composition constraints. The codon usage pattern of PV is mostly coincident with that of its host, while the codon usage pattern of HBV is antagonistic to that of its host [37, 38]. The codon usage pattern of HBV is a mixture of the two types of codon usage. The coincident portion of codon usage pattern for HBV enables the corresponding amino acids to be translated rapidly, the other antagonistic portion of codon usage pattern likely enable viral proteins to be folded properly, although the translation efficiency of the corresponding amino acids is decreased. Latent genes in Epstein-Barr virus deoptimize codon usage in order to evade competition for host protein translation  and attenuation of PV activity was performed by rare codon pairs inducing poor translation for sequences of viral proteins . These results suggested that disfavored codons coding for amino acids may not be a deleterious factor for viruses to adapt to its host cells.
According to the data of codon usage pattern of HBV isolated from different countries, the geographic factor fails to influence the formation of codon usage pattern of HBV. After all, with development of international communication and highly efficient dissemination of HBV through various approaches of transmission, the affection of geographic factor seems to be weak on the limitation of HBV distribution in different countries. It is interesting that the main four subtypes of HBV have no significant difference in genetic characteristic shaped by different human races. This result might suggested that translation selection from human is not a single factor to shape the overall codon usage pattern of this virus and mutation pressure from HBV itself is a main force to drive HBV evolution. Genotyping of HBV is of high interest because there is increasing evidence that HBV genotypes may be associated with HBeAg sero-conversion rates, mutation occurring in the procure and core promoter region, severity of liver disease and treatment response [15, 16, 39, 40]. There is a significant difference of the overall codon usage pattern of HBV between genotypes A, B, E and C, D, G. HBV genotypes and subgenotypes have been associated with differences in clinical and virological characteristics, showing that they may play a role in the virus-host relationship . It has been shown that genotypes C and D are associated with more serious liver injuries and with a higher incidence of HCC than genotypes A and B [42–44]. In addition, genotype C and D have a much lower rate in response to interferon therapy than those infected with A or B genotypes [40, 45]. Moreover, subtle differences in frequency and type of lamivudine resistant variants occur in genotype A and D infectious . An evolutionary approach to HBV infection, based on the principles of natural selection, may offer explanation for how modes of transmission may favor some genotypes and subgenotypes over others and influence HBV virulence.
The genetic diversity and codon usage patterns we proposed here are helpful to understand the processes of HBV evolution, especially the roles played by translation selection from host and mutation pressure from virus. Additionally, such information might benefit to understand the roles of geographic and subtype factors in influencing the process of HBV evolution.