Abstract
BackgroundHepatitis B virus (HBV) infection is one of the main human health problem and causes a large-scale of patients chronic infection worldwide.. As the replication of HBV depends on its host cell system, codon usage pattern for the viral gene might be susceptible to two main selections, namely mutation pressure and translation selection. In this case, a deeper investigation between HBV evolution and host adaptive response might assist control this disease.ResultRelative synonymous codon usage (RSCU) values for the whole HBV coding sequence were studied by Principal component analysis (PCA). The characteristics of the synonymous codon usage patterns, nucleotide contents and the comparison between ENC values of the whole HBV coding sequence indicated that the interaction between virus mutation pressure and host translation selection exists in the processes of HBV evolution. The synonymous codon usage pattern of HBV is a mixture of coincidence and antagonism to that of host cell. But the difference of genetic characteristic of HBV failed to be observed to its different epidemic areas or subtypes, suggesting that geographic factor is limited to influence the evolution of this virus, while genetic characteristic based on HBV genotypes could be divided into three groups, namely (i) genotyps A and E, (ii) genotype B, (iii) genotypes C, D and G.ConclusionCodon usage patterns from PCA for identification of evolutionary trends in HBV provide an alternative approach to understand the evolution of HBV. Further more, a combined selection of mutation pressure with translation selection on codon usage might shed a light on understanding the evolutionary trends of HBV genotypes.
Highlights
Hepatitis B virus (HBV) disease is one of the main global health problems that two billion people are infected and 350 million people undergo chronic infection as well [1]
Codon usage patterns from Principal component analysis (PCA) for identification of evolutionary trends in HBV provide an alternative approach to understand the evolution of HBV
A combined selection of mutation pressure with translation selection on codon usage might shed a light on understanding the evolutionary trends of HBV genotypes
Summary
Synonymous coodn usage in HBV The C% and U% were higher than A% and G%, and C3% and U3% were higher than A3% and G3% in HBV (Table 1). The genotypes A and B have an obviously different genetic characteristic with the rest, while genotypes C, D and G appear to have a relationship of evolution (Figure 3) These results indicated that the geographic distribution might be a limited factor to effect the codon usage of the whole HBV coding sequence, and the subtypes did not reflect the characteristic of HBV evolution to some degree. Comparative analysis of the RSCU values between HBV and human cell There is a resemblance of synonymous codons usage pattern between this virus and human cell, for example, the similar synonymous codon usage pattern includes all synonymous codons for Phe, Ile, Val, Ser, Ala, Tyr, His, Lys, Asp, Cys and Gly (Table 1) This may be explained that the codon usage of HBV adapting to its host under translation selection could result in the multiplication of progeny virus. The result suggested that these codons could influence the translational rate of the context flanking them, resulting in the viral product correct fold
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