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Open Access Research

The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern

Ming-ren Ma*, Xiao-qin Ha*, Hui Ling, Mei-liang Wang, Fang-xin Zhang, Shang-di Zhang, Ge Li and Wei Yan

Author Affiliations

Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command; Key lab of Stem cells and Gene Drugs of Gansu Province, Lanzhou 730000, China

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Virology Journal 2011, 8:544  doi:10.1186/1743-422X-8-544

Published: 15 December 2011

Abstract

Background

Hepatitis 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.

Result

Relative 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.

Conclusion

Codon 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.

Keywords:
Hepatitis B virus; codon usage pattern; evolution; mutation pressure; translation selection