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

Virology Journal

Wei Yan¹  Ge Li¹  Shang-di Zhang¹  Fang-xin Zhang¹  Mei-liang Wang¹  Hui Ling¹  Xiao-qin Ha¹  Ming-ren Ma¹ 

[1] 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

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

Others  :  1155467
DOI  :  10.1186/1743-422X-8-544

 received in 2011-09-06, accepted in 2011-12-15,  发布年份 2011

【 摘 要 】

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.

【 授权许可】

   
2011 Ma et al; licensee BioMed Central Ltd.

【 图 表 】

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