Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus

Abstract In this study, an abundant (A+U)% and low codon bias were revealed in duck hepatitis virus type 1 (DHV-1) and the new serotype strains isolated from Taiwan, South Korea and Mainland China (DHV-N). The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in these samples. By comparative analysis of the codon usage patterns of 40 ORFs of DHV, we found that all of DHV-1 strains grouped in genotype C; the DHV-N strains isolated in South Korea and China clustered into genotypes B; and the DHV-N strains isolated from Taiwan clustered into genotypes A. The findings revealed that more than one subtype of DHV-1 circulated in East Asia. Furthermore, the results of phylogenetic analyses based on RSCU values and Clustal W method indicated obvious phylogenetic congruities. This suggested that better genome consistency of DHV may exist in nature and phylogenetic analyses based on RSCU values maybe a good method in classifying genotypes of the virus. Our work might give some clues to the features and some evolutionary information of DHV.

[1]  S Karlin,et al.  Contrasts in codon usage of latent versus productive genes of Epstein-Barr virus: data and hypotheses , 1990, Journal of virology.

[2]  A. M. Lindberg,et al.  Recent Korean isolates of duck hepatitis virus reveal the presence of a new geno- and serotype when compared to duck hepatitis virus type 1 type strains , 2007, Archives of Virology.

[3]  Jian-hua Zhou,et al.  Analysis of codon usage in bovine viral diarrhea virus , 2010, Archives of Virology.

[4]  C. Tseng,et al.  Molecular analysis of duck hepatitis virus type 1 indicates that it should be assigned to a new genus. , 2007, Virus research.

[5]  P. Sharp,et al.  Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. , 1986, Nucleic acids research.

[6]  Marco Archetti,et al.  Codon Usage Bias and Mutation Constraints Reduce the Level of ErrorMinimization of the Genetic Code , 2004, Journal of Molecular Evolution.

[7]  M. Nei,et al.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.

[8]  Edward C Holmes,et al.  The extent of codon usage bias in human RNA viruses and its evolutionary origin. , 2003, Virus research.

[9]  R. E. Gough,et al.  An outbreak of duck hepatitis type II in commercial ducks. , 1985, Avian pathology : journal of the W.V.P.A.

[10]  Xia Li,et al.  Analysis of synonymous codon usage patterns in different plant mitochondrial genomes , 2009, Molecular Biology Reports.

[11]  Dabing Zhang,et al.  Molecular analysis of duck hepatitis virus type 1. , 2007, Virology.

[12]  F. Guo,et al.  Codon Usages of Genes on Chromosome, and Surprisingly, Genes in Plasmid are Primarily Affected by Strand-specific Mutational Biases in Lawsonia intracellularis , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.

[13]  T. Hyypiä,et al.  Tissue tropism of recombinant coxsackieviruses in an adult mouse model. , 2005, The Journal of general virology.

[14]  R. E. Gough,et al.  Astrovirus-like particles associated with hepatitis in ducklings , 1984, Veterinary Record.

[15]  C. Tseng,et al.  Molecular characterization of a new serotype of duck hepatitis virus. , 2007, Virus research.

[16]  Jian-hua Zhou,et al.  Analysis of codon usage in Newcastle disease virus , 2011, Virus Genes.

[17]  Xiao Sun,et al.  Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales , 2004, Virus Research.

[18]  Dabing Zhang,et al.  Classification of duck hepatitis virus into three genotypes based on molecular evolutionary analysis , 2008, Virus Genes.

[19]  P. Tien,et al.  Analysis of synonymous codon usage in classical swine fever virus , 2008, Virus Genes.

[20]  S. Kanaya,et al.  Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. , 2001, Gene.

[21]  Yanmin Li,et al.  Mutation pressure shapes codon usage in the GC-Rich genome of foot-and-mouth disease virus , 2007, Virus Genes.

[22]  Qin Zhang,et al.  Analysis of synonymous codon usage in 11 Human Bocavirus isolates , 2008, Biosystems.

[23]  Jae-Hong Kim,et al.  Molecular analysis of duck hepatitis virus type 1 reveals a novel lineage close to the genus Parechovirus in the family Picornaviridae. , 2006, The Journal of general virology.

[24]  Jian-hua Zhou,et al.  Analysis of synonymous codon usage in foot-and-mouth disease virus , 2010, Veterinary Research Communications.

[25]  Chengwei Wu,et al.  Codon usage bias and recombination events for neuraminidase and hemagglutinin genes in Chinese isolates of influenza A virus subtype H9N2 , 2010, Archives of Virology.

[26]  C. Dutta,et al.  Synonymous codon usage in adenoviruses: influence of mutation, selection and protein hydropathy. , 2006, Virus research.

[27]  B. Calnek,et al.  In vitro isolation, propagation, and characterization of duck hepatitis virus type III. , 1979, Avian diseases.

[28]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[29]  Dabing Zhang,et al.  Molecular detection and typing of duck hepatitis A virus directly from clinical specimens. , 2008, Veterinary microbiology.