During protein biosynthesis synonymous codon encoding amino acids are not used randomly, and some species or some gene always prefers to use of one or several particular synonymous codons, which is called as codon usage bias. Precious studies reveal that different genes from different species or the same one have obvious codon usage bias [21, 22] . Codon usage bias is influenced mainly by mutation bias [23, 24] , translation selection [25, 26] , secondary protein structure [20, 27] , replication and transcription selection [28] , secondary mRNA structure [29] , gene length [30] , tRNA abundance [31] , gene function and external environment [32] . However, most of these studies focus on some higher organism and many microorganisms with large genome and more genes, and there are few studies on virus with small genome and few genes or comparison between virus and host. Relatively, there are more reports on codon usage in genomes from viruses with great harm to mankind, such as SARS, human immunodeficiency virus, influenza virus A and hepatitis virus. PCV is a primary pathogen of postweaning multisystemic wasting syndrome (PMWS), which has threatened the development of pig feeding industry seriously because in recent year's occurrence of this disease has increased so as to bring about great economic loss in the world industry of pig feeding. Further studies on codon usage pattern in PCV have great significance on mutation pattern and molecular evolution of PCV. However, reports on codon usage pattern in PCV are rare, and this study is the first report. By comparison with reported DNA viruses such as Duck plague virus, Duck enteritis virus, Iridovirus, Herpesvirus [33] [34] [35] [36] , synonymous codon usage bias in the Table 4 The correlation analysis between the first two axes in CA and the nucleotide contents of PCV a b NS in superscript represent non-significant ***P-value < 0.001. **P-value < 0.01. *0.01 < P-value < 0.05 Figure 2 Correspondence analysis plot of relative synonymous codon usage in PCV. The first dimension variable f' 1 and the second variable f' 2 can reflect 39.87% and 23.83% of total mutation respectively. ). This suggests that low codon bias may result from increase in itself replication efficiency in PCV in order to adapt to replication system of its hosts. In this study, relation between main indices (f'1 and f'2)for the correspondence analysis on PCV usage cofon usage and its nucleotide composition (See Table 2 ) indicates, mutation pressure has a significant role in PCV codon usage. Other factors which can influence on PCV codon usage are also analysed and the initial results show that mutation pressure is the main factor to influence on PCV codon usage variation.