The analysis of codon bias of foot-and-mouth disease virus and the adaptation of this virus to the hosts

Abstract

The synonymous codon usage patterns of open reading frame (ORF) in foot-and-mouth disease virus (FMDV), the similarity degree of the synonymous codon usage between this virus and the hosts and the genetic diversities of FMDV ORFs and the viral functional genes in viral ORF have been investigated by some simply statistical analyses. As for the synonymous codon usage of FMDV, some over-represented and under-represented codons have a similar usage in all seven serotypes. 33 out of 59 synonymous codons are similarly selected between FMDV ORF and the hosts. It is interesting that the overall codon usage pattern of the strains of serotype O isolated from pigs is different with that of strains of the same serotype isolated from non-pig origin, suggesting that the factor of pigs takes part in the formation of codon usage of FMDV serotype O. Projection of codon usage of nine viral functional genes onto the two-dimensional map represents that even though viral functional genes have various genetic diversities and each gene is not separated from each other based on seven serotypes, the codon usage patterns of VP2, 2C, 3A, 3C and 3D genes belonging to serotype O strains isolated from pigs are different with those of the same serotype strains from non-pig origin. In addition, the interaction between GC12% and GC3% of viral functional genes indicates that the codon usage patterns of VP1, VP2, 2B, 3A, 3C and 3D genes are influenced by mutation pressure from virus. Furthermore, distribution plots of ENC value vs. GC3% for viral function genes indicate that mutation pressure is not the only factor in the formation of codon usage of these genes. The results suggest that both the mutation pressure from virus and the translation selection from the hosts take part in the evolution process of viral functional genes of FMDV.