Comprehensive analysis of the overall codon usage patterns in equine infectious anemia virus

Abstract

Background: Equine infectious anemia virus (EIAV) is an important animal model for understanding the relationship between viral persistence and the host immune response during lentiviral infections. Comparison and analysis of the codon usage model between EIAV and its hosts is important for the comprehension of viral evolution. In our study, the codon usage pattern of EIAV was analyzed from the available 29 full-length EIAV genomes through multivariate statistical methods.

Finding: Effective number of codons (ENC) suggests that the codon usage among EIAV strains is slightly biased. The ENC-plot analysis demonstrates that mutation pressure plays a substantial role in the codon usage pattern of EIAV, whereas other factors such as geographic distribution and host translation selection also take part in the process of EIAV evolution. Comparative analysis of codon adaptation index (CAI) values among EIAV and its hosts suggests that EIAV utilize the translational resources of horse more efficiently than that of donkey.

Conclusion: The codon usage bias in EIAV is slight and mutation pressure is the main factor that affects codon usage variation in EIAV. These results suggest that EIAV genomic biases are the result of the co-evolution of genome composition and the ability to evade the host's immune response.

Figure 1

The main forces that affect the codon usage of EIAV. (A) The relationship between the effective number of codons (ENC) and the GC content of the third codon position (GC₃). The continuous curve represents the expected curve between ENC value and GC₃% in the absence of selection. All of spots lie below the expected curve. (ENC, GC₃%) values of gag, pol and env were indicated by blue plot, green plot, and red plot respectively. (B) Correlation between G + C content at the first and second codon positions (GC₁₂%) and that at synonymous third codon positions (GC₃%). The line represents the correlation curve generated by the correlation analysis.

Figure 2

Genetic relationship based on synonymous codon usage in EIAV. (A) A plot of the values of the first axis and the second axis of gag, pol, and env in principle component analysis. EIAV field strain Miyazaki2011-A was indicated by black arrow. (B) A plot of the values of the first axis and the second axis of EIAV strains isolated from China (green), Japan (blue), and America (red) in principle component analysis. EIAV field strain Miyazaki2011-A was indicated by black arrow, EIAV strains V70 and V26 was indicated by blue arrow.