Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China.
Virol J. 2013 Dec 20;10:356. doi: 10.1186/1743-422X-10-356.
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.
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.
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.
马传染性贫血病毒（EIAV）是研究慢病毒感染过程中病毒持续存在与宿主免疫反应之间关系的重要动物模型。比较和分析 EIAV 与其宿主之间的密码子使用模型对于理解病毒进化很重要。在本研究中，我们通过多变量统计方法分析了来自 29 个全长 EIAV 基因组的 EIAV 的密码子使用模式。
有效密码子数（ENC）表明 EIAV 株之间的密码子使用略有偏向。ENC-plot 分析表明，突变压力在 EIAV 的密码子使用模式中起着重要作用，而地理分布和宿主翻译选择等其他因素也参与了 EIAV 进化的过程。EIAV 与其宿主之间的密码子适应指数（CAI）值的比较分析表明，EIAV 比驴更有效地利用了马的翻译资源。
EIAV 的密码子使用偏性较小，突变压力是影响 EIAV 密码子使用变化的主要因素。这些结果表明，EIAV 基因组的偏性是基因组组成与逃避宿主免疫反应能力共同进化的结果。
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