Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130117, China.
College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
Viruses. 2022 Jan 18;14(2):170. doi: 10.3390/v14020170.
Porcine parvovirus (PPV) is the main pathogen of reproductive disorders. In recent years, a new type of porcine parvovirus has been discovered and named porcine parvovirus 2 to 7 (PPV2-PPV7), and it is associated with porcine circovirus type 2 in pigs. Codon usage patterns and their effects on the evolution and host adaptation of different PPV sub-types are still largely unknown. Here, we define six main sub-types based on the Bayesian method of structural proteins of each sub-type of PPV, including PPV2, PPV3, PPV4, PPV5, PPV6, and PPV7, which show different degrees of codon usage preferences. The effective number of codons (ENC) indicates that all PPV sub-types have low codon bias. According to the codon adaptation index (CAI), PPV3 and PPV7 have the highest similarity with the host, which is related to the main popular tendency of the host in the field; according to the frequency of optimal codons (FOP), PPV7 has the highest frequency of optimal codons, indicating the most frequently used codons in its genes; and according to the relative codon deoptimization index (RCDI), PPV3 has a higher degree. Therefore, it is determined that mutational stress has a certain impact on the codon usage preference of PPV genes, and natural selection plays a very decisive and dominant role in the codon usage pattern. Our research provides a new perspective on the evolution of porcine parvovirus (PPV) and may help provide a new method for future research on the origin, evolutionary model, and host adaptation of PPV.
猪细小病毒（PPV）是引起繁殖障碍的主要病原体。近年来，发现了一种新型猪细小病毒，并将其命名为猪细小病毒 2 到 7（PPV2-PPV7），它与猪圆环病毒 2 型有关。不同 PPV 亚型的密码子使用模式及其对进化和宿主适应的影响在很大程度上仍然未知。在这里，我们根据每种 PPV 亚型结构蛋白的贝叶斯方法定义了六个主要亚型，包括 PPV2、PPV3、PPV4、PPV5、PPV6 和 PPV7，它们表现出不同程度的密码子使用偏好。有效密码子数（ENC）表明所有 PPV 亚型的密码子偏性都较低。根据密码子适应指数（CAI），PPV3 和 PPV7 与宿主的相似度最高，这与宿主在该领域的主要流行趋势有关；根据最优密码子频率（FOP），PPV7 具有最高的最优密码子频率，表明其基因中使用最频繁的密码子；根据相对密码子去优化指数（RCDI），PPV3 的程度更高。因此，确定突变压力对 PPV 基因的密码子使用偏好有一定影响，自然选择在密码子使用模式中起着非常决定性和主导作用。我们的研究为猪细小病毒（PPV）的进化提供了新的视角，并可能有助于为未来研究 PPV 的起源、进化模型和宿主适应提供新的方法。
