Yao Xiaoting, Pang Ming, Wang Tianxing, Chen Xi, Tang Xidian, Chang Jianjun, Chen Dekun, Ma Wentao
College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China.
Pathogens. 2020 Oct 27;9(11):888. doi: 10.3390/pathogens9110888.
Parapoxvirus (PPV) has been identified in some mammals and poses a great threat to both the livestock production and public health. However, the prevalence and evolution of this virus are still not fully understood. Here, we performed an in silico analysis to investigate the genomic features and evolution of PPVs. We noticed that although there were significant differences of GC contents between orf virus (ORFV) and other three species of PPVs, all PPVs showed almost identical nucleotide bias, that is GC richness. The structural analysis of PPV genomes showed the divergence of different PPV species, which may be due to the specific adaptation to their natural hosts. Additionally, we estimated the phylogenetic diversity of seven different genes of PPV. According to all available sequences, our results suggested that during 2010-2018, ORFV was the dominant virus species under the selective pressure of the optimal gene patterns. Furthermore, we found the substitution rates ranged from 3.56 × 10 to 4.21 × 10 in different PPV segments, and the PPV VIR gene evolved at the highest substitution rate. In these seven protein-coding regions, purifying selection was the major evolutionary pressure, while the GIF and VIR genes suffered the greatest positive selection pressure. These results may provide useful knowledge on the virus genetic evolution from a new perspective which could help to create prevention and control strategies.
副痘病毒（PPV）已在一些哺乳动物中被发现，对畜牧业生产和公共卫生都构成了巨大威胁。然而，这种病毒的流行情况和进化过程仍未完全明晰。在此，我们进行了一项计算机模拟分析，以研究副痘病毒的基因组特征和进化。我们注意到，尽管口疮病毒（ORFV）与其他三种副痘病毒在GC含量上存在显著差异，但所有副痘病毒都表现出几乎相同的核苷酸偏向性，即富含GC。副痘病毒基因组的结构分析显示了不同副痘病毒种类的差异，这可能是由于它们对自然宿主的特定适应性。此外，我们估计了副痘病毒七个不同基因的系统发育多样性。根据所有可用序列，我们的结果表明，在2010 - 2018年期间，在最优基因模式的选择压力下，口疮病毒是主要的病毒种类。此外，我们发现不同副痘病毒片段的替换率在3.56×10至4.21×10之间，且副痘病毒VIR基因的进化替换率最高。在这七个蛋白质编码区域中，纯化选择是主要的进化压力，而GIF和VIR基因受到的正向选择压力最大。这些结果可能从一个新的角度为病毒遗传进化提供有用的知识，有助于制定预防和控制策略。
