Hughes Austin L, Piontkivska Helen
Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, United States.
Infect Genet Evol. 2008 Mar;8(2):130-8. doi: 10.1016/j.meegid.2007.11.001. Epub 2007 Nov 17.
Analysis of nucleotide diversity within six species of circovirus showed consistently stronger purifying selection at nonsynonymous sites in the rep gene than on those in the cap gene. In addition, synonymous nucleotide diversity in the rep gene was significantly lower than that in the cap gene, suggesting functional constraint even at synonymous sites in rep, which was associated in all six species with strongly negative AT-skew. Of the six virus species examined, four species showed evidence of ongoing purifying selection at nonsynonymous polymorphic sites in the rep gene, indicating the presence of slightly deterious nonsynonymous variants in these populations. The rep gene of porcine circovirus 2 (PCV2) was unique, however, in showing a strong excess of rare nonsynonymous polymorphisms. The excess of rare nonsynonymous polymorphisms suggests a prolonged population bottleneck in PCV2, allowing slightly deleterious mutations to accumulate, followed by a population expansion during which selection to remove these variants has increased in effectiveness. Such a population history is consistent with the epidemiological evidence of a recent worldwide spread of PCV2.
六种圆环病毒核苷酸多样性分析表明，在rep基因的非同义位点上，净化选择始终比cap基因中的更为强烈。此外，rep基因中的同义核苷酸多样性显著低于cap基因，这表明即使在rep基因的同义位点也存在功能限制，在所有六个物种中这都与强烈的负AT偏斜相关。在所检测的六个病毒物种中，有四个物种在rep基因的非同义多态位点上显示出正在进行净化选择的证据，这表明这些种群中存在轻微有害的非同义变体。然而，猪圆环病毒2（PCV2）的rep基因是独特的，表现出强烈的罕见非同义多态性过剩。罕见非同义多态性的过剩表明PCV2存在长期的种群瓶颈，使得轻微有害突变得以积累，随后是种群扩张，在此期间去除这些变体的选择效率有所提高。这样的种群历史与PCV2近期在全球范围内传播的流行病学证据一致。
