Simmonds Peter
Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom.
J Virol. 2006 Nov;80(22):11124-40. doi: 10.1128/JVI.01076-06. Epub 2006 Sep 6.
Picornaviridae are a large virus family causing widespread, often pathogenic infections in humans and other mammals. Picornaviruses are genetically and antigenically highly diverse, with evidence for complex evolutionary histories in which recombination plays a major part. To investigate the nature of recombination and selection processes underlying the evolution of serotypes within different picornavirus genera, large-scale analysis of recombination frequencies and sites, segregation by serotype within each genus, and sequence selection and composition was performed, and results were compared with those for other nonenveloped positive-stranded viruses (astroviruses and human noroviruses) and with flavivirus and alphavirus control groups. Enteroviruses, aphthoviruses, and teschoviruses showed phylogenetic segregation by serotype only in the structural region; lack of segregation elsewhere was attributable to extensive interserotype recombination. Nonsegregating viruses also showed several characteristic sequence divergence and composition differences between genome regions that were absent from segregating virus control groups, such as much greater amino acid sequence divergence in the structural region, markedly elevated ratios of nonsynonymous-to-synonymous substitutions, and differences in codon usage. These properties were shared with other picornavirus genera, such as the parechoviruses and erboviruses. The nonenveloped astroviruses and noroviruses similarly showed high frequencies of recombination, evidence for positive selection, and differential codon use in the capsid region, implying similar underlying evolutionary mechanisms and pressures driving serotype differentiation. This process was distinct from more-recent sequence evolution generating diversity within picornavirus serotypes, in which neutral or purifying selection was prominent. Overall, this study identifies common themes in the diversification process generating picornavirus serotypes that contribute to understanding of their evolution and pathogenicity.
小核糖核酸病毒科是一个庞大的病毒家族，可在人类和其他哺乳动物中引发广泛的、通常具有致病性的感染。小核糖核酸病毒在基因和抗原方面具有高度多样性，有证据表明其进化历史复杂，其中重组起着主要作用。为了研究不同小核糖核酸病毒属血清型进化背后的重组和选择过程的本质，我们对重组频率和位点进行了大规模分析，按血清型在每个属内进行了分类，分析了序列选择和组成，并将结果与其他无包膜正链病毒（星状病毒和人诺如病毒）以及黄病毒和甲病毒对照组的结果进行了比较。肠道病毒、口疮病毒和猪水泡性疹病毒仅在结构区域按血清型显示出系统发育分类；其他区域缺乏分类是由于广泛的血清型间重组。非分类病毒在基因组区域之间还表现出一些特征性的序列差异和组成差异，而这些差异在分类病毒对照组中并不存在，例如结构区域的氨基酸序列差异大得多、非同义替换与同义替换的比率明显升高以及密码子使用的差异。这些特性与其他小核糖核酸病毒属（如帕里病毒和埃尔博病毒）相同。无包膜的星状病毒和诺如病毒同样显示出高重组频率、正选择的证据以及衣壳区域密码子使用的差异，这意味着驱动血清型分化的潜在进化机制和压力相似。这个过程与在小核糖核酸病毒血清型内产生多样性的更近的序列进化不同，后者中中性或纯化选择很突出。总体而言，这项研究确定了小核糖核酸病毒血清型多样化过程中的共同主题，有助于理解它们的进化和致病性。
