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Abstract：
Our current understanding of the natural evolution of RNA viruses comes largely from consensus level genetic analyses which ignore the diverse mutant swarms that comprise within-host viral populations. The breadth and composition of viral mutant swarms impact viral fitness and adaptation, and the capacity for swarm plasticity is likely to be particularly important for arthropod-borne viruses (arboviruses) that cycle between taxonomically divergent hosts. Despite this, characterization of the relationship between the selective pressures and genetic signatures of the mutant swarm and consensus sequences is lacking. To clarify this, we analyzed previously generated whole genome, deep-sequencing data from 548 West Nile virus samples isolated from avian tissues or mosquitoes in New York State from 1999-2018. Both consensus level (interhost) and minority level (intrahost) nucleotide and amino acid sequences were analyzed, and diversity at each position was calculated across the genome in order to assess the relationship between minority and consensus sequences for individual genes and hosts. Our results indicate that consensus sequences are an inept representation of the overall genetic diversity. Unique host and gene-specific signatures and selective pressures were identified. These data demonstrate that an accurate and comprehensive understanding of arbovirus evolution and adaptation within and between hosts requires consideration of minority genotypes.
摘要：
我们目前对RNA病毒自然进化的理解主要来自共识水平的遗传分析，该分析忽略了包含宿主内病毒种群的多种突变群。病毒突变群的广度和组成影响病毒的适应性和适应性，并且群体可塑性的能力可能对于在分类学上不同的宿主之间循环的节肢动物传播的病毒（虫媒病毒）尤为重要。尽管如此,缺乏突变群和共有序列的选择压力和遗传特征之间的关系的表征。为了澄清这一点，我们分析了以前产生的全基因组，从纽约州1999-2018年从鸟类组织或蚊子中分离出的548个西尼罗河病毒样本的深度测序数据.分析了共有水平（宿主间）和少数水平（宿主内）的核苷酸和氨基酸序列，并且在整个基因组中计算每个位置的多样性，以评估单个基因和宿主的少数和共有序列之间的关系。我们的结果表明，共有序列是整体遗传多样性的无能代表。鉴定了独特的宿主和基因特异性标记和选择压力。这些数据表明，对宿主内部和宿主之间的虫媒病毒进化和适应的准确和全面的理解需要考虑少数基因型。
