Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity
Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity
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DOI：
10.1128/jvi.00736-12
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发表时间：
2012-08-01
影响因子：
5.4
通讯作者：
Henn, Matthew R.
中科院分区：
文献类型：
--
作者：
Parameswaran, Poornima;Charlebois, Patrick;Henn, Matthew R.
类似于RNA病毒如人类免疫缺陷病毒的观察，与宿主内登革病毒（DENV）群体相关的遗传变异已被假定影响病毒适应性和疾病发病机制。以前研究DENV宿主内遗传变异的尝试仅表征了少数病毒基因或有限数量的全长基因组。我们开发了一种结合深度测序的全基因组扩增方法，以捕获DENV-2整个编码区的宿主内多样性。使用这种方法，我们从22名患有继发性DENV感染的巴布亚个体的血清中测序了DENV-2基因组，并在每个样品中捕获了类似于75%的DENV基因组（范围，40至98%）。我们使用高度敏感和特异性的方法鉴定和量化变异，并确定多样性程度大大低于先前的估计。宿主内多样性的显着差异，检测基因之间的抗原性不同的领域之间的包膜基因。有趣的是，一个强有力的协会之间的程度，在一些基因和病毒进化枝的身份宿主的多样性。此外，宿主内病毒变体的丰度，以及病毒突变对氨基酸编码和预测蛋白质功能的影响，决定了在循环的埃古安DENV-2群体中是否在宿主间水平上观察到宿主内变体，强烈暗示了跨传播事件的纯化选择。我们的数据说明了高覆盖率的全基因组分析宿主内多样性的高分辨率映射的宿主内多样性和病毒感染的临床，流行病学和病毒学参数之间的关系的价值。
Analogous to observations in RNA viruses such as human immunodeficiency virus, genetic variation associated with intrahost dengue virus (DENV) populations has been postulated to influence viral fitness and disease pathogenesis. Previous attempts to investigate intrahost genetic variation in DENV characterized only a few viral genes or a limited number of full-length genomes. We developed a whole-genome amplification approach coupled with deep sequencing to capture intrahost diversity across the entire coding region of DENV-2. Using this approach, we sequenced DENV-2 genomes from the serum of 22 Nicaraguan individuals with secondary DENV infection and captured similar to 75% of the DENV genome in each sample (range, 40 to 98%). We identified and quantified variants using a highly sensitive and specific method and determined that the extent of diversity was considerably lower than previous estimates. Significant differences in intrahost diversity were detected between genes and also between antigenically distinct domains of the Envelope gene. Interestingly, a strong association was discerned between the extent of intrahost diversity in a few genes and viral clade identity. Additionally, the abundance of viral variants within a host, as well as the impact of viral mutations on amino acid encoding and predicted protein function, determined whether intrahost variants were observed at the interhost level in circulating Nicaraguan DENV-2 populations, strongly suggestive of purifying selection across transmission events. Our data illustrate the value of high-coverage genome-wide analysis of intrahost diversity for high-resolution mapping of the relationship between intrahost diversity and clinical, epidemiological, and virological parameters of viral infection.