A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes
A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes
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DOI：
10.1371/journal.ppat.1007707
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发表时间：
2019-04-01
期刊：
影响因子：
6.7
通讯作者：
Lopez, Carolina B.
中科院分区：
文献类型：
--
作者：
Sun, Yan;Kim, Eun Ji;Lopez, Carolina B.
回拷型缺陷病毒基因组 (cbDVG) 是体外和体内呼吸道合胞病毒 (RSV) 感染期间抗病毒免疫反应的主要引发剂。然而，控制 cbDVG 生成的机制仍然未知，从而限制了我们操纵 cbDVG 内容以调节宿主对感染的反应的能力。在这里，我们报告了介导 RSV cbDVG 物种子集产生的特定基因组信号。使用定制的生物信息学工具，我们确定了 RSV 基因组中经常用于在感染过程中生成 cbDVG 的区域。然后，我们创建了一个小基因组系统来验证这些序列之一的功能，并确定特定核苷酸是否对于该位置的 cbDVG 生成至关重要。此外，我们创建了一种重组病毒，由于该序列中引入了突变，因此无法产生 cbDVG 的子集。还发现所鉴定的序列是自然 RSV 感染期间 cbDVG 生成的位点，并且在来自不同感染患者的样本中发现了源自该序列的常见 cbDVG。这些数据表明，病毒基因组中编码的序列决定了 cbDVG 形成的位置，因此，cbDVG 的生成不是一个随机过程。这些发现开启了通过基因操作 cbDVG 形成来调节感染结果的可能性。作者摘要 复制回缺陷病毒基因组 (cbDVG) 调节单链病毒目的感染和发病机制。 cbDVG 被认为是由病毒复制过程中发生的随机错误引起的，主要假设是病毒聚合酶是 cbDVG 生成的主要驱动力。在这里，我们描述了 RSV 基因组中的特定基因组序列，该序列对于感染期间存在的大部分 cbDVG 群体的产生是必需的。我们鉴定了特定的核苷酸，当对其进行修饰时，会改变该位置的 cbDVG 生成，并且我们创建了一种重组病毒，可以根据该序列中的突变选择性地产生 cbDVG。这些数据表明，RSV cbDVG 的产生受到特定病毒序列的调节，并且可以操纵这些序列来改变感染期间产生的 cbDVG 群体。
Defective viral genomes of the copy-back type (cbDVGs) are the primary initiators of the antiviral immune response during infection with respiratory syncytial virus (RSV) both in vitro and in vivo. However, the mechanism governing cbDVG generation remains unknown, thereby limiting our ability to manipulate cbDVG content in order to modulate the host response to infection. Here we report a specific genomic signal that mediates the generation of a subset of RSV cbDVG species. Using a customized bioinformatics tool, we identified regions in the RSV genome frequently used to generate cbDVGs during infection. We then created a minigenome system to validate the function of one of these sequences and to determine if specific nucleotides were essential for cbDVG generation at that position. Further, we created a recombinant virus unable to produce a subset of cbDVGs due to mutations introduced in this sequence. The identified sequence was also found as a site for cbDVG generation during natural RSV infections, and common cbDVGs originated at this sequence were found among samples from various infected patients. These data demonstrate that sequences encoded in the viral genome determine the location of cbDVG formation and, therefore, the generation of cbDVGs is not a stochastic process. These findings open the possibility of genetically manipulating cbDVG formation to modulate infection outcome.Author summary Copy-back defective viral genomes (cbDVGs) regulate infection and pathogenesis of Mononegavirales. cbDVG are believed to arise from random errors that occur during virus replication and the predominant hypothesis is that the viral polymerase is the main driver of cbDVG generation. Here we describe a specific genomic sequence in the RSV genome that is necessary for the generation of a large proportion of the cbDVG population present during infection. We identified specific nucleotides that when modified altered cbDVG generation at this position, and we created a recombinant virus that selectively produced cbDVGs based on mutations in this sequence. These data demonstrate that the generation of RSV cbDVGs is regulated by specific viral sequences and that these sequences can be manipulated to alter the population of cbDVG generated during infection.