Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.
Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.
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DOI：
10.1038/s41598-017-18791-z
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发表时间：
2018-01-10
影响因子：
4.6
通讯作者：
McHardy AC
中科院分区：
文献类型：
--
作者：
Klingen TR;Reimering S;Loers J;Mooren K;Klawonn F;Krey T;Gabriel G;McHardy AC
监测甲型流感病毒基因组的变化对于了解其快速进化和适应不断变化的条件（例如环境）至关重要。在新的宿主物种内建立。选择性清除代表一种快速适应模式，通常在人类甲型流感病毒中观察到。我们描述了扫描动力学（SD）图，这是一种将系统发育算法与统计技术相结合的计算方法，用于根据纵向序列数据来表征快速进化的病毒的分子适应。 SD 图有助于识别选择性扫描、发生这些扫描的时间段以及为病毒提供选择性优势的相关变化。我们研究了 2009 年大流行的 H1N1 甲型流感 (pH1N1) 和季节性 H3N2 甲型流感 (sH3N2) 病毒过去的全基因组适应性。 pH1N1 流感病毒显示多种蛋白质的氨基酸同时发生变化，特别是在 pH1N1 活性高的季节。在一定程度上，这些变化导致了功能改变，促进了持续的人际传播。在 sH3N2 流感病毒的进化过程中，我们检测到了疫苗株特征的变化，这些变化在 WHO 建议之前的一个季节的选择性扫描中偶尔被发现。总而言之，SD 图允许通过识别选择性扫描及其相关特征来监测和表征甲型流感病毒的适应性进化。
Monitoring changes in influenza A virus genomes is crucial to understand its rapid evolution and adaptation to changing conditions e.g. establishment within novel host species. Selective sweeps represent a rapid mode of adaptation and are typically observed in human influenza A viruses. We describe Sweep Dynamics (SD) plots, a computational method combining phylogenetic algorithms with statistical techniques to characterize the molecular adaptation of rapidly evolving viruses from longitudinal sequence data. SD plots facilitate the identification of selective sweeps, the time periods in which these occurred and associated changes providing a selective advantage to the virus. We studied the past genome-wide adaptation of the 2009 pandemic H1N1 influenza A (pH1N1) and seasonal H3N2 influenza A (sH3N2) viruses. The pH1N1 influenza virus showed simultaneous amino acid changes in various proteins, particularly in seasons of high pH1N1 activity. Partially, these changes resulted in functional alterations facilitating sustained human-to-human transmission. In the evolution of sH3N2 influenza viruses, we detected changes characterizing vaccine strains, which were occasionally revealed in selective sweeps one season prior to the WHO recommendation. Taken together, SD plots allow monitoring and characterizing the adaptive evolution of influenza A viruses by identifying selective sweeps and their associated signatures.
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影响因子：
5.5
作者：
Al Busaidy, Suleiman;Al-Gohary, Amany;Ziegler, Thedi
通讯作者：
Ziegler, Thedi
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
5.5
作者：
Bouvier NM;Palese P
通讯作者：
Palese P
影响因子：
3.7
作者：
Burke DF;Smith DJ
通讯作者：
Smith DJ