流感病毒重组模式在揭示跨物种传播事件时表现出偏好和连续性。

IF 6.8 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
Xiao Ding, Yun Ma, Shicheng Li, Jingze Liu, Luyao Qin, Aiping Wu
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引用次数: 0

摘要

基因组重组是流感病毒进化的关键驱动因素,也是大流行出现的主要因素,因为重组的毒株可表现出显著改变的抗原性。然而,由于技术和伦理的限制,对重组模式(RPs)的研究有限,阻碍了有效的监测和控制策略。为了解决这一差距,我们开发了FluRPId,这是一个基于流感病毒遗传多样性识别rp的框架。FluRPId整合了重排多样性最大化、优势度和流行病学可能性的原则,以评估检测到的重排事件的可信度。应用FluRPId,我们构建了一个全面的流感病毒重组景观,包括高可信度的广泛重组事件,其中也包括大多数先前报道的重组事件。我们的分析显示,NS基因经常与PA和NA重组,而涉及HA、NA和NS的重组发生的频率比预期的要高。此外,我们确定了在重排过程中表现出强连锁的特定位点组合,为片段关联偏好提供了见解。此外,在所有亚型中都观察到广泛的重组链,强调了流感病毒进化中重组的连续性。值得注意的是,我们发现了重大的跨物种重组事件,并表征了跨物种传播病毒的宿主适应变化。我们的研究提供了迄今为止最全面的流感病毒重组景观,揭示了关键模式、偏好和进化连续性。这些发现弥补了宏观尺度重组研究的关键空白,并为未来的研究和控制工作提供了见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Influenza virus reassortment patterns exhibit preference and continuity while uncovering cross-species transmission events.

Genomic reassortment is a key driver of influenza virus evolution and a major factor in pandemic emergence, as reassorted strains can exhibit significantly altered antigenicity. However, due to technical and ethical constraints, research on reassortment patterns (RPs) has been limited, impeding effective surveillance and control strategies. To address this gap, we developed FluRPId, a framework for identifying RPs based on the genetic diversity of influenza viruses. FluRPId integrates principles of reassortment diversity maximization, dominance, and epidemiological likelihood to assess the credibility of detected reassortment events. Applying FluRPId, we constructed a comprehensive reassortment landscape of influenza viruses, encompassing widespread reassortment events with high credibility, which also include most previously reported reassortment events. Our analysis revealed that the NS gene frequently reassorts with PA and NA, while reassortment involving HA, NA, and NS occurs more frequently than expected. Furthermore, we identified specific loci combinations that exhibit strong linkage during reassortment, providing insights into segment association preferences. Additionally, extensive reassortment chains were observed across all subtypes, underscoring the continuity of reassortment in influenza virus evolution. Notably, we identified significant cross-species reassortment events and characterized host adaptation changes in cross-species-transmitted viruses. Our study provides the most comprehensive reassortment landscape of influenza viruses to date, uncovering key patterns, preferences, and evolutionary continuity. These findings bridge a critical gap in macro-scale reassortment studies and offer insights for future research and control efforts.

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来源期刊
Briefings in bioinformatics
Briefings in bioinformatics 生物-生化研究方法
CiteScore
13.20
自引率
13.70%
发文量
549
审稿时长
6 months
期刊介绍: Briefings in Bioinformatics is an international journal serving as a platform for researchers and educators in the life sciences. It also appeals to mathematicians, statisticians, and computer scientists applying their expertise to biological challenges. The journal focuses on reviews tailored for users of databases and analytical tools in contemporary genetics, molecular and systems biology. It stands out by offering practical assistance and guidance to non-specialists in computerized methodologies. Covering a wide range from introductory concepts to specific protocols and analyses, the papers address bacterial, plant, fungal, animal, and human data. The journal's detailed subject areas include genetic studies of phenotypes and genotypes, mapping, DNA sequencing, expression profiling, gene expression studies, microarrays, alignment methods, protein profiles and HMMs, lipids, metabolic and signaling pathways, structure determination and function prediction, phylogenetic studies, and education and training.
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