减小尺寸可以提炼季节性流感和SARS-CoV-2的复杂进化关系
Sravani Nanduri1, Allison Black2, Trevor Bedford2,3
1Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
bioRxiv : the preprint server for biology
|September 10, 2024
概括
像MDS和t-SNE这样的尺寸缩小方法有效地识别病毒中的遗传组,为分析病毒基因组序列和传播动态提供了更简单的基因组学替代方案.
科学领域:
- 病毒学 病毒学
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 从病毒基因组中推断遗传学推断对于理解传播动态和识别样本集群至关重要.
- 流感A/H3N2和SARS-CoV-2等病毒的重组和重组复杂化了传统的遗传学分析.
- 遗传学方法可能很复杂,需要专门的知识,促使人们寻找替代分析方法.
研究的目的:
- 评估减小维度技术在捕获重新分类 (H3N2) 和重组 (SARS-CoV-2) 病毒中已知的遗传分组中的有效性.
- 确定这些方法是否可以准确地表示遗传距离,并识别与已建立的基因组或基因系相匹配的集群.
- 为病毒基因组序列分析提供可访问,开源的工具,当基因组学不合适或不必要时.
主要方法:
- 应用主要成分分析 (PCA),多维缩放 (MDS),t分布式随机邻居嵌入 (t-SNE),以及对病毒基因组序列的均多重近似和投影 (UMAP).
- 在低维嵌入中对对基因和欧几里德距离之间的计算相关性.
- 利用嵌入物上的层次聚类来识别序列聚类,并评估与已知的病毒群体,重新分类群体和复合系谱相对应的准确性.
主要成果:
- 多维缩放 (MDS) 嵌入精确地反映了双向遗传距离,包括SARS-CoV-2复合物的中间放置.
- t-分布式随机邻居嵌入 (t-SNE) 集群成功地对H3N2和SARS-CoV-2的已建立的基因组群以及重组和重组组合群进行了复制.
- 减小尺寸的方法在不依赖明确的生物模型的情况下表现出遗传关系的有效性.
结论:
- 简单的统计方法,特别是维度减小,可以准确地代表人类病原病毒的遗传关系,如H3N2和SARS-CoV-2.
- 这些方法为分析病毒基因组序列提供了一个可行的,可能更简单的基因组学替代方案,特别是在重新分类或重组的情况下.
- 开发的开源实现方便了这些技术的应用,以便在公共卫生和病毒学研究中得到更广泛的应用.
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