Revisiting the recombinant history of HIV-1 group M with dynamic network community detection.
Revisiting the recombinant history of HIV-1 group M with dynamic network community detection.
复制标题
DOI：
10.1073/pnas.2108815119
复制
发表时间：
2022-05-10
影响因子：
11.1
通讯作者：
中科院分区：
文献类型：
--
作者：
复制是HIV 1型（HIV-1）维持遗传多样性和干扰病毒根除工作的主要机制。越来越多的证据表明灵长类慢病毒包括HIV-1 M组（HIV-1/M）的重组起源。推断整个HIV-1/M基因组的重组程度非常重要，因为它可以更深入地了解全球流行病的起源，动态和演变。在这里，我们提出了一种替代方法，可以重建HIV-1全基因组重组的程度，揭示网状模式，并作为HIV-1分类的框架。我们的方法提供了一种替代的方法来了解其他新兴病毒的人畜共患病的早期进化史中的病毒重组的作用。全长HIV 1型（HIV-1）基因组序列的普遍丰度提供了一个机会，重新审视HIV-1 M组（HIV-1/M）多样性的标准模型，该模型将基因组聚类为主要非重组亚型，这与最近的证据不一致，猴免疫缺陷病毒（SIV）和其他HIV-1组的深度重组历史。在这里，我们开发了一种无监督的非参数聚类方法，它不依赖于预定义的非重组基因组，通过适应动态社会网络分析开发的社区检测方法。我们表明，这种方法（动态随机块模型[DSBM]）在检测模拟数据（拟二项式广义线性模型（GLM））中的重组断点时，与其他无参考重组检测程序（重组检测遗传算法[GARD]，重组检测程序4 [RDP 4]和RDP 5）相比，平均错误率显着降低。当这种方法被应用到一个有代表性的样本n = 525实际HIV-1基因组，我们确定k = 29作为DSBM簇的最佳数量，并使用变点检测估计，至少95%的这些基因组是重组。此外，我们确定了HIV-1基因组中已知和未记录的重组热点，以及HIV-1亚型参考基因组中亚型间重组的证据。我们建议DSBM产生的聚类可以为HIV-1分类提供一个信息框架。
Recombination is a major mechanism through which HIV type 1 (HIV-1) maintains genetic diversity and interferes with viral eradication efforts. There is growing evidence demonstrating a recombinant origin of primate lentiviruses including HIV-1 group M (HIV-1/M). Inferring the extent of recombination across the entire HIV-1/M genome is of great importance as it provides deeper insights into the origin, dynamics, and evolution of the global pandemic. Here we propose an alternative method that can reconstruct the extent of genome-wide recombination in HIV-1, uncover reticulate patterns, and serve as a framework for HIV-1 classification. Our method provides an alternative approach for understanding the roles of virus recombination in the early evolutionary history of zoonosis for other emerging viruses. The prevailing abundance of full-length HIV type 1 (HIV-1) genome sequences provides an opportunity to revisit the standard model of HIV-1 group M (HIV-1/M) diversity that clusters genomes into largely nonrecombinant subtypes, which is not consistent with recent evidence of deep recombinant histories for simian immunodeficiency virus (SIV) and other HIV-1 groups. Here we develop an unsupervised nonparametric clustering approach, which does not rely on predefined nonrecombinant genomes, by adapting a community detection method developed for dynamic social network analysis. We show that this method (dynamic stochastic block model [DSBM]) attains a significantly lower mean error rate in detecting recombinant breakpoints in simulated data (quasibinomial generalized linear model (GLM), ), compared to other reference-free recombination detection programs (genetic algorithm for recombination detection [GARD], recombination detection program 4 [RDP4], and RDP5). When this method was applied to a representative sample of n = 525 actual HIV-1 genomes, we determined k = 29 as the optimal number of DSBM clusters and used change-point detection to estimate that at least 95% of these genomes are recombinant. Further, we identified both known and undocumented recombination hotspots in the HIV-1 genome and evidence of intersubtype recombination in HIV-1 subtype reference genomes. We propose that clusters generated by DSBM can provide an informative framework for HIV-1 classification.
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DOI：
10.1109/34.865189
发表时间：
2000-07-01
影响因子：
23.6
作者：
Biernacki, C;Celeux, G;Govaert, G
通讯作者：
Govaert, G
影响因子：
1.1
作者：
Baudry, Jean-Patrick
通讯作者：
Baudry, Jean-Patrick
HIV-1跨型重组期间断点位置的序列决定因素。
影响因子：
14.9
作者：
Baird HA;Galetto R;Gao Y;Simon-Loriere E;Abreha M;Archer J;Fan J;Robertson DL;Arts EJ;Negroni M
通讯作者：
Negroni M
影响因子：
64.8
作者：
Gao, F;Bailes, E;Hahn, BH
通讯作者：
Hahn, BH
影响因子：
6.4
作者：
Angelis, Konstantinos;Albert, Jan;Paraskevis, Dimitrios
通讯作者：
Paraskevis, Dimitrios