Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples: a distance-based sequential-linking method
Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples: a distance-based sequential-linking method
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DOI：
10.1016/s0378-1119(03)00656-5
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发表时间：
2003-10-23
期刊：
影响因子：
3.5
通讯作者：
Tanaka, H
中科院分区：
文献类型：
--
作者：
Ren, FR;Ogishima, S;Tanaka, H
提出了一种从非同期样本重建宿主（患者）内病毒进化的系统发育关系的新方法。该方法有两个重要特点：可以通过简单的计算算法处理非同期病毒样本，并且可以估计病毒进化过程中出现的中性和适应性进化模式。在我们之前的研究中，我们提出了基于最大似然法的该算法的初步表述。然而，该初步公式很难使用，因为可能性的计算需要极大量的时间，并且可能的树拓扑的数量随着病毒变体数量的增加而呈指数增加。在本文中，我们提出了另一种新算法，称为基于距离的顺序链接算法，其中采用邻接方法从连续病毒样本中重建纵向系统发育树。该算法应用于单个患者感染 7 年后获得的 1 型人类免疫缺陷病毒 (HIV-1) env 基因（V3 区）的纵向数据集。结果表明，该方法可以在合理的计算时间内成功地从非同期病毒样本重建纵向系统发育树。这种修改后的方法被证明是估计宿主内病毒进化动态过程的有用工具。 (C) 2003 Elsevier B.V. 保留所有权利。
A new method for reconstructing phylogenetic relationships of within-host (patient) viral evolution from non contemporaneous samples is presented. This method has two important features: noncontemporaneous viral samples can be dealt with by a simple computing algorithm, and both neutral and adaptive evolution patterns occurring during the process of viral evolution can be estimated. In our previous study, we proposed a preliminary formulation of this algorithm that was based on the maximum likelihood method. However, that preliminary formulation was difficult to use because the calculation of the likelihood required an extremely large amount of time and the number of possible tree topologies increased exponentially according to the increase in the number of viral variants. In this paper, we propose another new algorithm, referred to as a distance-based sequential-linking algorithm, in which the neighbor-joining method is employed for reconstruction of the longitudinal phylogenetic tree from serial viral samples. This algorithm is applied to a longitudinal data set of the env gene (V3 region) of human immunodeficiency virus type 1 (HIV-1) obtained over 7 years after the infection of a single patient. The results suggest that this method can successfully reconstruct a longitudinal phylogenetic tree from noncontemporaneous viral samples within a reasonable calculation time. This revised method proved to be a useful tool for estimating the dynamic process of within-host viral evolution. (C) 2003 Elsevier B.V. All rights reserved.