Salemi Marco, Gray Rebecca R, Goodenow Maureen M
Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, College of Medicine, 1376 Mowry Road, P.O. Box 106633, Gainesville, FL 32610, USA.
Mol Phylogenet Evol. 2008 Nov;49(2):618-28. doi: 10.1016/j.ympev.2008.08.017. Epub 2008 Aug 31.
Since recombination leads to the generation of mosaic genomes that violate the assumption of traditional phylogenetic methods that sequence evolution can be accurately described by a single tree, results and conclusions based on phylogenetic analysis of data sets including recombinant sequences can be severely misleading. Many methods are able to adequately detect recombination between diverse sequences, for example between different HIV-1 subtypes. More problematic is the identification of recombinants among closely related sequences such as a viral population within a host. We describe a simple algorithmic procedure that enables detection of intra-host recombinants based on split-decomposition networks and a robust statistical test for recombination. By applying this algorithm to several published HIV-1 data sets we conclude that intra-host recombination was significantly underestimated in previous studies and that up to one-third of the env sequences longitudinally sampled from a given subject can be of recombinant origin. The results show that our procedure can be a valuable exploratory tool for detection of recombinant sequences before phylogenetic analysis, and also suggest that HIV-1 recombination in vivo is far more frequent and significant than previously thought.
由于重组会导致镶嵌基因组的产生，这违反了传统系统发育方法中序列进化可以由单一树准确描述的假设，基于包含重组序列的数据集进行系统发育分析得出的结果和结论可能会产生严重误导。许多方法能够充分检测不同序列之间的重组，例如不同HIV-1亚型之间的重组。更具问题的是在密切相关的序列中识别重组体，例如宿主内的病毒群体。我们描述了一种简单的算法程序，该程序能够基于分裂分解网络检测宿主内重组体，并对重组进行稳健的统计检验。通过将该算法应用于几个已发表的HIV-1数据集，我们得出结论，在先前的研究中宿主内重组被严重低估，并且从给定个体纵向采样的env序列中多达三分之一可能起源于重组。结果表明，我们的程序可以作为在系统发育分析之前检测重组序列的有价值的探索工具，并且还表明HIV-1在体内的重组比以前认为的要频繁和显著得多。
