Hassanin Alexandre, Rambaud Opale, Klein Dylan
Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Centre National de la Recherche Scientifique, École Pratique des Hautes Études, Muséum National d'Histoire Naturelle, Université des Antilles, 75231 Paris, France.
Viruses. 2022 Feb 21;14(2):440. doi: 10.3390/v14020440.
Recombination creates mosaic genomes containing regions with mixed ancestry, and the accumulation of such events over time can complicate greatly many aspects of evolutionary inference. Here, we developed a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes to highlight the regions supporting phylogenetic relationships. The method was applied to an alignment of 56 sarbecoviruses, including SARS-CoV and SARS-CoV-2, responsible for the SARS epidemic and COVID-19 pandemic, respectively. The SWB analyses were also used to construct a consensus tree showing the most reliable relationships and better interpret hidden phylogenetic signals. Our results revealed that most relationships were supported by just a few genomic regions and confirmed that three divergent lineages could be found in bats from Yunnan: , which groups SARS-CoV related coronaviruses from China; , which includes SARS-CoV-2 related coronaviruses from Southeast Asia and Yunnan; and , which contains a few highly divergent viruses recently described in Yunnan. The GB barcodes showed evidence for ancient recombination between and genomes, as well as more recent recombination events between and genomes. The recombination and phylogeographic patterns suggest a strong host-dependent selection of the viral RNA-dependent RNA polymerase. In addition, SARS-CoV-2 appears as a mosaic genome composed of regions sharing recent ancestry with three bat s from Yunnan (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia. Finally, our results suggest that viral circular RNAs may be key molecules for the mechanism of recombination.
重组产生了包含混合谱系区域的镶嵌基因组，随着时间的推移，此类事件的积累会使进化推断的许多方面变得极为复杂。在此，我们开发了一种滑动窗口自引导（SWB）方法来生成基因组自引导（GB）条形码，以突出支持系统发育关系的区域。该方法应用于56种沙贝病毒的比对，这些病毒分别导致了SARS疫情和COVID-19大流行，其中包括SARS-CoV和SARS-CoV-2。SWB分析还用于构建一棵共识树，以显示最可靠的关系并更好地解释隐藏的系统发育信号。我们的结果表明，大多数关系仅由少数基因组区域支持，并证实了在云南蝙蝠中可发现三个不同的谱系：一个谱系包含来自中国的与SARS-CoV相关的冠状病毒；另一个谱系包括来自东南亚和云南的与SARS-CoV-2相关的冠状病毒；还有一个谱系包含最近在云南描述的一些高度分化的病毒。GB条形码显示了和基因组之间古老重组的证据，以及和基因组之间较新的重组事件。重组和系统发育地理模式表明，病毒的RNA依赖性RNA聚合酶存在强烈的宿主依赖性选择。此外，SARS-CoV-2表现为一个镶嵌基因组，其组成区域与来自云南的三种蝙蝠（RmYN02、RpYN06和RaTG13）有近期共同祖先，或与来自云南和东南亚的蝙蝠中更古老的祖先相关。最后，我们的结果表明，病毒环状RNA可能是重组机制的关键分子。
