The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies. However, in case of the SARS-CoV-2, the low divergence of near-identical genomes sequenced over a short period of time makes conventional analysis infeasible. Using a novel method, we identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population. Bolotie is specifically designed to perform a rapid search for inter-clade recombination events over extremely large datasets, facilitating analysis of novel isolates in seconds. In cases where raw sequencing data was available, we were able to rule out the possibility that these samples represented co-infections by analyzing the underlying sequence reads. The Bolotie software and other data from our study are available at https://github.com/salzberg-lab/bolotie.

中文翻译：

---

使用 Bolotie 快速检测 SARS-CoV-2 中的进化枝间重组。


检测病原体基因组重组的能力对于系统发育分析的准确性至关重要，从而预测传染病的传播以及制定治疗方法和公共卫生政策。然而，就 SARS-CoV-2 而言，短时间内测序的几乎相同的基因组的低差异性使得传统分析不可行。使用一种新方法，我们从首批发布的 87,695 个基因组中鉴定出了 225 个可能源自重组的异常 SARS-CoV-2 基因组，其中一些基因组一直存在于人群中。 Bolotie 专门设计用于在极大的数据集上快速搜索进化枝间重组事件，从而有助于在几秒钟内分析新的分离株。在可以获得原始测序数据的情况下，我们能够通过分析基础序列读数来排除这些样本代表共同感染的可能性。 Bolotie 软件和我们研究的其他数据可在 https://github.com/salzberg-lab/bolotie 获取。