Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses ^1–4. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution ⁵. Here, we use a novel phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6M sample tree from May 2021, we identify 589 recombination events, which indicate that approximately 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3’ portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.

准确及时地检测重组谱系对于解释遗传变异、重建流行病传播、识别感兴趣的选择和变异以及准确地进行系统发育分析至关重要^1-4 。在 SARS-CoV-2 大流行期间，基因组数据生成超出了现有分析平台的能力，从而削弱了病毒进化的实时分析⁵ 。在这里，我们使用一种新颖的系统发育学方法来搜索重组谱系的近乎全面的 SARS-CoV-2 系统发育。在 2021 年 5 月的 160 万样本树中，我们识别出 589 个重组事件，这表明已测序的 SARS-CoV-2 基因组中约 2.7% 具有可检测的重组祖先。据推测，重组断点不成比例地出现在含有刺突蛋白的基因组 3' 部分。我们的结果强调需要及时分析重组，以查明可能增加病毒传播性或毒力的重组谱系的出现。我们预计这种方法将能够在 SARS-CoV-2 大流行期间及之后对病毒重组进行全面的实时跟踪。