Although recombination is a feature of coronavirus evolution, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation thus far. Here, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages to investigate the possibility of virus recombination among them. Our analyses reveal well-supported phylogenetic differences between the Orf1ab region encoding viral non-structural proteins and the rest of the genome, including Spike (S) protein and remaining reading frames. By accounting for several deletions in NSP6, Orf3a, and S, we conclude that the B.1.628 major cluster, now designated as lineage XB, originated from a recombination event between viruses of B.1.631 and B.1.634 lineages. This scenario is supported by the spatiotemporal distribution of these lineages across the USA and Mexico during 2021, suggesting that the recombination event originated in this geographical region. This event raises important questions regarding the role and potential effects of recombination on SARS-CoV-2 evolution.

尽管重组是冠状病毒进化的一个特征，但迄今为止检测到的 SARS-CoV-2 重组谱系的流通有限。在这里，我们对四个 SARS-CoV-2 谱系进行了详细的系统发育分析，以研究它们之间病毒重组的可能性。我们的分析揭示了编码病毒非结构蛋白的 Orf1ab 区域与基因组其余部分（包括 Spike (S) 蛋白和其余阅读框）之间的系统发育差异，这些差异得到了充分支持。通过考虑 NSP6、Orf3a 和 S 中的多个缺失，我们得出结论，B.1.628 主要簇（现在指定为谱系 XB）源自 B.1.631 和 B.1.634 谱系病毒之间的重组事件。2021 年这些谱系在美国和墨西哥的时空分布支持了这种情况，表明重组事件起源于该地理区域。这一事件提出了有关重组对 SARS-CoV-2 进化的作用和潜在影响的重要问题。