After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain¹. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave². Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.

在 2020 年春季出现第一波 SARS-CoV-2 感染后，欧洲从 2020 年夏末开始经历了病毒的死灰复燃，这种病毒更加致命且更难以控制¹。宽松的干预措施和夏季旅行被认为是第二波的驱动因素². 在这里，我们建立了一个系统地理模型来评估新引入的谱系，而不是重新点燃持久谱系，如何促成欧洲 COVID-19 的复兴。我们使用来自 10 个欧洲国家的基因组、流动性和流行病学数据为该模型提供信息，并估计在许多国家，夏末流行的血统中有一半以上是自 2020 年 6 月 15 日以来新引入的。新引入的血统继续传播的成功是在此期间与当地的 COVID-19 发病率呈负相关。2020 年夏季变体的普遍传播凸显了解除限制后病毒传播的威胁，在控制当前更易传播和/或逃避免疫的变体传播的战略中需要仔细考虑这一点。