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Untangling introductions and persistence in COVID-19 resurgence in Europe

Philippe Lemey
Nick Ruktanonchai
Samuel L. Hong
Vittoria Colizza
Chiara Poletto
Frederik Van den Broeck
Mandev S. Gill
Xiang Ji
Anthony Levasseur
Bas B. Oude Munnink
Marion Koopmans
Adam Sadilek
Shengjie Lai
Andrew J. Tatem
Guy Baele
Marc A. Suchard
Simon Dellicour
Nature (2021)


Following 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 phylogeographic model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the COVID-19 resurgence in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries over half of the lineages circulating in late summer resulted from new introductions since June 15th. The success in onward transmission of newly introduced lineages was negatively associated with local COVID-19 incidence 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 by 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 spread through cross-border travel even as vaccination begins to reduce disease burden.