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 and Simon Dellicour ()
Additional contact information
Philippe Lemey: Immunology and Transplantation, Rega Institute, KU Leuven
Nick Ruktanonchai: University of Southampton
Samuel L. Hong: Immunology and Transplantation, Rega Institute, KU Leuven
Vittoria Colizza: INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP
Chiara Poletto: INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP
Frederik Van den Broeck: Immunology and Transplantation, Rega Institute, KU Leuven
Mandev S. Gill: Immunology and Transplantation, Rega Institute, KU Leuven
Xiang Ji: Tulane University
Anthony Levasseur: UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), Aix-Marseille Université (AMU) and Institut Universitaire de France (IUF)
Bas B. Oude Munnink: WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Erasmus MC
Marion Koopmans: WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Erasmus MC
Adam Sadilek: Google
Shengjie Lai: University of Southampton
Andrew J. Tatem: University of Southampton
Guy Baele: Immunology and Transplantation, Rega Institute, KU Leuven
Marc A. Suchard: University of California Los Angeles
Simon Dellicour: Immunology and Transplantation, Rega Institute, KU Leuven

Nature, 2021, vol. 595, issue 7869, 713-717

Abstract: Abstract 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.

Date: 2021
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DOI: 10.1038/s41586-021-03754-2

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