Untangling introductions and persistence in COVID-19 resurgence in Europe

• Published in: Nature (London) Vol. 595; no. 7869; pp. 713 - 717
• Main Authors: Lemey, Philippe, Ruktanonchai, Nick, Hong, Samuel L., Colizza, Vittoria, Poletto, Chiara, Van den Broeck, Frederik, Gill, Mandev S., Ji, Xiang, Levasseur, Anthony, Oude Munnink, Bas B., Koopmans, Marion, Sadilek, Adam, Lai, Shengjie, Tatem, Andrew J., Baele, Guy, Suchard, Marc A., Dellicour, Simon
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29-07-2021; Nature Publishing Group
• Subjects: 631/181/757; 631/326/596/4130; 692/308/174; Bacteriology; Cardiology and cardiovascular system; Control; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 - prevention & control; COVID-19 - transmission; COVID-19 - virology; Datasets; Disease transmission; Distribution; Emerging diseases; Epidemics; Epidemiology; Europe; Europe - epidemiology; Forecasts and trends; Genome, Viral - genetics; Genomes; Human health and pathology; Humanities and Social Sciences; Humans; Incidence; Infections; Infectious diseases; Life Sciences; Locomotion; Microbiology and Parasitology; multidisciplinary; Parasitology; Phylogenetics; Phylogeny; Phylogeography; SARS-CoV-2 - classification; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; SARS-CoV-2 - pathogenicity; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Social networks; Summer; Time Factors; Travel - statistics & numerical data; Vaccination; Vaccines; Viral diseases; Virology; Europe; United Kingdom > UK; Belgium; Norway; Italy; France; Germany; Spain
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-021-03754-2

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 contain
1
. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave
2
. 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.
In many European countries, more than half of the SARS-CoV-2 lineages circulating in late summer 2020 resulted from new introductions, highlighting the threat of viral dissemination when restrictions are lifted.