SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data

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dc.contributor.authorLemey, Philippeen
dc.contributor.authorRuktanonchai, Nick W.en
dc.contributor.authorHong, Samuelen
dc.contributor.authorColizza, Vittoriaen
dc.contributor.authorPoletto, Chiaraen
dc.contributor.authorVan den Broeck, Frederiken
dc.contributor.authorGill, Mandeven
dc.contributor.authorJi, Xiangen
dc.contributor.authorLevasseur, Anthonyen
dc.contributor.authorSadilek, Adamen
dc.contributor.authorLai, Shengjieen
dc.contributor.authorTatem, Andrewen
dc.contributor.authorBaele, Guyen
dc.contributor.authorSuchard, Marcen
dc.contributor.authorDellicour, Simonen
dc.date.accessioned2022-09-12T11:55:22Zen
dc.date.available2022-09-12T11:55:22Zen
dc.date.issued2021-02-10en
dc.description.abstractFollowing the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting late summer that was deadlier and more difficult to contain. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave. 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 West European countries and estimate that in many countries more than 50% of the lineages circulating in late summer resulted from new introductions since June 15th. The success in onwards transmission of these lineages is predicted by SARS-CoV-2 incidence during this period. Relatively early introductions from Spain into the United Kingdom contributed to the successful spread of the 20A.EU1/B.1.177 variant. The pervasive spread of variants that have not been associated with an advantage in transmissibility highlights the threat of novel variants of concern that emerged more recently and have been disseminated by holiday travel. Our findings indicate that more effective and coordinated measures are required to contain spread through cross-border travel.en
dc.description.notesPreprint versionen
dc.description.sponsorshipThe research leading to these results has received funding from the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 725422-ReservoirDOCS) and from the European Union's Horizon 2020 project MOOD (grant agreement no. 874850), and the Bill & Melinda Gates Foundation (OPP1094793 and INV-024911). The Artie Network receives funding from the Wellcome Trust through project 206298/Z/17/Z. PL acknowledges support by the Research Foundation - Flanders ('Fonds voor Wetenschappelijk Onderzoek - Vlaanderen', G066215N, G0D5117N and G0B9317N). GB acknowledges support from the 'lnterne Fondsen KU Leuven'/Internal Funds KU Leuven under grant agreement C14/18/094, and the Research Foundation - Flanders ('Fonds voor Wetenschappelijk Onderzoek - Vlaanderen', G0E1420N). MAS acknowledges support from National Institutes of Health grant U19 Al135995 and R01 Al153044. SD is supported by the Fonds National de la Recherche Scienti(lque (FNRS, Belgium). We also gratefully acknowledge support from NVIDIA Corporation with the donation of parallel computing resources used for this research.en
dc.description.versionSubmitted versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.21203/rs.3.rs-208849/v1en
dc.identifier.urihttp://hdl.handle.net/10919/111791en
dc.language.isoenen
dc.publisherSpringeren
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectEpidemiologyen
dc.subjectStatistical Epidemiologyen
dc.subjectVirologyen
dc.subjectCOVID-19en
dc.subjectSARS-CoV-2en
dc.subjectSARS-CoV-2en
dc.subjectsecond waveen
dc.subjectphylogeographyen
dc.subjectinternational mobilityen
dc.titleSARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility dataen
dc.title.serialNatureen
dc.typeArticleen
dc.type.dcmitypeTexten

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