The origin and early spread of SARS-CoV-2 in Europe

The investigation of migratory patterns during the SARS-CoV-2 pandemic before spring 2020 border closures in Europe is a crucial first step toward an in-depth evaluation of border closure policies. Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimat...

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Published in:Proceedings of the National Academy of Sciences - PNAS Vol. 118; no. 9
Main Authors: Nadeau, Sarah A, Vaughan, Timothy G, Scire, Jérémie, Huisman, Jana S, Stadler, Tanja
Format: Journal Article
Language:English
Published: United States 02.03.2021
Subjects:
COVID-19 - epidemiology
COVID-19 - virology
Europe - epidemiology
Genome, Viral
Humans
Phylogeography
SARS-CoV-2 - genetics
SARS-CoV-2 - isolation & purification
Europe
disease import
SARS-CoV-2
transmission
phylogeography
ISSN:1091-6490, 1091-6490
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Summary:The investigation of migratory patterns during the SARS-CoV-2 pandemic before spring 2020 border closures in Europe is a crucial first step toward an in-depth evaluation of border closure policies. Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures. Based on SARS-CoV-2 genomes, we reconstruct a partial transmission tree of the early pandemic and coinfer the geographic location of ancestral lineages as well as the number of migration events into and between European regions. We find that the predominant lineage spreading in Europe during this time has a most recent common ancestor in Italy and was probably seeded by a transmission event in either Hubei, China or Germany. We do not find evidence for preferential migration paths from Hubei into different European regions or from each European region to the others. Sustained local transmission is first evident in Italy and then shortly thereafter in the other European regions considered. Before the first border closures in Europe, we estimate that the rate of occurrence of new cases from within-country transmission was within the bounds of the estimated rate of new cases from migration. In summary, our analysis offers a view on the early state of the epidemic in Europe and on migration patterns of the virus before border closures. This information will enable further study of the necessity and timeliness of border closures.
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ISSN:1091-6490
1091-6490
DOI:10.1073/pnas.2012008118