Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Mar 2;118(9):e2012008118.
doi: 10.1073/pnas.2012008118.

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

Sarah A Nadeau  1   2 , Timothy G Vaughan  1   2 , Jérémie Scire  1   2 , Jana S Huisman  1   2   3 , Tanja Stadler  4   2
Affiliations

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

Sarah A Nadeau et al. Proc Natl Acad Sci U S A. .

Abstract

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.

Keywords: SARS-CoV-2; disease import; phylogeography; transmission.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interest.

Figures

Fig. 1.
Fig. 1.
Maximum-clade credibility tree. The clade of A2a sequences analyzed is highlighted with dashed branches. The values above the branches are the posterior clade probabilities and the pale red bars show the 95% highest posterior density interval for node ages. The pie charts at nodes show posterior probability for the ancestor being located in each region (note that we assumed the root of the tree was in Hubei with probability 1). The region for each tip is the region in which the sequence was collected, irrespective of travel history. Tips are annotated with GISAID accession identifier.
Fig. 2.
Fig. 2.
Estimated rate of new cases arising from migration compared with the estimated rate of new cases arising from within-region transmission. For each day, we multiplied the (smoothed) number of newly confirmed cases in each source region by the posterior sample of migration rates from source to sink. The median of these rates is shown in the “Migration” row. We also multiplied the (smoothed) number of newly confirmed cases in each sink region by the posterior sample of transmission rates for the region. The median of these rates is shown in the “Within-region transmission” row. Gray shaded regions indicate dates on which new cases were reported in each region. Dates are lagged 5 d to account for a 5-d delay between infection and migration or onward transmission and daily case counts were smoothed by taking a rolling 7-d average. Case data comes from the Johns Hopkins Center for Systems Science and Engineering (https://github.com/CSSEGISandData/COVID-19).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Connor P., More than nine-in-ten people worldwide live in countries with travel restrictions amid COVID-19. Pew Research Center, https://www.pewresearch.org/fact-tank/2020/04/01/more-than-nine-in-ten-p.... Accessed 18 May 2020.
    1. WHO , Updated WHO recommendations for international traffic in relation to COVID-19 outbreak, https://www.who.int/news-room/articles-detail/updated-who-recommendation.... Accessed 18 May 2020.
    1. Wu F., et al. ., A new coronavirus associated with human respiratory disease in China. Nature 579, 265–269 (2020). - PMC - PubMed
    1. WHO , COVID-19 situation reports, https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situatio.... Accessed 20 April 2020.
    1. Spiteri G., et al. ., First cases of coronavirus disease 2019 (COVID-19) in the WHO European region, 24 January to 21 February 2020. Euro Surveill. 25, 2000178 (2020). - PMC - PubMed

Publication types

LinkOut - more resources