A comprehensive study of the phylodynamics of SARS-CoV-2 in Europe
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Date
2021-03-30
Publication Type
Master Thesis
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yes
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Abstract
The quick spread of SARS-CoV-2 in Europe in early 2020 shocked the continent. The short time to prepare for the pandemic resulted in rising case counts and stressed health care systems, while the knowledge about SARS-CoV-2 transmission and disease was pressingly seeked. Understanding of viral dynamics is critical to efective public health strategies and prevention of future outbreaks. In this project, we study the spatial dynamics of the early spread of SARS-CoV-2 in Europe from SARS-CoV-2 genomes. We apply a novel approach based on the multitype birth death phylodynamic model to infer geographically structured epidemic trajectories in a Bayesian framework. We integrate several sources of information: genetic sequence data, geographic distance, international travel fows and confirmed case numbers, to better understand the entry into and early spread of SARS-CoV-2 in Europe. We estimate the date of the European outbreak origin to be January 16, 2020 (95% HPD interval December 29, 2019 to January 21, 2020) seeded by several imported cases from China. We fnd that local transmission is responsible for the majority of infections as early as February 2020 while the first confirmed cases were being reported, and we infer that a wide range of infection numbers are compatible with the European outbreaks described by the analyzed genetic sequences.
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published
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ETH Zurich
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Subject
sars-CoV-2; COVID-19; Phylodynamics; Phylogenetics; Multi-type birth–death model; GLM
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09490 - Stadler, Tanja / Stadler, Tanja