{"id":{"repo_id":"ethz","oai_identifier":"oai:www.research-collection.ethz.ch:20.500.11850/570421"},"canonical_url":"https://search.dev.ndltd.org/etd/ethz/oai:www.research-collection.ethz.ch:20.500.11850/570421","repository":{"repo_id":"ethz","name":"ETH Zürich","base_url":"https://www.research-collection.ethz.ch/oai/request"},"display":{"title":"Pathogen phylogenies for public health","abstract":"An organism’s genome sequence is a rich source of information on its current characteristics and its evolutionary history. In this thesis, I refine and apply methods to extract information from pathogen genome sequences via phylogenetic reconstructions. I extend existing phylogeny-based models to new applications in genome-wide association studies (GWAS) and genomic epidemiology. First, I show that correlations in an infectious disease trait due to shared pathogen ancestry can reduce GWAS power. I extend a statistical model of evolution to estimate and correct for these correlations. Second, I apply a phylodynamic model to estimate the origin and early transmission patterns of the SARS-CoV-2 virus during the first European outbreaks of COVID-19. Third, I describe a data infrastructure we built to generate SARS-CoV-2 genome sequences from cases in Switzerland. Finally, I develop a phylogenetic and phylodynamic framework to perform a large-scale analysis on these data. In particular, I evaluate the effect of several major public health measures in Switzerland in 2020 on SARS-CoV-2 introduction and transmission dynamics. All together, this thesis aims to enhance our understanding of infectious diseases and how to combat them.","abstract_html":"An organism’s genome sequence is a rich source of information on its current characteristics and its evolutionary history. In this thesis, I refine and apply methods to extract information from pathogen genome sequences via phylogenetic reconstructions. I extend existing phylogeny-based models to new applications in genome-wide association studies (GWAS) and genomic epidemiology. First, I show that correlations in an infectious disease trait due to shared pathogen ancestry can reduce GWAS power. I extend a statistical model of evolution to estimate and correct for these correlations. Second, I apply a phylodynamic model to estimate the origin and early transmission patterns of the SARS-CoV-2 virus during the first European outbreaks of COVID-19. Third, I describe a data infrastructure we built to generate SARS-CoV-2 genome sequences from cases in Switzerland. Finally, I develop a phylogenetic and phylodynamic framework to perform a large-scale analysis on these data. In particular, I evaluate the effect of several major public health measures in Switzerland in 2020 on SARS-CoV-2 introduction and transmission dynamics. 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In this thesis, I refine and apply methods to extract information from pathogen genome sequences via phylogenetic reconstructions. I extend existing phylogeny-based models to new applications in genome-wide association studies (GWAS) and genomic epidemiology. First, I show that correlations in an infectious disease trait due to shared pathogen ancestry can reduce GWAS power. I extend a statistical model of evolution to estimate and correct for these correlations. Second, I apply a phylodynamic model to estimate the origin and early transmission patterns of the SARS-CoV-2 virus during the first European outbreaks of COVID-19. Third, I describe a data infrastructure we built to generate SARS-CoV-2 genome sequences from cases in Switzerland. Finally, I develop a phylogenetic and phylodynamic framework to perform a large-scale analysis on these data. In particular, I evaluate the effect of several major public health measures in Switzerland in 2020 on SARS-CoV-2 introduction and transmission dynamics. All together, this thesis aims to enhance our understanding of infectious diseases and how to combat them."]},{"key":"dc:format","label":"Dc Format","values":["application/application/pdf"]},{"key":"dc:title","label":"Title","values":["Pathogen phylogenies for public health"]}]}],"canonical_facts":{"dc:contributor":["Stadler, Tanja; id_orcid0000-0001-6431-535X","Neher, Richard","Fellay, Jacques"],"dc:creator":["Nadeau, Sarah"],"dc:date":["2022"],"dc:description":["An organism’s genome sequence is a rich source of information on its current characteristics and its evolutionary history. In this thesis, I refine and apply methods to extract information from pathogen genome sequences via phylogenetic reconstructions. 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