Project: Real-time phylogenetics and epidemiology in SARS-CoV-2 genome data
Davies Group
The ongoing COVID-19 pandemic has seen the generation of over 75,000 genomes of the causative agent, the virus SARS-CoV-2, across the globe. These data have been key to understand the spread and evolution of the virus, and ultimately provide information to develop a public health response. Phylogenetic methods can reveal the presence of transmission clusters and their dynamics, including their effective reproductive number (Re), and transmission rates. The crux of these methods is that transmission leaves a signature in pathogen genomes. However, such genomic signatures are elusive in the context of very rapid transmission.
This project will investigate the potential of hierarchical Bayesian models to estimate epidemiological parameters in outbreak clusters with rapid transmission. These models exploit different sources of information and are expected to outperform standard phylogenetic techniques. The student will benefit from curated genome data for SARS-CoV-2 and will focus on statistical modelling. This project will develop skills in programming, statistics, and infectious disease epidemiology.
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Davies Group
3 vacancies
The Davies group aims to apply genome sequencing methodologies and bioinformatics approaches to understand the evolution and transmission of bacterial pathogens. This knowledge can help facilitate a global understanding of pathogen evolution, in addition to informing public health intervention to reduce the disease burden associated with bacterial pathogens. Current projects address key research questions such as: is there a genetic difference between strains causing different disease manifestations? What is driving the emergence and dissemination of bacterial pathogens? Do host immune factors govern disease severity? Our research closely aligns with key international collaborators including the Wellcome Trust Sanger Institute in the United Kingdom.
Davies Group Current Projects
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Integrative infectious disease phylodynamics
PhD/MPhil
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Population genomics of endemic Streptococcus pyogenes
PhD/MPhil, Master of Biomedical Science, Honours
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Evolution of streptococcal pathovars
PhD/MPhil, Master of Biomedical Science, Honours
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Unravelling the drivers of group A streptococcal pandemics
PhD/MPhil, Master of Biomedical Science, Honours
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Using genomics to investigate the transmission of skin pathogens and antimicrobial resistance in a ‘One Health’ setting
PhD/MPhil, Master of Biomedical Science, Honours
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Detecting natural selection in bacterial genomic data
Master of Biomedical Science, Honours
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Real-time phylogenetics and epidemiology in SARS-CoV-2 genome data
PhD/MPhil, Master of Biomedical Science
Research degrees at the Doherty Institute are administered by the University of Melbourne.