Edinburgh Infectious Diseases
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PhD students rise to the challenge of Covid-19

Students from the Wellcome Trust PhD programme in Hosts, Pathogens and Global Health at the University of Edinburgh are taking on projects to help answer key questions in the Covid-19 pandemic.

The Hosts, Pathogens and Global Health PhD programme was established at the University of Edinburgh in 2016, and is led by directors Keith Matthews, Professor of Parasite Biology in the School of Biological Sciences, and Mark Woolhouse, Professor of Infectious Disease Epidemiology in the Usher Institute.

It provides broad, interdisciplinary training in all aspects of infectious disease research, from immunology to epidemiology, phylogenetics and evolutionary biology.
PhD students Alex Morgan and Áine O'Toole are working on projects that are providing insight into the effectiveness of different social distancing measures, and characterising the different lineages of SARS-CoV-2 present in UK coronavirus patients.
Alex Morgan and Aine O'Toole
PhD students Alex Morgan and Aine O'Toole.

Modelling social distancing measures

Alex Morgan is part of the second cohort of Hosts, Pathogens and Global Health PhD students.  He started his PhD project with Prof Mark Woolhouse and the Epigroup in September 2018, after completing his MSc by Research during his first year in Edinburgh. 

He is now is now working with others in Epigroup who are currently modelling the impact of different social distancing measures (SDMs) on the transmission dynamics of the COVID-19 outbreak.

We are exploring ways that the timing and magnitude of these SDM strategies translates into reductions in the burden of disease, in the overall population, in at-risk groups and to prevent health systems from being overwhelmed.

Alex MorganWellcome Trust 4-year PhD student, School of Biological Sciences


Mathematical models adapted from the tried and tested SIR (susceptible-infected-recovered/deceased) model structure have been used to explore these questions. These models do not aim to forecast the course of the outbreak, rather they allow us to explore a wide range of possible scenarios.

The results from these models are helping epidemiologists, public health practitioners and policy makers gain a better understanding of the role of SDMs in managing COVID-19 epidemics.

Whole genome sequencing of SARS-CoV-2

Áine O'Toole is now in her final year on the Hosts, Pathogens and Global Health PhD programme.  She began working with Prof Andrew Rambaut on viral evolution in the summer of 2017.

Along with several members of Andrew's group and others at the University, Áine is now part of the team working on the COVID-19 Genomics UK Consortium project. 

COVID-19 Genomics UK Consortium

This project aims to carry out whole genome sequencing of SARS-CoV-2 from coronavirus-positive patients across the UK.  Along with colleagues at the Wellcome Sanger Institute in Cambridge and a number of other UK universities, the project is now processing about 1000 samples each week and sequencing them on the MinION sequencing platform.

Áine has been setting up the bioinformatics system to allow the automated and efficient analysis of the huge amounts sequence data generated by the project.

I've been working on a lineage typing tool called pangolin (phylogenetic assignment of named global outbreak lineages) that will allow any research group to type their virus genome.  Hospitals and research centres across the UK can input their data and check if there are outbreaks in hospitals or if the infections are separate introductions of the virus.

Áine O'TooleWellcome Trust 4-year PhD student, School of Biological Sciences

The genome data provides insight into how the virus is moving within the community, and helps inform decisions on the most effective control measures to limit virus spread.  In particular, the classification of viruses within hospitals, gives invaluable information about levels of nosocomial transmission.

"Our Wellcome Trust HPGH programme was established to train exactly the sort of infectious disease researchers needed to tackle the unexpected challenges of emerging infections such as COVID19.  I am very proud that our young researchers are making such an important contribution to the effort to understand and control the impact of this global pandemic”

Prof Keith MatthewsCo-director Hosts, Pathogens and Global Health PhD programme

Related links

Hosts, Pathogens and Global Health PhD programme

School of Biological Sciences


Rambaut Lab