2021-22 Bloomsbury PhD Studentships (Round 2): Genomics & Epidemiology Project

The Bloomsbury Colleges group was set up in 2004 and consists five institutions: Birkbeck, London School of Hygiene & Tropical Medicine (LSHTM), the Royal Veterinary College (RVC), the School of Oriental and African Studies (SOAS), and the UCL Institute of Education (UCL–IOE). These studentships were set up to increase collaboration and interdisciplinary research opportunities across the colleges.

Applications are invited for a three-year full-time PhD studentship, to start in the academic year 2021-22 at the London School of Hygiene & Tropical Medicine (where LSHTM is the lead institution). 


This studentship will provide

for the duration of the award.


Combining data from genomics and epidemiology to understand and prevent emerging

Project Title

Combining data from genomics and epidemiology to understand and prevent emerging infectious viral disease

Supervisory Team

Principal Supervisor: Dr Oliver Brady (LSHTM)

Co-Supervisor: Dr Sarah Hill (RVC)

Co-Supervisor: Professor Oliver Pybus (RVC)

Project Description

This fully funded PhD project aims to better understand how emerging infectious diseases spread using a unique combination of epidemiological and genetic statistical methods.

YFV is thought to be maintained by “sylvatic” transmission cycles between non-human primates but spill-over events into humans are common and can lead to sustained human-to-human transmitted “urbanised” cycles with high case fatality rates. While only the sylvatic cycle is currently considered active in South America, since 2016 a series of major spill over events have occurred in the South-eastern region of Brazil and there is concern that urbanised cycles could re-initiate in the highly populous coastal cities. In Africa, it is expected that climate change will lead to more intense urban transmission of the virus. Once initiated, high human mobility increases the risk of introduction of YFV to new areas, where populations may be unvaccinated.

Understanding the routes and drivers of the emergence of YFV into new regions has been challenging because of the limited availability of human and non-human primate case data globally. Understanding how YFV has circulated in sylvatic cycles and how humans interacted with such cycles is critical for determining how the risk of YFV spill over from the sylvatic cycle is changing. Analysis of epidemiological and genomic data can provide complementary insights into current and historical transmission patterns and their combination can often compensate for temporal and spatial data gaps. This project aims to combine epidemiological and genomic data analysis techniques to better understand and predict the movement of sylvatic yellow fever virus, and determine how vaccinations could be more effectively targeted.

The project is flexible to expand to include focus on other emerging infectious viruses depending on the interests of the candidate, and datasets that become newly available throughout the course of the PhD.


The student will spend time training in complementary techniques at both LSHTM and the Royal Veterinary College (RVC). At RVC the student will develop skills in real-time genomic sequencing and virus genomic and phylodynamic analyses. At LSHTM the student will receive training on a range of mathematical and statistical modelling techniques as well as experience managing large multi-dimensional epidemiological datasets. This interdisciplinary PhD will require the student to develop and combine skills from both areas.

Key References

Faria, Nuno R., et al. “Genomic and epidemiological monitoring of yellow fever virus transmission potential.” Science 61(6405) (2018): 894-899.

Hill, Sarah C., et al. “Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2017-2018”. PLoS Pathogens. 16.8 (2020): e1008699.

Shearer, Freya M., et al. "Existing and potential infection risk zones of yellow fever worldwide: a modelling analysis." The Lancet Global Health 6.3 (2018): e270-e278.

Kraemer, Moritz UG, et al. "The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus." elife 4 (2015): e08347.


We are looking for a highly-motivated candidate with strong quantitative and analytical skills with a desire to conduct research that makes meaningful improvements to public health policy.

All applicants must meet minimum LSHTM entry requirements. In addition, the candidate must have evidence of outstanding academic performance and must have or be predicted to obtain a Master’s degree in a quantitative science-based subject, ideally epidemiology, public health, computational data science, bioinformatics, pathogen evolutionary genetics or modelling. Candidates without a Master’s degree will be considered if they can demonstrate relevant extended research experience, e.g. from time spent as a research assistant or from an extended undergraduate project. They should be able to demonstrate some early computational skills (e.g. baseline skills in computer coding). They also must demonstrate solid foundations in academic writing and presenting, and in independently organising aspects of their research.

Candidates wishing to conduct virus genomic sequencing should already have baseline molecular biology laboratory skills. Experience using genomic or statistical techniques to research zoonotic viruses or mosquito-borne pathogens would be desirable but not essential.

This studentship is only open to applicants who are assessed as Home fee status. For further information about Fee Status Assessment please see the School’s policy and procedure document.

To apply

Information about the MPhil/PhD programme structure at LSHTM, as well as application guidance and a link to the portal, can be found on the School’s Research Degrees and Doctoral College pages.

To apply for this studentship, applicants should submit an application for research degree study via the LSHTM application portal. The applicant should apply via the Faculty of Epidemiology and Population Health (EPH) for their proposed project. ‘2021-22 Bloomsbury PhD Studentship’ must be entered under the ‘Funding Section’ on the application. Students should submit a brief (1 page maximum) description of their current relevant research experience and the skills they have developed instead of a Research Proposal.

Applicants should note that automated requests for references are only sent to referees once an application for admission/study has been submitted. Therefore, we would advise applicants to submit their application as early as possible in order to give referees time to respond to their reference request before the closing date. We suggest that applicants also  liaise with their referees to ensure they are aware of this scholarship’s requirements and deadline. It is the applicant’s responsibility to ensure that references are submitted prior to the scholarship deadline.

Incomplete applications will not be considered for this studentship.

Applications for this project will only be reviewed and processed after the deadline. All applications that are submitted before the deadline will be considered equally, regardless of submission date.  

By submitting an application for this funding applicants agree to its Terms & Conditions.


Deadline for applications is 23.59 (BST) on Tuesday 6 April 2021.

Further information

For further details about the project, please contact Oliver Brady and Sarah Hill.