Why do viruses cross host species boundaries? And how have past infectious with viruses shaped immune responses? Animal genomes are littered with the remnants of ancient viral infections. Approximately 5-8% of the human genome is made up of endogenous retroviruses, a substantially larger proportion than is occupied by protein coding genes. This pattern holds throughout the vertebrates, with vertebrate genomes constituting a rich ‘fossil record’ of ancient viral infections. Other viruses can also occasionally form such genomic fossils, albeit more rarely, and we have shown that all known viral replication strategies are represented within animal genomes. The vast quantities of data made available as a result of genome scale sequencing projects has greatly facilitated progress in a field that is becoming known as paleovirology.
This project will use genome scale sequence data to study the evolutionary biology of viruses and address questions such as, for example, why are certain viruses more prone to crossing species boundaries causing novel emergent infections, and what is the extent and role of integrated viral sequences in animal evolution. The project can involve the use of computational and evolutionary analysis of genome sequence data, and can also focus on experimental virology to test specific hypotheses.
Aims
Key Objectives & Core Scope
- Mining the Virtual Fossil Record: Using computational biology and high-throughput genetic screening to analyse animal DNA databases.
- Characterizing EVE Diversity and transmission: Examining retroviral and non-retroviral elements (such as ancient lineages related to modern viruses such as Hepatitis B, Ebola,, Dengue, and HIV) integrated in host nuclear DNA.
- Virally Derived Immunity (Exaptation): Investigating how hosts have repurposed these ancient viral fragments into functional cellular genes that inhibit viral infections.
Methods
The project can involve either computation or experimental approaches. Computational methods will involve analysing existing public genomic and transcriptomic datasets, mining thousands of genomes to find viral sequences. Tasks involve running automated bioinformatic workflows using the lab’s custom HI-FEVER Nextflow pipeline, performing large-scale sequence alignments, building phylogenetic trees. They will also involve transcriptomic work to reveal function. You will write code, develop data visualization pipelines, and use statistical modelling to identify patterns of ancient host-switching, working closely with a team of computational biologists. Experimental approaches will involve cell culture virology, transfection, transduction, FACS, immunity assays and other laboratory techniques.
Project code
AK01
Funding
This project is part of the DPhil in Biology programme, and is not a funded course at the University of Oxford; as such, students are expected to explore options for funding. However, we anticipate being able to offer around 6 full graduate scholarships to incoming DPhil students in 2027/28.
You will be automatically considered for several Oxford scholarships, which cover fees and stipend, if you fulfil the eligibility criteria and submit your graduate application by 6 January 2026. Scholarships are awarded based on academic achievement and potential to excel as a DPhil student.
For further details about searching for funding as a graduate student visit the graduate study information on our website.
Eligibility
For full entry requirements and eligibility information, please see the main admissions page.
How to apply
The deadline for applications for 2027/28 entry is 6 January 2027. We will continue to accept applications submitted after this date, but these late applications will not be considered for scholarship funding.
You can find the admissions portal and further information about eligibility and the DPhil in Biology Programme at the University's graduate admissions page. Please quote the Project Reference Code alongside the title in the ‘Proposed field and title of research project, if applicable’ field in the application form.
Institution website: https://www.biology.ox.ac.uk/dphil
