PhD Studentship: Virus Diversity and Disease on UK Trout Farms: Metaviromic Approaches for Improved Fish Health

Supervisor

Dr Sarah Hill, SAHILL@rvc.ac.uk, Research Fellow in Genomic Epidemiology (Infectious Diseases), Royal Veterinary College

Project details

What problem will I be helping to solve?

We know that about a quarter of global greenhouse gas emissions come from food production. As the human population continues to grow, we urgently need to improve the sustainability of this sector. The main source of animal protein consumed globally is fish and seafood, most of which is farmed in aquaculture. In some forms of aquaculture, up to 40% of individual livestock die before they can be harvested for food – most of which are thought to be killed by viruses. Preventing deaths due to viruses in aquaculture can therefore contribute hugely to improving the sustainability of this important farming sector. Furthermore, it would improve food security, help national economies, improve fish welfare, and protect wild species from the possible threats of virus spillover from farming systems. 

Problematically, we know almost nothing about the genetic diversity and dynamics of most viruses that infect the world’s 35,000 aquatic vertebrate species – including those species that we farm. This makes it near-impossible to control outbreaks.

What approaches would I use? 

Traditional methods to detect pathogens, such as PCR tests or lateral flow tests, are typically limited to diagnosing a single pathogen per test, which restricts the number of viruses that can be monitored. In contrast, metagenomic sequencing of viruses (or “metaviromics”) enables the simultaneous detection of multiple pathogens in a sample, offering a powerful approach to enhance surveillance. Furthermore, metaviromic approaches can generate massive quantities of data on the genetic diversity of viruses, which could be analysed to inform about virus evolution, transmission, and virulence. Currently, metaviromic techniques are rarely used to detect and explain dynamics of viruses in wild or farmed animal populations, leading to huge gaps in our understanding of virus diversity and prevalence. You will therefore lead a pioneering study that bridges the fields of metagenomics, epidemiology, and computational analyses to unlock insights into viral disease dynamics. 

Your work will bridge wet-laboratory sequencing and computational analyses and can include elements of fieldwork if you aim to gain experience in that area. Depending on your interests and skills, this could include elements of (i) comparing environmental pathogen surveillance on water samples to individual-specific tests, (ii) discovery and genomic characterisation of new virus species, (iii) use of computational and mathematical approaches to link longitudinal changes in virus presence and abundance with population demographics and environmental changes, and observed disease. 

Despite the focus on fish here, the approaches and skills that you develop will be applicable in your future career to studying virus in any human or animal population. The primary supervisor, Dr Sarah Hill, studies virus outbreaks in various host species.

What support and opportunities will I get? 

We will provide you with excellent training in the field, and a vibrant environment in which to conduct your research. You will gain expertise in metaviromic sequencing and computational analysis of viromes and virus genetic sequences. We will encourage and support you to learn a wide range of cutting-edge computational approaches to analyse complex viromic data, including exploring machine learning techniques. 

We will help you to publish your research in leading journals (e.g., see Dr Hill’s current publication history https://scholar.google.co.uk/citations?user=kNtlfaEAAAAJ&hl=en). We will also fund you to attend international meetings to present your work (typically once or twice per year – current group members have recently travelled to Canada, Hong Kong, Bangladesh and Norway). We hold fortnightly laboratory meetings together with several other similar research groups at the Royal Veterinary College, and you can also choose to take part in activities such as a regular “Coding in R” club. 

We work closely with internationally leading research groups and with governmental surveillance organisations in the UK and abroad, and will help you to meet with relevant researchers in our network.  

As this research project is a collaboration between academia (Royal Veterinary College, LIDo DTP) and industry (Esox Biologics), you will gain valuable experience of working in both environments. You will have access to excellent modern facilities at the Royal Veterinary College’s Hawkshead campus, and Imperial College London’s Translation and Innovation Hub (the headquarters of Esox Biologics). This includes both newly built laboratories housing all necessary facilities to conduct environmental and targeted sequencing of viruses. You will be provided with access to a centralised high-performance cluster and cloud-based computing to allow you to perform powerful analyses on large datasets. 

How can I apply?

This industrial collaborative (iCase) PhD project is offered via the BBSRC London Interdisciplinary Doctoral Training Programme (LIDo DTP). We recognise that you may not yet have had experience in all research areas described in the “Project Details”, but we expect that candidates will have a very strong track record. You should have, or be expected to achieve, a first or high upper second-class undergraduate honours degree or equivalent, or a Masters degree with distinction in a related subject. We seek applicants who have a demonstrable aptitude for research, including aspects of computing or mathematics. In addition, we value personal traits that will allow you to succeed in this PhD, such as intellectual curiosity, perseverance, and enthusiasm. 

To apply, please visit the LIDo’s Apply website at the apply button above, and apply to this named iCase project. Shortlisted candidates will have two interviews – the first with the LIDo panel, and (if successful at that stage) the second with Dr Hill, Dr Pope and Dr Xia. Please email Dr Sarah Hill (sahill@rvc.ac.uk) if you have questions about the potential scope of the work before applying. 

The Royal Veterinary College and Esox Biologics are committed to equality and diversity. Funding to cover fees for international students is available on a competitive basis to support applications from students across the w