EASTBIO: Genomic epidemiology of viral pathogens in Atlantic salmon aquaculture at the University of Edinburgh

Supervisors:  Prof. Dan Macqueen, Dr Samantha Lycett.

Background:

The global aquaculture sector is expanding rapidly to meet the nutritional demands of a growing human population. Atlantic salmon is among the highest value aquaculture species, with the UK and Norwegian sectors producing 0.2 million and 1.3 million tonnes per annum, respectively (with a combined value of ca. 7-billion GBP). Disease outbreaks are a major barrier to the sustainability of salmon aquaculture. Viral diseases have limited treatment options, and outbreaks on salmon farms are very damaging financially and in terms of animal welfare. Therefore, tools to support the control of viral disease in salmon aquaculture will be vital to achieve ongoing sustainable growth of this important industry.

Viruses evolve rapidly and accumulate genetic variation over relatively short timescales. Exploiting this property, genome sequencing is now widely applied for human and animal viral pathogens. Such efforts are best illustrated by current global initiatives to sequence SARS-CoV-2 genomes from human samples, which has revealed COVID-19 transmission routes, identified variants of concern, and contributed data in support of vaccine design and efficacy testing. Viral genomic sequencing offers huge potential to support disease control in salmon farming, but to date has been used to a limited extent in aquaculture field situations.

The primary objective of this project is to develop robust, high-throughput assays to sequence the genomes of salmonid viruses, including salmonid alphavirus (SAV), piscine orthoreovirus (PRV) and infectious pancreatic necrosis virus (IPNV). Using field samples from infected fish derived from field locations in Norway and the UK, we will build up a large repertoire of new genome sequences, which will be used to provide novel insights into viral spread and evolutionary dynamics in aquaculture, providing valuable information for fish farmers and decision makers in support of disease outbreak mitigation.

Candidate and training: We seek a student with experience in genomics, bioinformatics, and/or pathogen biology, ideally with an interest in applying research into practise, which will be done in collaboration with an industry partner (Pharmaq Analytiq, part of Zoetis). The student will learn how to sequence viral pathogen genomes using Illumina and Nanopore platforms and analyse the resultant data. They will be trained in design of sequencing assays, sequencing library preparation, bioinformatics, and genomic epidemiology / phylodynamic modelling analyses. The student will benefit from an extended placement of at least 6 months with Pharmaq Analytiq in Bergen, Norway, where they will be exposed to a commercial R&D setting.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership (DTP) http://www.eastscotbiodtp.ac.uk/how-apply-0 .

EASTBIO Application and Reference Forms can be downloaded via   http://www.eastscotbiodtp.ac.uk/how-apply-0

Please send your completed EASTBIO Application Form along with a copy of your academic transcripts to [email protected]

You should also ensure that two references have been send to [email protected]  by the deadline using the EASTBIO Reference Form.

This opportunity is open to UK and international students and provides funding covering stipend and UK level tuition fees.  The University of Edinburgh covers the difference between home and international fees meaning that the EASTBIO DTP offers fully-funded studentships to all appointees.  There is a cap on the number of international students the DTP recruits.  It is therefore important for us to know from the outset which fees status category applicants will fall under when applying to our university.

Please refer to UKRI websiteand Annex B of the UKRI Training Grant Terms and Conditionsfor full eligibility criteria.