MinION sequencing of Tilapia Lake Virus. BioSciences PhD (Self-Funded) Ref: 3191

About the Research Project

Supervisors

Lead supervisor: Dr Ben Temperton (University of Exeter)

Co-supervisors:
Professor Charles Tyler (University of Exeter),
Dr David Verner-Jeffreys (Cefas),
Dr Richard Paley (Cefas),
Dr Chadag Vishnumurthy Mohan (WorldFish)

Location: Streatham Campus, University of Exeter, EX4 4QJ

Project Description:
Aquaculture is of major and increasing importance to global food security, particularly in Low Income, Food Deficit Countries (LIFDCs), where it also serves as a significant contribution to poverty alleviation. Tilapia are the second most important aquaculture species in volume globally and particularly in developing countries, due to their affordable price, omnivorous diet and high-tolerance to intensive farming methods. In 2015, tilapia production from both aquaculture and capture was 6.5 million tonnes, with an industry value of $9.8 billion (FAO).  Recently, the FAO issued an alert for a highly contagious and lethal virus infecting tilapia stocks, known as Tilapia Lake Virus (TiLV) that has now been reported in 5 countries (Colombia, Ecuador, Egypt, Israel and Thailand), with more countries implementing TiLV surveillance (China, India and Indonesia). A 2015 outbreak in Egypt affected 37% of aquaculture farms, with an estimated economic impact of $100 million. TiLV represents a new genus in the single-stranded RNA virus family Orthomyxoviridae, which also includes influenza viruses and Infectious Salmon Anaemia Virus, one of the most feared viral diseases in the marine farmed salmon industry.

Genome sequencing of pathogens is critical for understanding evolutionary rates, mechanisms of host adaptation, transmission routes and the phylogeography of outbreaks. However, traditional sample-to-sequence times are often prohibitively long to facilitate real-time, data-driven management and deployment of control measures, particularly in developing countries where availability of continuous power and laboratory facilities is limited. Recently, a new portable sequencing device from Oxford Nanopore was used for field-based, real-time tracking of Ebola and Zika outbreaks, providing a step-change in real-time disease monitoring and management. In this PhD project, we will leverage Nanopore technology to develop the genomic tools for field-based screening of the TiLV outbreak in South East Asia and beyond. Cultured TiLV isolates accessed via WorldFish will be used to develop and optimise MinION sequencing using a range of techniques including cDNA libraries, primer amplification and direct RNA sequencing. The student will optimise bioinformatic analyses to meet the demands of real-time outbreak management. Once developed, these protocols will be field-tested in collaboration with WorldFish - linked through an ongoing funded BBSRC GRP project, for in situ real-time sequencing of a TiLV outbreak. In situ identification of TiLV will be supported by isolation of TiLV strains to validate long-read sequencing against axenic cultures, to couple phenotypic and genotypic traits, and to evaluate the extent of reassortment in natural TiLV populations – a critical step for the development of an effective vaccination program.

The student will join Exeter’s Effective Researcher Development Programme, and will benefit from in-house training in cutting edge molecular genetics and statistics at Exeter and in disease (histo)pathology, pathogen culture, aquaculture and business operations at Cefas. The student will spend time at both Exeter and Cefas, balanced by the needs of the experimental work and skills training.  S/he will also accompany the PIs to Malaysia on visit(s) as part of the GRP project and will interact with WorldFish partners and gain experience on ground operations in tilapia aquaculture and disease surveillance.

For more information about the project and informal enquiries, please contact the primary supervisor Dr Ben Temperton:

Things to consider:
Information about current fees : https://www.exeter.ac.uk/pg-research/money/fees/
Information about possible funding sources: http://www.exeter.ac.uk/pg-research/money/alternativefunding/
Information about Doctoral Loans: http://www.exeter.ac.uk/pg-research/money/phdfunding/postgraduatedoctoralloans/

Entry requirements

You should have or expect to achieve at least a 2:1 Honours degree from a UK university, or equivalent, in Biological Sciences. Experience in molecular techniques is desirable.

If English is not your first language you will need to meet the English language requirements and provide proof of proficiency. Click here for more information and a list of acceptable alternative tests.

How to apply

You will be asked to submit some personal details and upload a full CV, covering letter and two academic references. Your covering letter should outline your academic interests, prior research experience and reasons for wishing to undertake this project. You may also be asked to upload verified transcripts of your most academic qualification.

Please quote reference 3191 on your application and in any correspondence about this project.

Summary

Application deadline:24th September 2018
Value:This project is self-funded
Duration of award:Not applicable
Contact: PGR Enquiries pgrenquiries@exeter.ac.uk