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  IAFRI PhD Studentship: Using multiplex-amplicon sequencing for broad spectrum targeted detection of plant viruses and vectors

   School of Natural and Environmental Sciences

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  Prof Neil Boonham  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project


Interested in understanding how rapid sequencing technology can help the UK protect against alien pests and diseases? Working in collaboration with Defra, this PhD will investigate the potential of nanopore sequencing to rapidly detect plant pathogens and their vectors. 

Oxford Nanopore Technology (ONT) Minion has been used for sequencing from PCR amplicons, giving a rapid sequence based confirmation of the presence of high risk pathogens such as COVID and Ebola, but it’s application in plant health has been limited. The studentship would investigate applications of this technology both in the labs at Fera and for deployment with inspectors. The aims of the studentship would be to: (1) Investigate the detection of whole genomes and their use as a proxy indication of pathogen viability, using a tiled amplicon sequencing approach for the detection and identification of tomato brown rugose fruit virus, including comparing the results for biologically viable and non-viable virus. (2) The simultaneous detection and sequence confirmation of suites of pathogens and pests, using multiplexed amplicon sequencing approach for the detection of viruses in soft fruits.

Number Of Awards


Start Date

1st January 2024 

Award Duration

3 years


Department for Environment Food & Rural Affairs (Defra) 


Dr Ines Vazquez Iglesias (Fera), Aimee Fowkes (Fera), Dr Ian Adams (Fera), Dr Adrian Fox (Fera), Prof. Neil Boonham (Newcastle University)

Eligibility Criteria

You must have, or expect to gain, a minimum 2:1 Honours degree or international equivalent in a subject relevant to the proposed PhD project (e.g. biological sciences, plant pathology, virology, biotechnology, molecular biology).  

Applicants whose first language is not English require an IELTS score of 6.5 overall with a minimum of 5.5 in all sub-skills.  

The studentship covers fees at the Home rate (UK and EU applicants with pre-settled/settled status and meet the residency criteria). International applicants are welcome to apply but will be required to cover the difference between Home and International fees. 

International applicants may require an ATAS (Academic Technology Approval Scheme) clearance certificate prior to obtaining their visa and to study on this programme. 

How To Apply

You must apply through the University’s Apply to Newcastle Portal 

Once registered select ‘Create a Postgraduate Application’. 

Use ‘Course Search’ to identify your programme of study: 

  • please apply for 2023 academic year for January 2024 start 
  • search for the ‘Course Title’ using the programme code: 8010F 
  • select ‘Agriculture’ in the ‘Research Area’ field 
  • select PhD Agriculture and Rural Development (full time) as the programme of study 

You will then need to provide the following information in the ‘Further Details’ section: 

  • a ‘Personal Statement’ (this is a mandatory field) - upload a document or write a statement directly in to the application form 
  • the studentship code snes266 in the ‘Studentship/Partnership Reference’ field 
  • when prompted for how you are providing your research proposal - select ‘Write Proposal’. You should then type in the title of the research project from this advert. You do not need to upload a research proposal.

Contact Details

Ines Vazquez ([Email Address Removed]) or Neil Boonham ([Email Address Removed])  

Agriculture (1) Biological Sciences (4)

Funding Notes

100% of home tuition fees covered, and a minimum tax-free annual living allowance of £18,622 (2023-24 UKRI rates). Also significant additional funding provided to cover research costs and local, national and international travel (e.g. conferences).