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A 3-year PhD Studentship funded by NIHR, is available in the Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street UCL Institute of Child Health. The studentship is available to start between April-October 2022 under the supervision of Prof. Judith Breuer and Dr Sofia Morfopoulou (GOS ICH, UCL) and Dr Ines Ushiro-Lumb, NHS Blood and Transplant.
This computational project will investigate bioinformatically the presence, viral loads and transcriptional activity of viruses in a range of human tissues and organs through the use of untargeted metagenomic high throughput sequencing (HTS) methods. Bioinformatics tools for taxonomic classification and pathogen discovery (metaMix) will be applied to detect viruses in sequencing data from clinical blood and transplant specimens, including potentially unexpected pathogens. The performance of agnostic metagenomic sequencing will be compared to methods using targeted enrichment panels and both approaches will be assessed for their analytical sensitivity and specificity. Long read methods will also be evaluated. Persistent viruses in donor and archived tissues, such as human herpesviruses, adenoviruses, polyomaviruses and parvoviruses, will be further characterised by whole genome sequencing methods and transcriptome analysis. Transmission risk by organ transplantation will be investigated and bioinformatics tools for haplotype reconstruction (HaROLD) will be applied to investigate the occurrence of mixed infections in recipients after organ transplants, including HCMV and EBV with documented transmission risks.
The project will address major gaps in understanding of the transmission risk of cell-associated viruses, health impacts and prevention or mitigation through donor/recipient matching. Related work will focus on the development of bioinformatics methods for analysis of HTS data from clinical metagenomics samples and viral populations and scoping its future implementation for donor screening. The work will address computational and throughput challenges and incorporate new ethical guidelines for identification and reporting strategies for adventitiously detected viruses.
Developments in these areas will add substantially to knowledge of the human virome and the evaluation of transmission risk for different viruses and donor / recipient backgrounds.
The candidate will be analysing sequencing data generated by a wet-lab postdoctoral researcher, to address the experimental questions posed during the PhD.
- Bioinformatics: Acquisition of expertise in metagenomics and pathogen genomics and transcriptomics sequencing data analysis.
- Shared working with other PhD/MPhil students in the wider programme investigating a range of other aspects of transfusion-related microbiology
- Programmes of presentations, seminars and attendance at national and international scientific meeting to present research findings
- Working within a combined University / NHSBT environment, the latter providing knowledge of how a large scale, healthcare-based service provider works and delivers to patients and the donor community.
The student will receive a starting stipend of £18,000 per annum (including London weighting) as well as the cost of tuition fees based on UK fee status.
Personal Specification
Applicants should have a good first degree (UK 1st class or upper 2nd class honours degree or equivalent from abroad) and a Master’s degree is desirable (or equivalent work experience) in a quantitative discipline or a biomedical sciences degree with scientific programming experience by the time of registration.
Eligibilty
This studentship covers the cost of tuition fees based on the UK (Home) rate. Non-UK students can apply but will have to personally fund the difference between the UK (Home) rate and the overseas rate where they are not eligible for UK fee status.
NB: You will be asked about your likely fee status at the interview so we would advise you to contact the UCL Graduate Admissions Office for advice should you be unsure whether or not you meet the eligibility criteria for Home fee status. Further information on Brexit and the definitions for fee status assessment can be found on the UCL website and also the UKCISA website (Higher Education: Definitions for fee status assessment).
Application
To apply, please send a current CV including the contact details of two professional referees as well as a cover letter to ich.iii.programme@ucl.ac.uk. Students should contact Prof. Judith Breuer (j.breuer@ucl.ac.uk) and Dr Sofia Morfopoulou (sofia.morfopoulou.10@ucl.ac.uk) to discuss their interest.
Applications also welcome from students who may be graduating in Summer 2022.
Deadline for receipt of applications: 31st January 2022
Interview date: TBC