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Development of a single NGS pipeline using a novel universal virus enrichment panel for the detection and typing of viral pathogens.

  • Full or part time
    Prof L Scobie
    Dr R Gunson
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

About This PhD Project

Project Description

Project reference number: SHLS19001

Background

Current routine virology diagnostics rely upon serological methods and novel molecular methods such as real time PCR. These methods are rapid and highly sensitive. Sanger sequencing is also available in some laboratories for specialist work including antiviral resistance and typing. Next generation sequencing (NGS) methods have the potential to impact routine virology. First they will likely replace Sanger sequencing by providing more detailed typing data that could be used to determine antiviral resistance more accurately. NGS will also allow laboratories to study the epidemiology of particular, monitor outbreaks and investigate potential transmission events in more detail than currently achievable. NGS may also complement existing diagnostic methods as it could be used to detect pathogens that are missed by current methods. In future, it may become the test of choice for the diagnosis of viral pathogens. However, currently NGS methods are expensive, highly complicated, and have multi step methods that require significant user expertise. As a result any technical advances that can make these methods more routine ready would be welcomed.

Investigation

Enrichment panels are an alternative pre NGS approach that enables the user to positively select/target particular pathogen sequences in a sample of interest. When hybridised with a sample they can bind to/select any viruses within the sample. The unbound probe and nucleic acid is then washed away and the selected nucleic acid is then used for NGS. Enrichment panels have been shown to improve sensitivity and ease of use as one method can theoretically be used for the detection and typing of all viral pathogens. The aim of this project is to develop and evaluate an enrichment method for the universal detection and subtyping of human viral infections. We will develop a panel that will target all clinically relevant viruses known to infect humans. We will also include variants of each virus in order to detect subtypes. We will first work up this method to be used prior to NGS sequencing using the MISEQ NGS platform. This initial work up will use a small panel of samples containing known viral pathogens. Each panel will contain a particular virus at variable concentrations (as determined by real time PCR). Divergent subtypes will also be included in each panel. Testing these panels will be used to compare the sensitivity and specificity of the new method with real time PCR and will also provide a measure of how well the method types the various viral targets. We aim to assess the pipeline on panels containing the following pathogens: norovirus, influenza A and B, enterovirus, RSV, Hepatitis A, adenovirus and hepatitis B. We will also examine the cost effectiveness of the method in comparison to existing methods. Should the assay prove to be sensitive and truly universal then we envisage it may be applied to "real" clinical situations should they arise during the project. It is hoped that the PhD will result in the utilisation of NGS methods in the virus department alongside existing diagnostic methods.

This proposal is a collaboration of the West of Scotland Specialist Virology Centre (WoSSVC) and Glasgow Caledonian University. WoSSVC is based at Glasgow Royal Infirmary and provides virology services for the whole of Glasgow. The department also acts as a referral laboratory for the West of Scotland. The laboratory has an international reputation for its work on molecular methods, in particular multiplex real time PCR. This PhD is a unique opportunity to work in a leading NHS virology laboratory and to gain experience of using novel, cutting edge molecular technology with the support of an academic environment.

Research Strategy and Research Profile

Glasgow Caledonian University’s research is framed around the United Nations Sustainable Development Goals, We address the Goals via three societal challenge areas of Inclusive Societies, Healthy Lives and Sustainable Environments. This project is part of the research activity of the Research Group – Molecular Mechanisms of Diabetes and Long Term Conditions.
https://www.gcu.ac.uk/hls/research/researchgroups/molecularmechanismsofdiabetes/
https://www.gcu.ac.uk/hls/staff/drlindascobie/

How to Apply

This project is available as a 3 year full-time PhD study programme with a start date of 1st October 2019
Candidates are requested to submit a detailed research proposal (of a maximum of 2000 words) on the project area as part of their application.

For information on how to apply and the online application form please go to
https://www.gcu.ac.uk/research/postgraduateresearchstudy/applicationprocess/

Funding Notes




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