The use of next generation sequencing in the diagnosis and typing of viral infections

Thorburn, Fiona (2016) The use of next generation sequencing in the diagnosis and typing of viral infections. PhD thesis, University of Glasgow.

Abstract

Viral respiratory infections are associated with substantial mortality, morbidity, and a vast economic and healthcare burden. The diagnosis of such infections has been revolutionised by the introduction of molecular methods such as RT-PCR. This has resulted in high levels of sensitivity and specificity along with a rapid turnaround time in comparison to previous methods. As a product of this success, the diagnosis of respiratory infections makes up a large proportion of the workload in most diagnostic laboratories.
The development of next generation sequencing (NGS) may be the next revolution in the field of virus diagnostics. This allows a metagenomic approach to specimen processing whereby target independent sequencing of all genetic material is carried out.
The research presented in this thesis initially sought to examine if NGS would be feasible in the field of respiratory virus diagnostics. The aim was to apply NGS to clinical specimens in parallel with the current diagnostic RT-PCR assays employed by the West of Scotland Specialist Virology Centre (WoSSVC) to determine if NGS could give the same level of results as RT-PCR and whether the sequence information generated in the process could be used in further characterising the detected pathogens. Further to this, the NGS method was then applied to the detection of norovirus from faecal specimens to demonstrate the utility in other areas of viral diagnostics.
The results show that multiple viral pathogens can be detected from clinical specimens without specific virus targeting. The method was less sensitive than RT-PCR but sequence data generated during the process was utilised viral detection, subtyping and phylogenetic analysis. We also demonstrated that a single workflow could be applied to multiple specimen types in the detection of RNA viral pathogens.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Keywords: Virus, respiratory, norovirus, sequencing, diagnostics.
• Subjects: Q Science > QR Microbiology; Q Science > QR Microbiology > QR355 Virology
• Colleges/Schools: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Supervisor's Name: Gunson, Dr. Rory and Murcia, Dr. Pablo
• Date of Award: 2016
• Depositing User: Dr Fiona Thorburn
• Unique ID: glathesis:2016-7838
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 15 Feb 2017 09:51
• Last Modified: 01 Aug 2022 08:41
• URI: https://theses.gla.ac.uk/id/eprint/7838