Enhanced surveillance for foot-and-mouth disease using field-based viral sequencing
Foot-and-mouth disease (FMD) remains an important disease in low and middle-income countries (LMICs), as well as representing a continuous threat to disease free countries such the UK. Understanding the epidemiology of FMD in an ecosystem needs access to samples from domestic anaimls as well as wildlife that may act as important reservoir species. However, the collection of sufficient data presents major logistical challenge and it is therefore a global priority to establish novel approaches to capture viral sequences from infected animals. The primary goal of this project is to develop a low-cost non-invasive sample-processing pipeline to generate high quality nucleic acid extracts and to amplify whole-genome seqeunce (WGS) of the FMD virus (FMDV) in real-time by applying molecular techniques adapted for field conditions. Consensus-level WGS data will be used to reconstruct within-herd dynamics (at high resolution) from samples collected from an intensive longitudinal study located in Uganda. We anticipate that this pipeline will be suitable for application to coutries within the FMD control pathway in Africa with the potential to improve our understanding of FMD epidemiology in endemic settings.
The main objectives of the project are:
• To develop a sample processing pipeline based on LAMP and CRISPR (SHERLOCKv2) to enrich viral sequence load
• Generate pilot data from within-herd infections to validate the resolution of the Nanopore system for molecular epidemiology of FMDV compared to Sanger sequencing
• In collaboration with EuFMD develop the wider field protocols needed to allow safe collection and processing of field samples to be sequenced in LMICs
• Through our strong links with the European Commission for the Control of FMD and as part of the Real-Time training course, we will further run a workshop to transfer the technology and knowledge derived from this study to LMICs in Africa for establishing cost effect surveillance systems.
Other projects available:
We would encourage applicants to list up to three projects of interest (ranked 1st, 2nd and 3rd choice) from those listed with a closing date of 10th January 2020 at https://www.ed.ac.uk/roslin/work-study/opportunities/studentships
3.5 year PhD
Applications including a statement of interest and full CV with names and addresses (including email addresses) of two academic referees, should be emailed to [Email Address Removed].
When applying for the studentship please state clearly the project title/s and the supervisor/s in your covering letter.
All applicants should also apply through the University's on-line application system for September 2020 entry via http://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=830
Hansen et al., (2019) Serotyping of foot-and-mouth disease virus using oxford nanopore sequencing. J. Virol. Methods. 263: 50-53
Lycett et al., (2019) The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa. Sci Rep. 9: 5614.
Cottam et al., (2008) Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007. PLoS Pathogens 18: e1000050