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EASTBIO Rapid mobile diagnostics for zoonotic pathogens in LMICs

Project Description

Royal (Dick) School of Veterinary Studies / The Roslin Institute

Zoonotic diseases are a major concern for poor livestock keepers in lower- & middle-income countries (LMICs) where they are exposed to a huge range of pathogens many of animal origin. The weak overstretched health systems in such setting means that most of these zoonotic diseases remain undiagnosed making their management and surveillance extremely complicated. This in-turn makes evidence-based policy and control programmes in these countries very difficult. For example; 60.7% of fevers treated in Tanzania are diagnosed and managed as malaria, while malaria is the true diagnosis for only 1.6%. Large scale non-selective malarial treatement could explain the currently reported increase in resistance to anti-malarials. This also has major implications for the development and spread of antimicrobial resistance (AMR) given the blanket use of broad-spectrum antibiotics. There is therefore need to develop and or adapt current available techniques to address to answer the following questions;

a) What is the level of mis-diagnosis and management of pyrexic conditions
b) What is the diagnostic performance, of newer, more affordable and less labour-intensive diagnostic tools.
c) How can they be used to improve diagnostic accuracy of pyrexic conditions.

Rapid on-site diagnosis would be a major step forward, and small portable PCR and LAMP devices exist and these are valuable tools for understanding where to direct resources for the control of infectious diseases.
In this project you will investigate the use of nanopore sequencers, LAMP and new credit card sized PCR systems with field samples and compare to conventional diagnostic tests.

Initial pathogen samples will include samples from pyrexic human cases from an ongoing One Health project on AMR in Uganda and samples from livestock in Cameroon, Kenya and Tanzania, but there will be opportunity to collect additional samples and try your protocols and algorithms in the field in later years. In particular this project will build upon existing Roslin-African collaborations including the National ANIMAL Disease Diagnostics and Epidemiology Centre (NADDEC)

Ministry of Agriculture, Animal industry and Fisheries, Uganda.

This project combines sequencing technology, PCR, and field epidemiology and the student will be trained in laboratory, field work, computer programming and data science.

All candidates should have or expect to have a minimum of an appropriate upper 2nd class degree. To qualify for full funding students must be UK or EU citizens who have been resident in the UK for 3 years prior to commencement.

Funding Notes

Completed application form along with your supporting documents should be sent to our PGR student team at

Please send the reference request form to two referees. Completed forms for University of Edinburgh, Royal (Dick) School of Veterinary Studies and the Roslin Institute project should be returned to by the closing date: 5th January 2020.

It is your responsibility to ensure that references are provided by the specified deadline.
Download application and reference forms via:
View Website


[1] Crump et al. (2013) Etiology of Severe Non-malaria Febrile Illness in Northern Tanzania: A Prospective Cohort Study. PLoS Negl Trop Dis 7(7): e2324.
[2] Real-time, portable genome sequencing for Ebola surveillance, Quick et al, Nature 530, 228–232 (2016)

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