In recent viral outbreaks of Ebola, MERS-CoV and Zika, viral genome sequencing revealed critical insights into the evolution and transmission of the virus, offering tantalizing examples of the potential value of this for future outbreak control efforts. To maximize the utility of this information, it needs to be achieved in real-time, providing virus genome data and actionable analysis and interpretation within hours of patients being sampled. The ARTIC project, funded by The Wellcome Trust, will achieve this by producing a mobile virus sequencing system, including statistically rigorous analysis frameworks, to prepare for the next outbreak and ensure that viral genome sequencing is positioned to have full impact on the public health response.

The aim of the project is to create a sample-to-response molecular epidemiology system for acute RNA virus outbreaks in resource-limited locations. Based on the Oxford Nanopore Technology’s MinION portable sequencing platform, the system will include a ‘lab-in-a-suitcase’ for virus isolation and sequencing, in-country bioinformatics of MinION data, real-time phylodynamic analysis, integration of epidemiological data, and interpretation and visualization of the results to inform public health responses. The position advertised here will focus on the computational and statistical aspects of the project including the development of phylodynamic analyses of outbreaks capable of updating in real-time as new data becomes available.

Candidates will have a PhD in a relevant field (computational biology, computer science, mathematical biology or statistics), experience of developing statistical models of molecular epidemiology, phylodynamics and phylogography, and/or demonstrable knowledge and experience of software development, High Performance Computing, and GPGPU development. The candidates will have a track-record of publishing in peer-reviewed, academic journals, excellent communication skills, and the ability to deal with a variety of tasks to set deadlines. The project will involve working with project team members including virologists, bioinformaticians and epidemiologists to create an integrated, practical system for public health emergencies.