How can real-time sequencing of viral genomes help inform epidemiology and public health of acute viral epidemics?

his project will use the extensive set of virus genome sequence data, collected as part of the international response to the 2013-2016 Western African Ebola virus epidemic, to understand the spatial epidemiology and transmission dynamics of the virus. In particular, this will focus on the movement of the virus between administrative districts and the proliferation within these areas. The project will involve a combination of virus genome phylogenetic analysis (often referred to as 'phylodynamics'), epidemiological modelling and agent-based simulation of the epidemic. Although some of the viral genetic data was compiled in retrospect as a research tool, a significant proportion was sequenced in the affected countries and made available rapidly during the course of the epidemic. This approach, facilitated by recent technological developments in sequencing (in particular the highly portable Nanopore sequencing), has the potential to turn virus genetic analysis into a primary tool of outbreak response.

The aims are: 1) To understand the drivers of the spread and persistence of the epidemic by integrating geographical, demographic, climatic and other data with viral genetic analysis. 2) To examine how the contact-network structure may have contributed to the longevity of the epidemic. 3) To explore how interventions could be prioritized and tuned for an improved response to such epidemics in future. And finally, 4) to investigate how real-time sequencing (sequencing of viral genomes within days or hours of diagnostic sample being taken) could provide this information whilst an epidemic is occurring.