29 August 2014
The outbreak of the Ebola virus in west Africa is being described by WHO as an international public health emergency. In the space of a few months over 1500 people who have contracted this terrible infection have died. As the spread of the virus shows no signs of abating, medical professionals, epidemiologists and scientists are battling to manage the health of patients who are infected, trace the transmission of the infection across many countries and attempt to introduce public health measures to control its further spread.
Against this background a paper was published yesterday in Science describing the genome sequencing and analysis of nearly 100 isolates of Ebola from patients infected in Sierra Leone. The authors have combined detailed field epidemiological information - which had already traced the introduction of Ebola into Sierra Leone from a small number of individuals who had travelled to a funeral in neighbouring Guinea - with deep sequencing of the genomes of the Ebola viruses that infected these early cases and many subsequent ones. This "real time genomic epidemiology” analysis has revealed information vital to informing public health efforts to control this outbreak.
Detecting the origins and evolution of the Ebola virus
By analysing the ancestry of the Ebola viruses in the current outbreak and comparing these with those from other recent outbreaks researchers have traced the origins of the current outbreak-causing virus to central Africa. Perhaps more importantly they have also been able to confirm that all the examined viruses from patients in Sierra Leone are so similar to one another that they have almost certainly arisen from human to human transmission, following a single earlier transmission of animal to human , reinforcing the need to focus efforts on preventing the former.
Worryingly the analysis of the Ebola virus genomes also suggests it is mutating quite rapidly. It is crucial to track these mutations using genomics to ensure that rapid molecular diagnostic tests can be adapted to continue to detect the virus, and so that any therapeutic strategies being developed (such as this experimental vaccine are not thwarted by their failure to target viruses that have undergone significant change in their sequence. The ultimate concern is that some of these mutations may change the functions of the virus, for example by allowing it to better adapt to sustain its transmission between humans, but further research will have to be undertaken before it can be determined whether this is actually occurring.
Lessons for realising the benefits of genomic epidemiology
This new publication describing the genomic epidemiology of the Ebola virus outbreak in Sierra Leone offers many lessons to those implementing and using genomics to manage infectious diseases:
Despite the availability of genomic data and the insights gleaned from it, the Ebola outbreak continues apace. This is a stark demonstration of the futility of acquiring knowledge and understanding where the means to act on it are limited. Without investment in the infrastructure, people and practices needed to improve existing programmes to manage infectious disease outbreaks, and without the development of policy at a governmental and international level to boost support to these programmes in times of crisis, genomics cannot be expected to impact on the resolution of outbreaks such as the one currently afflicting the population of west Africa.