Tracking Ebola: Real time genomic epidemiology offers lessons for global health

Leila Luheshi

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: 

  • Make data available at time of collection  The authors submitted their genomic data to public repositories as soon as it was collected and did not wait to publish it first. Therapeutics manufacturers were able to take this new information into account when designing interventions; it allowed other groups to compare their data and look for important emerging patterns that could inform outbreak control; and it maximised the number of people who could contribute insight to its analysis. As the lead author Dr. Sabeti said: “We’ve got to crowdsource the epidemic”.
  • Genomic data is of limited value without clinical and epidemiological context Vital to interpreting the Ebola virus genomes has been the knowledge derived from epidemiologists who, at great personal risk, have travelled around west Africa tracing contacts and piecing together possible chains of transmission. The success of genomic epidemiology in outbreak detection analysis and resolution depends on the effective combination of this ‘shoe leather’ epidemiology with rapid and accurate genomic analysis.
  • Capacity building to enable emergency response is crucial – Ebola genome sequencing, whilst an international collaborative effort between scientists and healthcare professionals in Sierra Leone, Nigeria, the UK and the USA, was all undertaken at an American genomics research institute. Moreover, the accompanying commentary   to the publication notes that other samples collected from Liberia and Guinea have been sent to a research lab in Germany but have not as yet been sequenced. The researchers simply don’t have the time to do it, as they have to prioritise epidemiological contact tracing. These observations suggest that national and international health organisations must pay serious attention to the development of genomic epidemiology infrastructure with surge capacity that can be deployed rapidly to respond to future outbreaks of emerging disease. It is not sustainable to rely on the good will and grant funding of researchers to provide what is emerging as a potentially vital public health function in the battle against infectious disease.
  • 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.