Edinburgh researchers help analyse Ebola genome sequences from current outbreak in West Africa

Recent work by University of Edinburgh researchers, analysing the genome sequence of the deadly Ebola virus isolated from patients in the recent outbreak in West Africa, has just been published in the journal Science.

The international team also included researchers from Harvard University, the Broad Institute, and colleagues in Sierra Leone and Nigeria.  Together they sequenced and analysed 99 Ebola genomes from 78 patients in Sierra Leone to aid better understanding of the disease and the development of future therapies to combat the currently incurable infection.

By generating extremely detailed maps of the virus's genome sequence the researchers were able to track the genetic changes of the virus as it moved from patient to patient, and determine how the virus has spread through the population.

(Right:  electron micrograph of Ebola; credit: CDC/Cynthia Goldsmith).

Gytis Dudas, the graduate student from Andrew Rambaut's lab at the University of Edinburgh, who worked on the project explained

When we looked at the origin of the sequences, we noticed there are subtle differences between the sequences collected in Sierra Leone. We found three genetic clusters of the virus, which allowed us to track the virus as it spread through Sierra Leone. We could also ascertain that the outbreak there was caused by the same strain as the one in Guinea, where the outbreak began.

The evidence suggests that the current epidemic stems from a single introduction of the Ebola virus into humans, before it began the subsequent spread through Guinea to neighbouring countries.

Right:  Diagram showing the mutations in the seuqences Ebola viruses from patients in Sierra Leone 2014 outbreak - one patient pre row.  Left:  Phylogenetic tree showing the descent of Sierra Leone strains from Guinea strains and the estimated dates of the beginning of the outbreak in West Africa and the introduction of the virus from Guinea to Sierra Leone in 2014. Credit: Gytis Dudas.

Gytis Dudas and Andrew Rambaut have already published a separate paper on the work in the journal PLoS Currents: Outbreaks, which gives clues about how the virus originally reached Guinea.

Their research showed that all of the viruses which have caused epidemics in the past have descended from a strain very similar to the one that caused the very first Ebola outbreak in the Democratic Republic of Congo in 1976.  Gytis Dudas says

By analysing the sequences and producing genetic trees showing the branches of different genetic strains of the virus, we estimated that the virus causing the current outbreak, the West Africa outbreak, split off from the Central Africa outbreak in 2004.

The analysis also shows that the virus then crossed from Guinea to Sierra Leone in May 2014 and has subsequently exhibited sustained human-human transmission, with no evidence of further zoonotic trasmission.  Bats are likely to be the natural reservoir for the virus, but scientists understand little about how the virus is evolving among them.

The team is now working to obtain the sequences of a different Ebola strain which is causing a separate outbreak of disease in the Democratic Republic of Congo.  Gytis Dudas concludes

The Congo strain is unrelated to the strain in West Africa, so that outbreak gives us another glimpse into what's going on in the virus reservoir.  Without more sequences, especially sequences from the bat reservoir, there is very little we can tell about how the virus is moving through Africa, and whether the current outbreak was preventable, since we are completely reliant on samples from infected humans.


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