An international research team has rapidly sequenced 99 Ebola virus genomes collected in the 2014 outbreak. The team, including members from the Broad Institute and Harvard University in the US and the Sierra Leone Ministry of Health and Sanitation, hopes the findings will help multidisciplinary, international efforts to understand and contain the unprecedented epidemic that is growing in West Africa.
The researchers report their findings in the journal Science. Five team members died of Ebola virus disease before the manuscript was published, and their fellow authors honor their memory in the study report.
The 99 genomes came from 78 patients diagnosed with Ebola virus disease in Sierra Leone during the first 24 days of the outbreak. Some patients gave more than one sample, allowing the team to see how the virus changed over the course of a single infection.
Using deep sequencing techniques, the team increased the amount of data available on the Ebola virus by four-fold. The results show the 2014 Ebola virus genomes contain over 300 mutations that distinguish them from previous outbreaks.
The team also found clues to suggest the 2014 outbreak started from a single introduction into humans and then spread among them over many months.
According to Doctors without Borders/MSF, fruit bats are thought to be the natural host of the Ebola virus, which first appeared among humans in simultaneous outbreaks in Nzara in Sudan, and in Yambuku in the Democratic Republic of the Congo (DRC), in 1976. The DRC outbreak occurred in a village near the Ebola river, hence the name of the virus.
The 2014 outbreak is unprecedented in both its size and the fact it emerged in several highly populated areas in West Africa, and not in sparsely populated areas in Middle Africa, as before. Previously, the largest outbreak was in 1976 and reported 318 cases. The current outbreak has reported over 2,000 cases since it emerged in Guinea, including over 1,000 deaths.
The World Health Organization (WHO) say the current outbreak has infected 240 health care workers in Guinea, Liberia, Nigeria and Sierra Leone, and more than 120 have died.
The new study shows that the 2014 Ebola strains likely have a common ancestor back in the 1976 outbreak. It also suggests the strains in the current West African outbreak separated from the Middle African version in the last 10 years and were brought to Sierra Leone by 12 people who attended the same funeral in Guinea.
The mutations in the 2014 Ebola strains are mostly in genes that code for proteins. This is important information for researchers developing diagnostic tests who need to keep track of how the virus is changing. With this in mind, the researchers released the genome sequences to the international scientific community before publishing the study.
Co-senior author Pardis Sabeti, associate professor at Harvard University and a senior associate member at the Broad Institute, says:
“By making the data immediately available to the community, we hope to accelerate response efforts. Upon releasing our first batch of Ebola sequences in June, some of the world’s leading epidemic specialists contacted us, and many of them are now also actively working on the data.”
The study presents a catalog of 395 mutations, of which over 340 distinguish the current outbreak from previous ones, and over 50 have occurred within the current outbreak. The team believes they serve a starting point for further research, as first author Stephen Gire, a research scientist in Sabeti’s lab, explains:
“Although we don’t know whether these differences are related to the severity of the current outbreak, by sharing these data with the research community, we hope to speed up our understanding of this epidemic and support global efforts to contain it.”
The National Institutes of Health, the Department of Health and Human Services, the National Science Foundation, the European Union Seventh Framework Programme, the World Bank and the Natural Environment Research Council all helped fund the study.
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