The Ebola virus sweeping through West Africa has mutated repeatedly during the current outbreak, a fact that could hinder diagnosis and treatment of the devastating disease, according to scientists who have genetically sequenced the virus in scores of victims.
The findings, published Thursday in the journal Science, also offer new insights into the origins of the largest and most deadly Ebola outbreak in history, which has killed more than 1,500 people in four countries and shows few signs of slowing. It also provided another reminder of the deep toll the outbreak has taken on health workers and others in the affected areas, as five of the paper’s more than 50 co-authors died from Ebola before publication.
In a collaboration led by scientists at Harvard University and aided by officials at Sierra Leone’s health ministry, researchers sequenced Ebola virus genomes from 78 patients beginning in the early days of the outbreak this spring. Those 99 samples — some patients were tested more than once — suggested that the outbreak began with a single human infection before spreading rapidly, like a spark that grows into a wildfire.
Ebola’s arrival in Sierra Leone in May started with a funeral, according to Thursday’s findings. A young pregnant woman tested positive for the virus and was treated at Kenema Government Hospital. Health workers who traced her contacts discovered that she and more than a dozen other women recently had attended the burial of a traditional healer who had been treating Ebola patients near the Sierra Leone-Guinea border. All of them had been infected.
“They realized she was not an isolated case,” said Pardis Sabeti, an associate professor at Harvard whose lab sequenced the Ebola genomes and quickly made public the data earlier this summer.
The genomic sequencing also offers hints as to how the Ebola “Zaire” strain at the heart of the current outbreak — one of five types of Ebola virus known to infect humans — likely ended up in West Africa in the first place. Researchers said the data suggests that the virus spread from an animal host, possibly bats, and that diverged around 2004 from an Ebola strain in central Africa, where previous outbreaks have occurred.
“We don’t actually know where the virus has been since then,” said Sabeti, referring to the time between 2004 and when the virus resurfaced earlier this year. “We’re trying to piece together an historical record.”
Thursday’s study also details hundreds of genetic mutations that make the current Ebola outbreak different from any in the past. Some of those changes have the potential to affect the accuracy of diagnostic tests or the effectiveness of vaccines and treatments under development for the disease.
“We’ve uncovered more than 300 genetic clues about what sets this outbreak apart from previous outbreaks,” Stephen Gire, one of the study’s co-authors and an infectious disease researcher at Harvard, said in an announcement about the findings. “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.”
Sabeti said researchers are expecting to receive additional Ebola samples soon from Nigeria. They plan to sequence those, as well, and release the data as soon as possible.
“The fact that we can do this in real time while the outbreak is still going is breathtaking,” said Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases at the National Institutes of Health, said of the group’s rapid genomic sequencing of the virus, which he said could have taken two years or longer in the past. “We didn’t have this technology years ago. What they did was really extraordinary.”
Fauci said Thursday’s findings also underscore the necessity to get the outbreak under control before the Ebola virus continues to morph.
“We’re left with a situation where if, in fact, this thing smolders on and on, we know mutations will accumulate,” he said. “And that has its own set of problems. We’ve really got to get this thing shut off.”
Sabeti said she that since she and her colleagues published the sequencing data, they have heard from companies working on vaccines and treatments, as well as by researchers developing new diagnostic tests, who want to understand how the mutations could affect those efforts. Only through such collaboration, she said, can scientists tackle the current outbreak with the speed it deserves.
“There’s nothing you should crowdsource more than an epidemic. It has this urgency where we need every person working on it,” Sabeti said. “It took a village to make this paper happen. It will take a planet to help get this virus under control.”