During the course of the current West African outbreak of Ebola virus disease, the US Army has put troops, medical personnel, building and medical supplies on the ground to fight the epidemic. Now, another critical piece of the medical arsenal has been sent—genomic sequencing capabilities and viral geneticist Captain Jeffrey Kugelman to track genetic changes in the virus as they happen in real-time.
“This virus mutates rapidly and it’s an ongoing concern,” says Kugelman, from Charlesville, Liberia, where he is working at the Liberian Institute for Biomedical Research. He and his collaborators published findings in mBio this week showing that the Ebola virus variant from the current outbreak has acquired genetic changes over the last four decades that might interfere with some therapies currently being tested in humans. Their study highlights the importance of ongoing biosurveillance of the virus’s genome to check for mutations that might disrupt the ability of medical workers to diagnose or treat the disease.
“There is an increasing need to have genomics biosurveillance during outbreaks,” says Gustavo Palacios, senior author on the study and director of the Center for Genome Sciences at the U.S. Army Medical Research Institute of Infectious Diseases in Frederick, Maryland where the analysis was done. “Especially when sequence-based therapies offer promising ways to attack the virus, constant surveillance is needed to see if those therapies are compromised by the natural genetic drift of the pathogen.”
Many of the most promising drugs being developed to fight Ebola are such sequence-based therapies that bind and target a piece of the virus’s genetic sequence or a protein sequence derived from that genetic sequence. These include monoclonal antibody, siRNA (small-interfering RNA) and PMO (phosphorodiamidate morpholino oligomer) drugs currently being used experimentally to treat a handful of patients. None of these drugs have been approved by the US Food and Drug Administration, but are being used under the emergency containment protocol of the World Health Organization.
“We wanted to highlight where genetic drift, the natural process of evolution on an RNA virus genome, could affect the development of these countermeasures,” says Palacios. The specific binding sites that each therapy targets have already been published. “Our work was to highlight the genetic changes in the current Ebola virus strain that could affect these sequence-based drugs that were designed using previous strains.”
He and Kugelman, along with USAMRIID colleagues and collaborators at Harvard University and the Massachusetts Institute of Technology, both in Cambridge, Massachusetts, compared the current strain, named EBOV/Mak, with two previous strains that caused smaller outbreaks in 1976 and 1995 in Zaire (now the Democratic Republic of the Congo). In each comparison, they found more than 600 genetic mutations in the form of single nucleotide polymorphisms (SNPs).
Next, they zoomed in on just the mutations that occurred in the genetic sequences targeted by the therapeutics. Of those, they found 10 new mutations that might interfere with the actions of the sequence-based drugs currently being tested. Three of these mutations appeared during the current West African outbreak.
“The virus has not only changed since these therapies were designed, but it’s continuing to change,” says Kugelman. All of the therapies were designed in the early 2000’s based on the 1976 or 1995 Ebola virus strains.
He and Palacios say that drug developers need to assess their therapies for efficacy against these mutations to ensure that resources are not wasted further developing a drug that might be less effective or not effective at all against the current virus variant. Palacios adds that regulatory agencies must also take into account the speed with which virus pathogens can evolve.
“If we agree that sequence-based, targeted therapies are a tool for the future, then we also need to change the way they are approved to allow for more flexibility,” he says. A more agile regulatory system is needed to respond to genetic changes that might require updated versions of sequence-based therapies.
Two of the therapies, TKM-Ebola, a combination of siRNA components, and ZMapp, a combination of antibodies, have already been used to treat a few patients in the US and Europe in combination with standard medical care. A clinical trial of TKM-Ebola will start in Sierra Leone in the coming months, which Palacios says is key: “Clinical trials are so important because they have the statistical power to determine if the survival rates are directly related to the drug, beyond supportive care.”
Palacios notes that real-time biosurveillance of the virus’ genome is needed to make sure that current diagnostic tests and therapies remain effective. In the current study, Palacios and Kugelman analyzed patient samples mostly from May to July 2014. However, they would like to monitor genetic changes as the epidemic continues to unfold. That is why Kugelman is now on the ground in Liberia, tracking the genetic changes that might occur in the virus as it is transmitted from human to human in near real-time.
“It’s not fast enough to help the current patients, but within 4-5 days after we get patient samples, we can characterize the outbreak genetically as it happens,” says Kugelman. “We will have virus sequence information within a week, instead of a months-long wait.”