Ebola’s Genomic Drift

A group of scientists from the Center for Genome Sciences at the US Army Medical Research Institute of Infectious Diseases (USAMRIID) say they have identified several mutations in the genetic makeup of Ebola that could shine a light on drug development. Their work describes the “genomic drift” of the virus and how this may affect therapies that target the virus’s genetic sequence (1). We spoke with Army Captain Jeffrey R. Kugelman, a viral geneticist at the USAMRIID in Fort Detrick, MD, US. Kugelmn works with Gustavo F. Palacios, who directs the Center, and Army Captain Suzanne E. Mate, who worked alongside Kugelman at the Liberian Institute for Biomedical Research (LIBR).

What lessons have been learnt from your research?

The first conclusion that we drew was that the description of the viral changes needed to keep pace with the outbreak, which highlighted the need for ongoing genomic characterization. This would inform treatment facilities about the effectiveness of their diagnostics (which are the basis for quarantine decisions), and inform pharmaceutical companies and regulatory agencies about the effectiveness of therapeutics. The second point, and one that will be a challenge to overcome in the future (if we move forward with these types of interventions) is that we need a more flexible regulatory approach to approval for human use. Targeted therapeutics, while having desirable traits in efficaciousness and for potentially limiting off-target effects, will also need to be continually monitored and possibly redesigned in the midst of an outbreak. This raises questions as to how much safety and efficacy testing, and regulatory review, would be required to use the redesigned therapeutic. If it follows the normal course, the outbreak would likely be over before the process can be completed.

What can pharma companies do to keep pace with genomic drift?

Questions of resistance development – also known as target erosion – are at the forefront of target therapeutic review for viral pathogens. Make plans early to study these effects to protect the efficacy of your investment, or trigger a move to another platform if there are questions of rapid resistance development.

Can you tell us about the genomic differences that you’ve identified?

Each of the therapeutics and diagnostics for Ebola virus disease has differing fidelity requirements when analyzing binding target erosion. Target erosion, very simply, is the accumulation of mutations that can lead to a loss of efficacy. Some therapeutics are nucleotide-targeted and tolerate very little change, so developers try to choose sites that have high conservation. These sites are protected by the biology of the virus, in that mutations would not be beneficial to the virus and are selected against in a normal setting. Introducing limiting factors, like therapeutics and environmental stressors, can increase the selection rates and lead to drug resistance, which is a primary study focus of our center. Other protein-based targets can tolerate far more change, as redundancy in amino acid encodings can result in a nucleotide change with no effect on the protein sequence. Our research shows that PMO sites have remained static, largely due to their location at the conserved translational start sites of the genes they target. The sites targeted by antibody-based therapeutics appear to have the most changes but also the greatest ability to tolerate those changes. Finally, siRNA targets have also seen changes. Based on these findings, which were disseminated immediately to pharma companies working on Ebola drugs, Tekmira indicates that the sequences of the company’s TKM-Ebola therapeutic have been updated (2).

Studying Ebola must present certain challenges...

Viral RNA isolation from a priority pathogen with no approved vaccine or treatment requires high-level containment and raises difficulties in logistics for any sequencing effort. So the primary challenge is actually the transport and agreements to move samples back to containment labs supporting sequencing studies. This process took months and, while necessary, reduced the timeliness of the reporting. Most of the diagnostic work to date has been with quantitative PCR, which shares the same starting material needed for sequencing. Thus, a natural evolution of this report was to forward deploy a sequencing center to provide near real-time updates to the report, providing information on target signal erosion as it was happening. We addressed this issue by setting up a sequencing center at the LIBR in Charlesville (3).

What is the main technology deployed?

The lab is directed by Fatorma Bolay, and uses Illumina MiSeq chemistry to assay viral genomes. The capacity currently stands at 20 samples per week, or approximately 20–24 GB of sequence data. Analysis assets were deployed alongside the sequencer and a sample can go from isolation to sequence in approximately 5–7 days depending on ongoing runs. The aim is to provide near real-time data during the outbreak to analyze sequences for target erosion of diagnostics and therapeutics. The assay is not specific to Ebola virus, so this LIBR sequencing center will be a part of several surveillance studies to determine the prevalence of pathogens found in insects and small mammals in Liberia, as well as supporting public health for determining the causative agents of unknown febrile illness. It is hoped this capacity will be an asset to West Africa in determining what diagnostics, therapeutics and public health education will be needed to reduce the severity of future outbreaks of disease.