The Ebola Outbreak Alarms the International Community

October 9, 2019

How Next Generation Sequencing and Synthetic Biology Are Changing the Paradigm of Outbreak Response

Ebola Outbreak

Ebola Outbreaks 

Ebola Virus Disease (EVD) rightfully strikes fear: it’s a horrible disease with an average case fatality ratio (CFR) around 50%. EVD CFRs have varied from 25% to 90% in past outbreaks[1]—a stark contrast to the deadliest influenza pandemic in 1918 when the average CFR was around 2.5%.[2] The virus threatens the entire globe with a potential pandemic as it crosses porous borders and spreads through imported cases. From 2014 to 2016, the world witnessed one of the worst EVD outbreaks, originating from Western Africa. The Ebola Zaire outbreak started in Guinea and quickly spread to Liberia and Sierra Leone. In the end, that outbreak infected 28,616 people and killed 11,310 victims (CFR of approximately 39.5%).[3]

The ongoing outbreak in the Democratic Republic of the Congo (DRC) has alarmed the international community with its increasing toll since the start of the outbreak in August 2018.[4] As of September 18, 2019, there were 3,150 identified cases, including 2,108 total deaths, with a CFR of approximately 67%. In anticipation a potential pandemic, the World Health Organization declared the current outbreak a public health emergency of international concern on July 17, 2019, an unusual and unexpected move.[5] 

Lessons Learned from Past Outbreaks 

The rapid evolution of the viral genome within the infected population can lead to genetic changes that enable the virus to evade existing diagnostic tests and therapeutics, rendering them ineffective.[6] Accordingly, there is a need to constantly evaluate assay effectiveness. To facilitate such evaluations, the whole genome sequence of the circulating virus is required. Armed with a full spectrum of next generation sequencing (NGS) data, researchers can easily compare the assay signatures or medical counter measure targets via computer simulation—in silico—to predict whether diagnostics and therapeutics will be effective. Rapid and accurate diagnosis is critical for appropriately triaging patients and preventing disease spread.

Researchers need reference materials—such as patient specimens (blood, serum, other body fluids, tissues, etc.) or viral isolates—from patient samples to understand the biology of the rapidly evolving virus, develop tools to combat new variants, and improve old medical countermeasures. However, getting reference materials out of the affected countries to isolate the virus and develop countermeasures is an arduous and time-consuming endeavor because of logistics, safety, and security concerns. 

Next Generation Sequencing Technologies 

The advent of NGS technology about 15 years ago has revolutionized many areas of clinical medicine, from pathogen discovery to disease diagnosis to personalized medicine. Rather than trying to import reference material samples to conduct research in U.S. labs, new efforts focus on generating viral genome sequences from patient samples in the country of origin by deploying NGS technologies and training laboratory personnel with support from the U.S. Department of Defense’s Targeted Acquisition of Reference Materials Augmenting Capabilities (TARMAC) program. Developing such capabilities in the affected countries has enabled the rapid generation of whole genome sequence data from patient samples, in some instances within 24 hours from sample receipt. The data could be transmitted and deposited in public databases to enable researchers worldwide to validate or develop new assays and medical countermeasures. 

Uses of Sequence Data 

How do we validate assay and medical countermeasure efficacies in silico? Defense Biological Product Assurance Office, a national resource for the biological defense community, developed the PCR Signature Erosion Tool (PSET) in 2014 in collaboration with Noblis.[7] This tool allows the in silico validation of the assay signatures and modification of the assays as needed.[8] Similar approaches have been taken for validating the effectiveness of medical countermeasures, including monoclonal antibodies.[9],[10]

The Centers for Disease Control and Prevention (CDC) recently employed synthetic biology techniques to recreate the virus. High-quality sequence data generated by the Institut National de Recherche Biomédicale in Kinshasa, DRC, with support from scientists at the U.S. Army Medical Research Institute of Infectious Diseases, were posted online. Access to that data enabled the CDC team to recreate the virus—a significant step toward a rapid response to an outbreak in real time.[11] The virus can be used in studies for developing and testing new medical countermeasures.

Real time pre-symptomatic diagnosis and point-of-care treatment of infections are within reach. Containing the outbreak won’t be an easy task, but NGS and synthetic biology techniques give us a chance to get ahead of the virus and slow the spread of EVD before it infects more individuals. These methods could even help develop medical countermeasure on the fly for diseases that do not yet have treatments, protecting the world’s citizens from future infectious disease threats.














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