The recent Ebola epidemic brought doctors and scientists from all corners of the world to West Africa, as aid groups and government rushed to stop the deadly spread of the disease. Now, that flood of resources is producing technology that could have implications far beyond just Ebola. A paper published today in Nature details a new system for analyzing genetic samples in the field, a tool that provided crucial data for tracking Ebola last year and could prove even more powerful in tracking future epidemics.
The instruments fit into three airline-ready bags, weighing less than 50 kilograms together, which allowed scientists to take them to remote clinics on the front lines of the outbreak. Between March and October of 2015, the team collected 142 different Ebola samples, typically returning a result in two working days, with longer delays if the researchers struggled with power outages or connectivity problems. Those samples provided valuable information as to how the disease was traveling on the border between Guinea and Sierra Leone.
Tommy Trenchard / European Mobile Laboratories
The new system tackles one of the central problems in public health: how to track a virus as it spreads. Typically, scientists track that movement by looking for mutations in the virus genome, running genetic scans of individual instances of the virus to see how different cases are related to each other. That technique was particularly effective for studying the recent Makona strain of Ebola, which showed between 16 and 27 mutations in each copy of its genome. But that work traditionally requires a full lab setup, which wasn’t available in the regions where Ebola-tracking was most urgent, so scientists had to improvise, building a so-called "lab in a suitcase."
"This opens up genomic research to far more applications around the world," said Jared Simpson of the Ontario Institute for Cancer Research, one of 102 separate co-authors on the paper. "We look forward to building upon the work done in this study and applying it to other fields, including cancer research."
a palm-sized genome analyzer
The key to the setup was the MinION MkI, a palm-sized genome analyzer that connects to a conventional laptop over USB. The device has a much higher error rate than conventional sequencers, but researchers were able to mitigate the errors by running each sample multiple times. The result wasn’t as comprehensive as data from traditional lab equipment, but it was accurate enough to track the spread of the disease. "This kind of ultra-portable sequencing setup is only made possible with the MinION," said Nicholas Loman of the University of Birmingham, another co-author on the paper. "Sequencers have been getting smaller… in the past five years, but they are still significantly more costly and bulky."
It’s early days for portable genome sequencing rigs, and Loman and others are looking forward to future systems that can operate entirely offline. Still, once the rig is small enough and independent enough, it could provide a new way to track even non-epidemic diseases. "It is still not very clear where exactly and in which animals Ebola persists between outbreaks," said Loman. "The ease of getting this system set up means you could potentially establish genome surveillance observatories all over the globe."