To Respond to a Disease Outbreak, Bring in the Portable Genome Sequencers
Using a genome sequencer smaller than a stapler, geneticists have demonstrated the role they can play in combating outbreaks of infectious disease. An eight-month experiment in Guinea during the tail end of the Ebola outbreak, described today in a the journal Nature, showed the potential of a genome sequencing technology that can be packed inside a suitcase and deployed in rural outposts.
With the Zika virus outbreak gaining momentum in the Americas, the Ebola experiment may offer useful lessons. “Having genome data is becoming part of the fundamental response to an outbreak,” says lead researcher Nick Loman, a geneticist at the University of Birmingham. By studying the genetic material of the virus across many patients, researchers can look for telltale mutations that reveal the paths of transmission. And if those routes are discovered quickly enough, public health officials could make decisions to change the course of the epidemic.
In the Ebola study, Loman and his colleagues used the MinIon sequencer from Oxford Nanopore Technologies. This diminutive device plugs into a laptop via a standard USB port, through which it both transmits data and draws power. The researchers packed three of these devices, three laptops, and all the other equipment and reagents they’d need into the suitcases shown in the photo below—“the rucksack on top just contains pants and socks,” says Loman. “This was the first time we could put an entire genome sequencing laboratory into aircraft-hold luggage.”
Photo: Joshua Quick Everything you need to track Ebola’s genome, including extra pants and socks.
One of Loman’s graduate students, Joshua Quick, brought the gear to Guinea in March 2015, and worked with the European Mobile Lab project to get set up quickly. Within two days, the team was sequencing samples of the Ebola virus drawn from local patients. The Ebola virus’s genome is composed of about 19,000 “letters” of genetic material called RNA; sequencing is the task of putting all those letters in the proper order. Then researchers could compare the genome sequences of different patients, looking for mutations that have reordered those letters along some stretches of the RNA strand. If patients have a virus with the same mutations, they were likely part of the same person-to-person chain of transmission.
The Guinea team regularly gave their results to public health officials to help them draw conclusions about the virus’s spread. “This started as a test run, and turned into real-time surveillance that was feeding into the epidemiology,” Loman says. For the most part, the results just confirmed known chains of transmission. But as the outbreak drew to a close in late 2015, the team provided useful intelligence on final flare-ups. “Occasionally a case comes out of the blue, and the question is, where did that case come from?” Loman says. “With genome sequencing you can say, it’s linked to this cluster.” Then public health officials can take the necessary steps to isolate the area.
During the West Africa Ebola outbreak, researchers tried out a mobile genetics lab that allowed them to study the Ebola virus’s genome on the ground in Guinea. Photo: Tommy Trenchard/European Mobile Laboratories
Between March and October 2015, researchers analyzed samples from 142 Ebola patients to gain information about the chains of transmission. Photo: Tommy Trenchard/European Mobile Laboratories
Using the portable MinIon genome sequencer from Oxford Nanopore Technologies, shown here, researchers established their lab in the epidemic’s center. They generated results within days of when samples were taken. Photo: Tommy Trenchard/European Mobile Laboratories
This experiment was the first example of real-time genetic surveillance during an infectious disease outbreak. The researchers provided data to public health officials combatting the Ebola epidemic. Photo: Tommy Trenchard/European Mobile Laboratories
The trickiest part of the experiment wasn’t the genome sequencing, it was maintaining a steady supply of electricity in the mobile lab in Guinea. The researchers had to buy a backup power device to keep freezers and cetrifuges running. Photo: Tommy Trenchard/European Mobile Laboratories