A genome sequencing kit that fits into an airplane suitcase has been successfully used for the first time to monitor the development of an outbreak of a lethal disease.
The equipment consists of a 100g MinION DNA sequencer by Oxford Nanopore Technologies and a laptop providing power to the kit through a USB connection. The whole kit, weighing less than 50kg, can provide information about the DNA of a virus in a patient’s sample within 24 hours, thus allowing researchers to monitor almost in real time the evolution of the virus. This information is crucial for medical professionals to gain control over the spreading outbreak. By analysing how the DNA of the virus differs in individual samples, the researchers can gain an in-depth understanding about where the disease has spread from and what the major transmission routes are.
In a study published in the latest issue of the journal Nature, an interdisciplinary team of researchers from the University of Birmingham and the Ontario Cancer Research Institute described how they used the equipment to monitor the spread of Ebola during the last year’s epidemic in Guinea.
“While sequencing has until now been confined to a lab, this opens up genomic research to far more applications around the world,” said Jared Simpson from the Ontario Institute for Cancer Research, a co-author of the study. “We look forward to building upon the work done in this study and applying it to other fields, including cancer research."
By sequencing 142 samples from Ebola patients in the Conakry region, the researchers were able to track how individual cases were related. The data helped World Health Organisation epidemiologists get a better understanding of the evolution of the outbreak.
Previously, samples would have to be shipped to laboratories abroad, which would result in several days of delay. In the case of a disease such as Ebola, a day’s delay could mean dozens of new cases and likely deaths.
"Genome sequencing information is valuable for researchers and epidemiologists during an epidemic,” said Nick Loman, from the Institute of Microbiology and Infection at the University of Birmingham. “Yet, generating such information is a laborious process typically performed in well-equipped laboratories using large, delicate and expensive hardware. Having a portable DNA sequencing system opens up the possibility to do outbreak genome sequencing in real time, which can directly impact the response on the ground, as well as provide a wealth of information about pathogen evolution.”
The portable DNA sequencer continues its mission in Guinea, currently in the Nongo region, where new cases of the lethal disease were reported this January, only a few hours after the epidemic was officially declared to be over.
The Ebola outbreak in West Africa was the deadliest since the disease was discovered in 1976. 11,000 people have died since 23 March 2014 when the first confirmed case was reported.