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Portable DNA Test Can Detect Ebola and Other Acute Infections

Posted September 29, 2015

A group of scientists, led by colleagues from the University of California, San Francisco (UCSF), completed a proof-of-concept study on real-time DNA sequencing that can be used to rapidly detect Ebola and many other known pathogens present in a blood sample from an infected individual.

The portable metagenomic test developed by Charles Chiu and his team can detect the Ebola virus and many other known pathogens in less than an hour. Image credit: NIAID via, CC BY 2.0.

The portable metagenomic test developed by Charles Chiu and his team can detect the Ebola virus and many other known pathogens in less than an hour. Image credit: NIAID via, CC BY 2.0.

Using the new technique, study lead author Charles Chiu, MD, PhD, and his team were able to detect the genetic fingerprints of Ebola in stored blood samples from two African patients with severe symptoms in five hours, with the sequencing itself taking only 10 minutes.

Detailed in a paper published in Genome Medicine on September 28th this technology could prove highly useful in settings where lab equipment and medical infrastructure is in short supply.

While most other commercially available diagnostic tests target specific pathogens, the method used in the study, called “metagenomics”, does not require any guesswork, and is capable of analysing all the DNA present in a sample.

To obtain such quick results the researchers developed new analysis and visualization software and used it on a laptop computer to leverage an emerging DNA-sequencing technology known as nanopore sequencing.

“This point-of-care genomic technology will be particularly attractive in the developing world, where critical resources, including reliable electric power, laboratory space, and computational server capacity, are often severely limited,” said Chiu.

Nanopore technology, currently under development by many private enterprises, distinguishes individual nucleic acids by the distinctive perturbations they create in electric currents as they pass through microscopic pores. The USB-powered sequencer used by Chiu’s research team, dubbed MinION, was made by Oxford Nanopore Technologies and is no larger than a modern cell phone.

Although the technology is still new and thereby prone to error, Chiu claims it’s becoming faster and more accurate by the month. With the sequencing part cut down to mere minutes, the team has now set its sights on streamlining the sample preparation technique, which still requires several hours, regardless of the setup.

“To our knowledge, this is the first time that nanopore sequencing has been used for real-time metagenomic detection of pathogens in complex clinical samples in the setting of human infections,” claims Chiu. “Unbiased point-of-care testing for pathogens by rapid metagenomic sequencing has the potential to radically transform infectious disease diagnosis in both clinical and public health settings.

Proving the robustness of their invention, the researchers successfully used their sequencing kit to detect Hepatitis C in the blood of an infected UCSF patient, and the Chikungunya virus in a man who was asymptomatic at the time, but eventually reported having a fever and joint pains.


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