Portable, rapid DNA test to detect Ebola, Chikungunya and Hep C in the making

Scientists have developed a new blood test based on DNA sequencing that can be used to rapidly diagnose Ebola and other pathogens such as Chikungunya and hepatitis C virus.

Researchers at the University of California - San Francisco said that the test can be used even where lab space and medical infrastructure are scarce.

They detected the genetic fingerprints of Ebola in stored blood samples from two African patients who had acute hemorrhagic fever, completing the diagnosis within five hours of opening the samples - the DNA sequencing itself took just 10 minutes.

Most commercially available or research-based genetic diagnostic tests target specific pathogens.

The team has pioneered techniques that do not require suspected pathogens to be identified beforehand in order to detect their unique genetic fingerprints.

This unbiased approach of analysing all DNA in a clinical sample without knowing which species are present, which was used in the Ebola detection, is called “metagenomic” analysis.

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

In the same set of experiments, published in the journal Genome Medicine, the researchers were able to detect Chikungunya virus, from a Puerto Rican outbreak, just as quickly in a blood sample from a donor with no symptoms, but who eventually reported having fever and joint pains.

In another example of the technique’s power, detection of hepatitis C virus in blood from an infected patient, present at a much lower concentration than the other viruses, took just 40 minutes from the start of 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 Charles Chiu, associate professor of laboratory medicine at UCSF, who led the team.

Chiu’s lab group was one of the first to pay USD 1,000 for access to an experimental DNA nanopore sequencer made by Oxford Nanopore Technologies, called the MinION.

The device is small enough to fit in the palm of the hand and is powered by a USB connection to a laptop.

Last year, using a similar metagenomic approach to pathogen detection, the researchers used their software and another DNA-sequencing technology to analyse all DNA in a spinal fluid sample, leading to the diagnosis of an unusual but treatable bacterial cause of encephalitis in a critically ill Wisconsin boy whose health had been worsening for months.

That earlier analysis took two days. The detection of Ebola in the new study was more rapid because nanopore sequencing yields data immediately and in real time, unlike the technology used in the Wisconsin case, which takes much longer to provide data for analysis.