Who: A team of researchers from UCSF
What: Developed DNA sequencing-based blood test
When: 28 September 2015
Why: To diagnose Ebola and other pathogens
A team of researchers completed a proof-of-principle study on a DNA sequencing-based real-time blood test that can be used to rapidly diagnose Ebola and other pathogens. The study was published online in Genomic Medicine on 28 September 2015.
The team was led by Charles Chiu, associate professor of laboratory medicine at University of California San Francisco (UCSF).
The study combined nanopore sequencing with metagenomic analysis for detection of pathogens in complex clinical samples in the setting of human infections.
First, the team pioneered a technique called metagenomic analysis that do not require suspected pathogens to be identified beforehand in order to detect their unique genetic fingerprints. This is unlike most commercially available or research-based genetic diagnostic tests that target specific pathogens.
Secondly, to obtain the quick results from the blood test of the Ebola-affected patient, the team then using the combination of pioneered technique and visualization software in a laptop to leverage an emerging DNA-sequencing technology known as nanopore sequencing.
Nanopore sequencing technology is a new technique which distinguishes individual nucleic acids by the distinctive perturbations they create in electric currents as they individually pass through microscopic pores.
The team sourced the experimental DNA nanopore sequencer called MinION from the Oxford Nanopore Technologies. The device is small enough to fit in the palm of the hand and is powered by a USB connection to a laptop.
Results of the Study
First, the team detected the genetic fingerprints of Ebola in stored blood samples from two African patients, who had severe hemorrhagic fever. The entire diagnosis was completed in 5 hours of opening the samples, out of which the DNA sequencing took only 10 minutes.
Second, 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.
Third, in another example of the technique’s power, detection of hepatitis C virus in blood from an infected UCSF patient, present at a much lower concentration than the other viruses, took just 40 minutes from the start of sequencing.
Why the study is unique?
The study is unique because for the first time nanopore sequencing was combined with metagenomic analysis for detection of pathogens in complex clinical samples in the setting of human infections.
The specialty of the test is that it can be used even where lab space and medical infrastructure are limited.