This hybrid device integrates a microfluidic chip for sample preparation and an optofluidic chip for optical detection of individual molecules of viral RNA. [Joshua Parks]
This hybrid device integrates a microfluidic chip for sample preparation and an optofluidic chip for optical detection of individual molecules of viral RNA. [Joshua Parks]

The 2014 outbreak of Ebola hemorrhagic fever that killed more than 11,000 people exposed a simple if not frightening truth: much of the world is ill-prepared for a larger outbreak of this deadly virus. To fill in the gaps of the infectious disease ramparts, scientists have reenergized efforts to understand the molecular mechanisms that underlie the virulent nature of Ebola. Simple, fast, accurate, and low-cost detection methods are an area in need of innovation for infectious diseases and lie at the center of these renewed initiatives.   

Now, a team of researchers led by scientists at the University of California Santa Cruz has developed chip-based technology, which they hope will allow for the reliable detection of Ebola and other viral-based pathogens. The new device uses direct optical detection of viral molecules and can be integrated into a simple, microfluidic device for use in field situations where rapid, accurate detections of Ebola infections are needed to control outbreaks.

The current gold standard for Ebola detection relies on RT-PCR methods for amplification of viral genes. While this method has been a proven diagnostic technique for infectious diseases like Ebola, it requires the use of specialized equipment and laboratory settings that are often incompatible with field setups.  

“Compared to our system, PCR detection is more complex and requires a laboratory setting,” explained senior author Holger Schmidt, Ph.D., professor of optoelectronics at UC Santa Cruz. “We're detecting the nucleic acids directly, and we achieve a comparable limit of detection to PCR and excellent specificity.”

The findings from this study were published recently in Nature Scientific Reports through an article entitled “Optofluidic analysis system for amplification-free, direct detection of Ebola infection.”

When the investigators tested the new system in the laboratory, they observed sensitive detection of the Ebola virus, without any false positive detection of two related viruses—Sudan and Marburg. Moreover, the device was able to accurately quantify the Ebola virus over six orders of magnitude.

“The measurements were taken at clinical concentrations covering the entire range of what would be seen in an infected person,” Dr. Schmidt noted.

The system combines two small chips, a microfluidic chip for sample preparation and an optofluidic chip for optical detection. Dr. Schmidt’s laboratory has been developing optofluidic technology for over a decade and decided to collaborate with researchers at UC Berkeley to design the microfluidic chip portion of the device, which is composed of a silicon-based polymer with microvalves and fluidic channels to transport the sample between nodes for preparation steps.

The device detects Ebola viral RNA by binding to a matching sequence of synthetic DNA oligonucleotide attached to magnetic microbeads. The microbeads are collected with a magnet, nontarget biomolecules are washed off, and the bound targets are then released by heating, labeled with fluorescent markers, and transferred to the optofluidic chip for optical detection.

Dr. Schmidt and his colleagues were excited by the devices capabilities and accuracy. However, they noted that they have not yet been able to test the system starting with raw blood samples, which will require additional sample prep steps and the use of a biosafety level 4 laboratory in Texas. 

“We are now building a prototype to bring to the Texas facility so that we can start with a blood sample and do a complete front-to-back analysis,” Dr. Schmidt stated. “We are also working to use the same system for detecting less dangerous pathogens and do the complete analysis here at UC Santa Cruz.”

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