E-Beacon Method May Provide Faster, More Accurate Test for Coronavirus

New research from Binghamton University Associate Professor of Chemistry Brian Callahan could be a game-changer on the detection of Coronavirus. He uses a new methodology to detect SARS-CoV-2 that can produce reliable results more quickly than other methods.

His article, “Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid,” was accepted for publication by the journal ChemBioChem. Co-authors include graduate student Xiaoyu Zhang, postdoctoral researcher Venubabu Kotikam and Chemistry Professor Eriks Rozners. A two-year pilot grant for $150,000 from the National Institute of Allergy and Infectious Diseases helped fund the research.

Methods to detect SARS-CoV-2, the virus that causes COVID-19, come in two types. The first detects the virus protein or “antigen,” the basis of the rapid tests found at local stores, with results typically coming back in around 15 minutes. The second type are molecular tests designed to detect virus nucleic acid, which can take anywhere from one to three days to return results.

Why so long? In the very specific and sensitive molecular tests, specimens must be shipped to testing labs, where the samples are then processed and analyzed by technicians with specialized training. As a result, they’re considered by scientists as the gold standard for testing due to their reliability, although their long wait time makes them cumbersome for patients.

“We focused on cutting down the wait time for molecular testing. We developed a nucleic acid sensor — we call it an E-beacon — that has the potential to speed sample turn-around time while maintaining the sensitivity and specificity parameters that make molecular testing so powerful,” Callahan said.

Enzymatic beacons

Enzymatic beacons are engineered “bioconjugates” with two key components: a light-generating enzyme and a DNA probe, Callahan explained. The components are stitched together via a recently-patented method.

In the E-beacons prepared for SARS-CoV-2, the DNA probe recognizes a specific sequence in the virus’ spike gene; that recognition event in turn causes the light output from the attached enzyme to increase. The more virus nucleic acid in a sample, the brighter the light signal from the enzyme component of the E-beacon, Callahan explained.

E-beacons can provide positive or negative results more rapidly than molecular tests, and without the expensive instrumentation required by polymerase chain reaction (PCR) based testing.

“As of now, our E-beacons appear to be just as specific and even more sensitive than detection methods used in current SARS-CoV-2 molecular tests,” said Callahan.

He acknowledged that the E-beacon experiments haven’t yet been done outside the lab, which is the likely next step.

Where could this lead? Imagine a walk-up, automated testing device that somewhat resembles a vending machine. Users would deposit a testing swab into a collection port. The molecular tests would then run autonomously within the machine, sending out the results via cell phone in about two hours.

E-beacons represent an attractive alternative to the current testing methods, and not just for SARS-CoV-2. Because of their modular design, they can be reconfigured easily for detecting other viral or bacterial pathogens, Callahan said.

“I am an eternal pessimist, so anytime a project works as well as the E-beacons, I’m surprised,” Callahan said.

There were setbacks, of course, including delays for materials and supplies they needed. Those delays led to a collaboration with Rozners, whose lab began preparing a vital component for the E-beacons. The project began to progress more quickly as a result.

Another essential ingredient to the research project’s pace and success: Zhang, whose efforts proved critical.

“Early mornings, late nights, weekends in the lab — he really hustled,” Callahan said.

Source: Binghamton University 

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Rochester Students Develop Game Changing Technology that Instantly Detects Sepsis Via Sweat

Sepsis is the body’s extreme response to an infection. It is a life-threatening medical emergency.  Sepsis happens when an infection you already have triggers a chain reaction throughout your body.  Infections that lead to sepsis most often start in the lung, urinary tract, skin, or gastrointestinal tract. Without timely treatment, sepsis can rapidly lead to tissue damage, organ failure, and death.

Undergraduate students at the University of Rochester recently developed a game changing technology that can instantaneously detect sepsis biomarkers in sweat. 

The following overview is from U of Rochester's News Center.

Every year, approximately 1.7 million American adults develop sepsis, a life-threatening complication that arises when the body has an overwhelming immune response to an infection. According to the Centers for Disease Control and Prevention, sepsis causes more than 20 percent of all deaths worldwide and one in every three deaths in US hospitals.

A crucial aspect of treating sepsis is to catch it at an early stage when a patient’s infection is still curable. Current methods to diagnose sepsis, however, rely on tests that can take days to yield results, while early sepsis can turn into full-blown septic shock within only one hour after the first symptoms emerge.

In order to address this problem, a team of 12 undergraduate students at the University of Rochester developed a novel device that instantaneously diagnoses sepsis based on biomarkers in a person’s sweat. The device offers a noninvasive way to monitor sepsis in real-time and uses materials that are environmentally friendly and affordable, making the device easily deployable in low-income countries.

The team recently entered their device in the International Genetically Engineered Machine (iGEM) competition, where it was nominated for best diagnostics project, best hardware, and best education awards and won a gold medal, making the team the second-most-awarded iGEM team in North America.

“After researching statistics on sepsis and talking to a variety of medical experts, we got a sense of its immense medical and economic impacts and the need to develop better options for sepsis diagnosis,” says iGEM team member Amanda Adams ’22, a biomedical engineering major. “Our goal was to create a biosensor that could provide up-to-date information about a patient’s condition. Getting to work in a student-led team where we were directly responsible for the entire project from planning it to presenting it was very rewarding.”

Worldwide synthetic biology competition

In 2020, Rochester launched an undergraduate class composed of students who compete in a worldwide synthetic biology competition with the goal to solve a real-world problem using innovative biological ideas. (Synthetic biology involves creating new biological parts or systems using materials already found in nature.) During the iGEM competition, held in mid-November, the undergraduates present to a panel of judges the projects they have spent the year designing and implementing.

“This year’s iGEM team tackled a problem that has a huge impact on society,” says Anne S. Meyer, an associate professor of biology, and one of the advisors for Rochester’s iGEM team. “The students realized that a patient’s sweat contains specific biomarkers that can report on whether or not the patient has sepsis. So, monitoring the levels of these biomarkers in patient sweat would be an easy and noninvasive way to diagnose sepsis in real time to get instant information.”

Overcoming the limitations of current sepsis diagnostic tools

Doctors use many different tools to diagnose patients, one of which is the presence and concentration of certain biomarkers—molecules such as proteins or sugar that are associated with a particular disease, condition, or biological process. There are several ways to measure biomarker concentrations, including test strips and lab-on-a-chip devices, but many of these approaches only show biomarker concentrations at one specific point in time. These methods can also be expensive, and many take hours to perform.

“This means that doctors often need to wait for the results of a test, and the results may not even be accurate if the patient developed a condition after the sample was taken,” Adams says.

The Rochester students consulted with sepsis survivors, scientists, and clinicians at the University of Rochester Medical Center to design a sepsis-sensing device, which they named “Bio-Spire,” a combination of “biology” and “perspire.” Bio-Spire is a biosensor that continuously monitors the levels of biomarkers in sweat. Unlike blood, sweat is a noninvasive medium to collect, and unlike saliva or urine, biomarkers in sweat can be continuously analyzed. The levels of biomarkers in blood and in sweat are correlated, so changes in the amount of biomarkers in sweat are indicative of changes in the blood.

That is, a change in biomarker levels in a patient’s sweat can signify a deterioration of the patient’s condition—and may signify sepsis.

Designing a ‘game-changer’ diagnostic device

Bio-Spire is designed to collect a tiny amount of sweat from a patient’s skin and wick the sweat past an integrated set of electrodes covered in biomarker detectors. The biomarker detectors consist of short pieces of DNA receptors attached to a small sheet of graphene—an ultra-thin layer of material that is highly conductive. The students synthetically created their own graphene and DNA in an environmentally-friendly manner by using engineered biological components.

When the sleeve-like device is placed on a patient’s arm, biomarkers associated with sepsis bind to the DNA receptors, changing the conductivity of the graphene sheet and triggering an electrical resistance in the electrodes, which is then recorded on a computer. The students created software that displays the concentrations of sepsis biomarkers in real time, permitting health care workers to receive up-to-the-minute updates on a patient’s condition.

“The Rochester team’s real-time sepsis diagnosis device is a game-changer because all of its parts can be created in an accessible, inexpensive way,” Meyer says. “Plus, it is the fastest sepsis diagnostic device ever created.”

In addition to developing the device, the team worked to increase awareness of sepsis and synthetic biology in the local community and beyond through a variety of education and outreach programs, including interactive science lessons with children’s summer camps in Rochester. The team also collaborated with an iGEM team from the Ohio State University to virtually publish a children’s book called A Trip to the Hospital: Randall’s Lesson on Sepsis, which is available on Amazon and Apple Books.

“We are excited by the promising results of this project and honored to be recognized for our efforts in addressing such an important, interdisciplinary issue in the medical community,” Adams says.

Because iGEM is an open-source competition, the team’s work is documented and available on their Bio-Spire Wiki page. This format allows future students or developers to take up the design and build upon the ideas.

Source: University of Rochester News Center

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