We’ll Need More than Vaccines to Vanquish the Virus: New COVID-19 Testing Technology at Penn

In January 2020, when we were yelling across crowded restaurants, elbow to elbow in darkened movie theaters, and shaking hands with strangers, the idea that we would face a global pandemic was unthinkable.

A year later, we live in a changed world.

Infections with the coronavirus are currently spreading at a rate of more than a million new recorded cases every three days, as the worldwide case total approaches 100 million. In the United States more than 350,000 people have succumbed to COVID-19.

Incredible medical breakthroughs have occurred — the FDA authorizations of two mRNA vaccines in only nine months — and vaccinations are underway, but the development of herd immunity and the quelling of the pandemic will take time. In the meantime, there will be a pressing need for methods to detect people infected with the virus to better protect healthy individuals and prevent super spreader events in public spaces.

Across the University of Pennsylvania and in the Perelman School of Medicine, researchers are collaborating across schools and departments to develop novel ways to detect SARS-CoV-2, the virus that causes COVID-19. Penn Medicine News rounded up some of the leading COVID-19 test development projects happening on campus.

A Low-Cost, Rapid Test

A team led by César de la Fuente, Ph.D., a Presidential Assistant Professor in Psychiatry, Microbiology, and Bioengineering, is developing a low-cost, rapid diagnostic test for COVID-19. An electrode printed using a screen printer — many thousands of which can be printed in a day at very low cost — will directly detect the virus in nasal secretions with no sample preparation and can be read on a desktop instrument or on a telephone in minutes.

This technology transforms the biochemical information from a binding event between the SARS-CoV-2 viral spike protein and its natural receptor into an electrical signal that clinicians and technicians can detect. That signal allows the test to discriminate between infected and healthy human samples. The research team had previously been working on diagnostics for bacterial infections and, right at the onset of the pandemic, de la Fuente said, “we felt a responsibility to think creatively about how we could contribute potential solutions.”

The team got together and we came up with the idea for the COVID-19 test they are currently developing. The $80,000 Nemirovsky Prize and funding from PSOM through the Dean’s Innovation Fund helped accelerate the work, and the team currently has a prototype test.

A Saliva-Based Test for Large-Scale Screening

Led by Frederic Bushman, PhD, chair of Microbiology and co-director of the Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Scott Sherrill-Mix, PhD, a postdoctoral researcher of Microbiology, and Arupa Ganguly, PhD, a professor of Genetics 

In April 2020, a Penn Medicine research team was assembled to come up with an assay for COVID-19 testing that would be reliably available without impact from the supply chain issues that have caused temporary shortages of so many necessary items during the pandemic, both medical/scientific and otherwise. Frederic Bushman, Scott Sherrill-Mix and Arupa Ganguly led the team to create a method called LAMP BEAC. LAMP stands for Loop-Mediated Isothermal Amplification, which is a method of amplifying DNA in a sample.  However, the LAMP method also gives background noise, complicating detection of the viral genetic sequences. So the team invented a way, using molecular beacons, of reading out the correct sequence that makes the assay a lot more specific.  The BEAC in their test’s name represents the molecular beacons designed by the researchers to obtain sequence-specific detection of SARS-CoV-2 genomes with improved discrimination.

LAMP BEAC allows the assay to be run from a saliva sample an individual can provide themselves rather than a nasal swab that needs to be collected by a clinician. Because reagents used in traditional clinical PCR tests are expensive and subject to supply chain disruptions, a team led by Gregory Van Duyne, PhD, a professor of Biochemistry and Biophysics at the Perelman School of Medicine engineered novel reagents, allowing inexpensive local production of the required enzymes. The reaction set up and incubation can be done in a couple of hours, allowing rapid turnaround.

This novel, inexpensive saliva-based test is part of a study, led by Mitesh Patel, MD, MBA, MS, an assistant professor of Medicine and Healthcare Management, and Allison Oakes, PhD, an advanced postdoctoral fellow of Medical Ethics and Health Policy. It is now being widely used at Penn for surveillance testing. Faculty, staff, and trainees associated with the Penn are asked to participate and complete a saliva-based COVID-19 test approximately every week for about six months. Researchers are using this to identify COVID-19 cases earlier and prevent its spread.

The study, called COVID SAFE, has enrolled more than 3,000 individuals, with more than 7874 tests performed over four weeks ending on Dec 30, 2020. So far, they have identified 15 positives —  which is a 0.2 percent positivity rate among totally asymptomatic people who otherwise might have spread the disease undetected. In an effort to make the test meet clinical standards, Ganguly’s Genetic Diagnostic Laboratory applied for and received Clinical Laboratory Improvement Amendments (CLIA) approval — designed to regulate clinical laboratory testing and ensure the accuracy, reliability and timeliness of test results — from the state to run tests beyond the clinical trial.

“The more asymptomatic people can be tested, the better chance we have at stopping the spread,” Ganguly said.

A Handheld, COVID-19 “Odor” Detecting Test

From the labs of Benjamin Abella, MD, MPhil, a professor of Emergency Medicine, and A.T. Charlie Johnson, PhD, Rebecca W. Bushnell Professor of Physics and Astronomy

A team led by physicists at the University of Pennsylvania and physicians at the University’s Perelman School of Medicine is developing a handheld device that can detect the signature “odor” of people with COVID-19, the illness caused by the coronavirus SARS-CoV-2. Johnson and Abella envision their “sniffer” device as one such tool.

“Our goal is a system that can be easily and cost-effectively deployed in workplaces, restaurants, retail stores, stadiums — anywhere — to help get the world back to something that resembles normal,” said project principal investigator A. T. Charlie Johnson.

Humans, like other animals, breathe out and emit from their skin various carbon-based chemical compounds that are byproducts of bodily processes and exist as gases at ordinary room temperatures. Some of these volatile organic compounds, or VOCs, are detectable by the human nose as body odor. Other VOCs are not sensed by humans, although they may be detectable by other animals. In part due to reports of dogs, cats and other animals using their powerful senses of smell to detect diseases in humans, researchers in recent decades have been developing electronic sniffer devices that can accomplish similar feats.

The device will be prototyped and tested with support from a grant from the National Institutes of Health’s National Center for Advancing Translational Sciences. It uses a nano-sensor array that was developed in the Johnson lab and can detect VOCs in the air close to people or their clothing. The team will collect t-shirts from people with and without COVID-19, and will use them to optimize the set of chemical sensors and train an AI algorithm to identify and recognize a COVID-19 VOC signature.

The team also includes Carrie Lynn Kovarik, MD, a professor of Dermatology, Cynthia Otto, DVM, PhD, a professor at the School of Veterinary Medicine, and Lyle H. Ungar, PhD, a professor of Computer and Information Science.

Preliminary tests using clothing from 30 people with or without COVID-19 indicate that it detects the chemical signature of a COVID-19-positive person with more than 90 percent sensitivity, and correctly detects COVID-19 negatives at a similar rate — with results being available in seconds.

“We’re hoping to scale this up rapidly, and we think the technology could be useful not just against COVID-19, but also against future pandemic illnesses,” Abella said.

An At-Home, Multi-Pathogen Test

From the lab of Haim Bau, PhD, a professor Mechanical Engineering and Applied Mechanics

When Haim Bau first heard about the COVID-19 epidemic in the Wuhan province in January 2020, he said, “it was clear it was only a matter of time before the virus would arrive in the USA, and inexpensive diagnostics, preferably ones that can be used at home, would be critical for controlling the spread of the disease and enabling rational policies.”

So Bau’s lab set to work. The team designed an isothermal amplification LAMP test and adapted their custom designed two-stage amplification method dubbed Penn-RAMP, for SARS-CoV-2. The researchers chose to focus on the LAMP method to amplify genetic material because it can be carried out with minimal or no instrumentation. They designed Penn-RAMP to enable co-detection of multiple co-endemic pathogens such as SARS-Cov-2 and various influenza strains.  

Although the results of Bau’s LAMP assay can be seen by the naked eye without a need for a reader, the test still requires incubation at 65 degrees Celsius. Typically, incubators are electrically powered heat blocks with temperature control. However, such incubators may cost dozens of dollars and may take time to manufacture in quantity, which presents a barrier for quick adaptation for home use. So the Penn researchers replaced the electrical heating with an exothermic (heat producing) chemical reaction — a concept well known to hikers and members of the military - and a phase change material for temperature regulation.

Their reagents can be stored in dry form, refrigeration-free. With further development, they hope their assay and incubator can provide an inexpensive test for use outside the clinical laboratory. Their work has been supported, in part, by a gift from from Mr. Jeff Horing to Penn School of Engineering for COVID-19 Research.

A Rapid Test Using a Metagenomics Approach

From the lab of Erle S. Robertson, Ph.D., Harry P. Schenck Professor in Otorhinolaryngology

Researchers in the lab of Erle Robertson are developing a rapid test with high sensitivity and accuracy that could eventually use a couple drops of blood or plasma for direct detection of this virus, or any other respiratory pathogen with potential for triggering a worldwide pandemic.

The test uses a microarray platform comprising 60,000 probes on eight replicate arrays for detection of all known viruses and other pathogenic bacteria, fungi and parasites. The test will have increased sensitivity and accuracy, through the use of multiple probes across the genome in regions that are unique as well as probes that are conserved for all known coronaviruses. This metagenomics approach includes probes which cover all known pathogenic respiratory pathogens, including other coronaviruses from bats, and other mammals providing accurate and efficient detection of SARS-CoV-2 as well as the potential for detection of other respiratory pathogens as co-infecting agents that may contribute to severity of disease.

The benefit of this test is in the sensitivity and accuracy, which is achieved by using multiple probes across the genome to minimize false negative results from probe failure. The overall screen requires expertise which could be quickly acquired with training, and can be transitioned from a research lab setting to a diagnostic lab for rapidly testing clinical samples with the appropriate resources in place.

“We are interested in understanding the association of distinct microbiota with different diseases and responses to therapy,” Robertson said. “Our goal was to identify the specific microbial signature that may contribute to disease severity. Thus, understanding the role of the underlying microbiota in a microenvironment and the changes that occur in the disease state to design effective therapeutic approaches.”

A Highly-Sensitive Digital Test

From the lab of Ping Wang, PhD, DABCC, FAACC, an associate professor of Pathology and Laboratory Medicine

Ping Wang’s research team is developing a COVID-19 test based on a microbubbling digital assay — a novel technology Wang developed that can detect a very low amount of biomarkers in human samples, using images of tiny microbubbles on a smartphone camera as a “cue.”

Wang developed the test before the pandemic as a point-of-care tool for detecting protein biomarkers in a highly sensitive way. Her team in Pathology and Laboratory Medicine have previously used the test to detect prostate cancer recurrence in patients who had had prostatectomies. Patients with prostatectomies have prostate-specific antigen (PSA) levels close to zero, and they use this test to detect early increases in levels of the PSA molecule, which could be used as a marker for early recurrence of the cancer.

When the COVID-19 pandemic occurred, Wang knew this test would be a perfect fit for detecting the COVID-19 virus antigens during acute infection phase, when they first show symptoms or before patients were symptomatic. Detection of such low levels of antigens is not possible through most routine technologies, but this can be achieved through Wang’s technology due to its higher analytical sensitivity.