You wake up one morning with a fever and a cough. Where can you get a rapid, accurate COVID-19 test?
The answer has plagued many people in the U.S., where the FDA has been slow to approve at-home, rapid tests, many of which suffer from high false-negative rates. And the more-accurate polymerase chain reaction (PCR) COVID-19 test preferred by clinics and health care providers takes many hours to perform and days for results to reach the patient.
Now, a team of Virginia Commonwealth University researchers has published a paper providing a framework for increasing the speed of the accurate PCR test by removing a timely and expensive step. Another paper by the same research team proposes an easier method for identifying variants like Delta.
“Having a quicker methodology that could get the test performed, at the PCR standard, in five to ten minutes would be a big improvement for COVID-19 diagnostics,” said Jared Farrar, Ph.D. “And the framework developed in the paper could be easily updated for detecting future variants and new infections in future pandemics.”
Ordinarily, to get the accurate PCR test at your local pharmacy or clinic, you’d have a nasal swab. The swab would go in a tube with liquid and be sent to a centralized lab. At the lab, they’d perform an RNA extraction and eventually they’d get a result that travels back to the doctor or patient. It can take days to get a result.
It’s the same at a hospital like VCU Health, though the lab is in-house. The RNA extraction part can take hours and requires specialized equipment that many small hospitals, clinics and local pharmacies don’t have.
Farrar and the team have provided a framework for turning those days or hours into minutes by removing the extraction step.
The framework shows that a test can detect SARS-CoV-2, the virus that causes COVID-19, without extracting and isolating the RNA, a step that was previously required. A tester can move straight from the patient sample to detection.
“It will get a result in less than 20 minutes, and is comparable to other COVID-19 PCR tests with the extraction step,” Farrar said. “By removing that step that had previously been required and the required hands-on time and reagents, you can do these things a whole lot faster.”
The rapid take-home tests (15-30 minutes) that are currently available at local pharmacies suffer from high false negatives. Compared to PCR testing, they can miss about 35% of true COVID-19 in individuals that are sick and about 65% of true COVID-19 in asymptomatic individuals.
“The danger with this form of testing in the general public is that many individuals may only take the rapid antigen test and if the result is negative assume they have a common cold,” Farrar said. “They then could spread COVID-19 to other people, or not seek medical care early when treatment options are more effective.”
Labs can use their existing PCR test instruments to do the diagnostics, which could translate in the future to simple instruments and tests that could be, for example, placed at offices, airports or schools.
The team’s new method would not be one that you could purchase and take home – at least not for now. But it simplifies PCR testing for COVID-19, removing a step in the typical process, thus decreasing the time and complexity of testing at hospitals, clinics and pharmacies.
In the same paper, the team also showed that using extracted RNA from COVID-19, PCR can be completed in less than 1 minute – the world’s fastest published COVID-19 PCR test.
“Ideally, in the not-so-distant future, you could walk into your doctor’s office, they could swab you and you could have results within five to 10 minutes, using the gold standard PCR methodology,” Farrar said. “It reduces patient anxiety, and it improves patient care at the point of need.”
Farrar was joined by co-first author Joseph Lownik, M.D., Ph.D., now a first-year clinical pathology resident in the Pathology Physician Scientist Training Program at Cedars-Sinai Medical Center in Los Angeles, Grayson Way, a current student in the VCU Wright Center for Clinical and Translational Research Ph.D. program in clinical and translational science, and Rebecca Martin, Ph.D., in publishing “Extraction-free rapid cycle RT-qPCR and extreme RT-PCR for SARS-CoV-2 virus detection” in the Journal of Molecular Diagnostics in August.
The same team, along with collaborators at the University of Washington Medical Center, published another paper, “Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting,” in September in Diagnostics.
The second paper develops a methodology to detect changes to the virus using common instruments and a simple process.
Right now, only a small portion of positive COVID-19 tests are sent to undergo whole-genome sequencing of viral RNA – in order to identify variants like Delta. Sequencing machines are costly, starting at hundreds of thousands of dollars, and require experts and enormous computing power to operate.
VCU Health sequences some positive tests but not very many of them. Smaller hospitals don’t have the equipment or expertise and send some positive tests to state or national labs.
“We were interested in trying to develop a method that was more, I would say, democratizing — a method that could be used anywhere,” Farrar said. “It could be used on instrumentation that’s inexpensive and doesn’t require a huge amount of expertise to run. You could find the equipment to do it in an undergraduate or graduate biology lab.”
The test would detect changes to the virus’s spike protein, and other important changes and help researchers understand how the COVID-19 virus functions and changes. Farrar notes that the method would adapt easily to new viruses and variants that may emerge.
“It would be valuable in a low-resource and low-laboratory-capacity country that could easily have this equipment in their labs,” Farrar said. “They could do surveillance on positive samples.”
Both Lownik and Farrar are graduates of the VCU Wright Center for Clinical and Translational Research Ph.D. program in clinical and translational science. Farrar is working on his medical degree, part of VCU’s M.D.-Ph.D. program for training clinician-researchers.
Martin, an assistant professor in the VCU School of Medicine’s Department of Microbiology and Immunology, and her team were the recipients of a VCU COVID-19 Rapid Research Funding grant last year, supported by the VCU Wright Center for Clinical and Translational Research and the Office of the Vice President for Research and Innovation.
Virginia Commonwealth University
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Goal 1: Train and Cultivate the Translational Science Workforce
Goal 4: Innovate Processes to Increase the Quality and Efficiency of Translational Research, Particularly of Multisite Trials