Researchers at the Public Health Agency of Canada National Microbiology Laboratory (PHAC-NML) in Winnipeg are developing a fast, highly accurate, low-cost test that identifies if a person is infected with the COVID-19 virus, which is critical to controlling its spread.
When someone tests positive for COVID-19, they can be isolated, and public health authorities can follow up with close contacts so those people can self-isolate, monitor for symptoms and get tested themselves.
Testing also helps officials understand where and how much of the virus may be circulating, informing public health actions to keep the virus in check.
Speed and accuracy
To be as effective as possible, testing needs to be fast and accurate—the faster test results are available, the faster public health officials can respond with measures to limit further infection.
Currently, as PHAC-NML senior research scientist Dr. Jim Strong explains, when it comes to testing for a virus like COVID, speed and accuracy is an either/or proposition.
"The most accurate test available uses a polymerase chain reaction—the PCR test," says Dr. Strong. "However, because it requires specialized equipment and a trained scientist doing hands-on work in the lab, it can take 24 hours or more to get the results. There is a test that takes 15 minutes, but there are questions about its sensitivity—it's not very good at picking up the virus in the early stages of infection."
To address the need for speed with accuracy, Dr. Strong and PHAC biologist Dr. Alex Bello, in collaboration with scientists at the Canadian Food Inspection Agency, are working on a CRISPR-based test for COVID.
The CRISPR advantage
"Clustered regularly interspaced short palindromic repeats (CRISPR) is what you might call bacteria's immune system," explains Dr. Bello. "When a bacterium comes in contact with a virus or other pathogen, it copies a bit of the pathogen's RNA or DNA into its own genome. Then, the next time the bacteria runs into that pathogen, it recognizes that DNA sequence. This activates an enzyme that cuts that sequence of the virus DNA or RNA, making it difficult for the virus to reinfect the bacteria."
Since these enzymes can be "programmed" to recognize and cut specific DNA sequences in all kinds of organisms, including humans, CRISPR is valued as an easy-to-use and accurate gene-editing tool.
Prior to COVID, with funding from the Government of Canada's Genomics Research and Development Initiative (GRDI), the PHAC researchers were using CRISPR technologies to develop a test to identify the Ebola virus. With the advent of the pandemic, GRDI quickly approved the researchers' request to apply their funding to a CRISPR-based test for COVID.
How it works
"CRISPR allows us to program a specific bacterial enzyme to recognize COVID nucleic acid. When it does, the enzyme activates and chops up the viral nucleic acid," says Dr. Strong. "The test we are developing will allow us to see that reaction."
Although there's a lot of complex genomics and other science behind it, the test itself would not require any special equipment or skills to run it. "We're aiming for a one-tube test," says Dr. Strong. "Drop a sample of blood or saliva into the tube, wait a few minutes and check the result—a lot like a do-it-yourself pregnancy test."
Dr. Duane Funk, associate professor of anesthesiology and critical care medicine at the University of Manitoba, says the CRISPR-based test being refined by Drs. Strong and Bello would be a "game-changer for pathogen diagnostics."
Along with speed, accuracy and ease of use—making it ideal for use in the field—Dr. Funk notes the test could be adapted to identify other pathogens, and potentially more than 1 at a time. "Infection can move very quickly to overwhelm the body's defences," says Dr. Funk. "This technology could enable a single test that would check for a whole panel of pathogens. In a matter of minutes, physicians would know what they were dealing with, choose the most appropriate course of action, and be able to start treatment immediately—instead of waiting hours and even days for the results of conventional tests."
Fast, sensitive, accurate, accessible
While still being refined in the lab, the CRISPR-based test provides results in about 30 minutes. It is highly sensitive—able to detect the COVID virus in very small concentrations—and as accurate as the PCR test. It's also expected to be highly accessible, at a cost of about a dollar per test.