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Tuesday, May 28, 2024

How does a COVID-19 test work?

How do COVID-19 tests work? This coronavirus question is longer and more complicated than one might imagine. Choosing the correct test to use for a given population is an important question to look at first.

Keith Poulsen, Director at the Wisconsin Veterinary Diagnostic Laboratory, says that they, along with the Wisconsin State Lab of Hygiene, work to produce Coronavirus test results for the UW campus. Poulson says they have been asked constantly, what is the right test to run?

According to the FDA, there are three main types of tests being widely run. These include molecular tests, which detect virus genome in a patient's sample, and an antigen test, which searches for proteins found on the virus’s surface. Both of these tests are diagnostic, meaning they look for the live virus in a patient at the time of testing. The third type of test searches for the presence of antibodies in the blood. These antibodies are created by the immune system as a response to an infection. Using an antibody test, patients can then know if they had a past infection of the coronavirus.

Poulsen said that WVDL runs a molecular test called reverse transcriptase real-time polymerase chain reaction, or PCR. He says they use PCR because it is both a sensitive and specific test. Sensitivity refers to how well a test can find a positive person, meaning they are very unlikely to return a false negative. Specificity refers to how well a test avoids reporting false positives, meaning a non-infected person returns as infected.

Poulsen also says PCR works well for handling a large volume of tests, which is important for a large college campus like UW-Madison. WVDL now has the ability to process 384 samples at a time. This amounts to over 1,000 tests during an eight hour shift. 

Poulsen says WVDL’s goal is to be processing 1,200 tests per day by the end of September to serve the university of over 40,000.

Dr. Collin Pitts, chief resident at the Preventive Medicine Residency program at UW-Madison supports UHS’s testing strategy for UW’s Smart Restart this year. Pitts says the campus’ tests are processed at WVDL and their results verified by Exact Sciences, a molecular diagnostics company in Madison. Currently, UHS is working on getting FDA approval to run all tests at WVDL. At this time, WVDL is running a surveillance based strategy, leaving results to be verified through Exact Sciences. WVDL is working to show that their tests return the same results as verified labs.

Now that the correct test has been chosen, it’s time to implement the process. Testing samples are taken at a campus testing site, where patients are able to administer their own nasal swabs. 

Kelsey Anderson, Health Communications Specialist for UHS, said there will be four testing sites in total. The Ogg Hall and Holdt testing sites will be reserved for students in university housing for required scheduled testing. The site at Henry Mall will be open to all UW employees and students from 8:30 a.m. to 4:30 p.m. Monday through Friday. When the Fluno Center site opens, it will offer testing beginning at 6:30 a.m. for all UW employees and students.

After sampling, the swabs are transported to the laboratory. Using an app on their smartphone that scans a barcode on the samples test tube, the patient will be able to drop off their testing material to be analyzed. These samples are collected during the day to be shipped in coolers and dropped off at WVDL to be run.

But Running the PCR equipment is the easy part, Poulsen says. The real work in testing comes with making sure that the information coming into the lab is accurate as possible. UHS’s coronavirus dashboard serves as a record-keeping mechanism, according to Poulsen, ensuring that samples do not get lost from test site to laboratory and confirming samples have two unique identifiers. Once a sample is linked by those identifiers to the patient it came from, then the laboratory work begins.

After this, Poulsen says the samples are transferred to WVDL’s BSL-2 certified laboratory, the kind of lab that handles human pathogens. Then, automation takes over. The machines were developed for animal pathogens and are used by the WVDL to look at Bovine Viral Diarrhea virus, a disease found in cattle. Poulsen emphasized that as the number of tests being run increases, that automation becomes all the more necessary.

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“This is monumental in terms of the response to be able to test 100 students a day. Logistically to support that; hiring the personal, getting sites set up, to the completion of the tests is phenomenal that we would be able to do that” Dr. Pitts said. “To get this up and running in the timeline that we have is truly amazing.”

The first step in the laboratory process the sample media is pipeted to an automated nucleic acid extraction instrument, pulling the virus RNA out. Next, the sample runs in an instrument called a thermocycler. This process uses enzymes in the reaction to add fluorescent tags to the viral nucleic acid in the sample. Next the goal is to amplify the nucleic acid in the sample. Poulsen explains that by using a cycle of temperatures along with enzymes in the sample, the nucleic acid will duplicate. With every duplication, a fluorescent tag will be attached to the new nucleic acid. A laser in the PCR machine will monitor the fluorescence in the sample as it grows, this is why the test is called “real-time”. This goes on for 37 cycles. If a threshold is not reached in those 37 cycles, the sample is considered negative. A readout of the test results is given to the microbiologist in charge to make sure that the controls did what was expected and that the results look good. The results are then updated to UHS’s database.

Poulsen says that currently in his lab they can do this run two to four times per day. They hope to be processing 1,000 to 2,000 tests per day without working overtime or adding more equipment.

Dr. Pitts says that the goal for UHS’s Smart Restart program is to reduce turnaround time as much as possible. Once the results are in hand, then getting the infectious campus members to quarantine and getting contact tracers involved are the next steps. Pitt emphasized that testing is just one part of the Smart Restart Mitigation tactics; other parts include encouraging students to wear masks, enforcing the mask mandate in UW buildings, reducing class sizes and social distancing.

Poulsen says the lab’s goal is to get results back to patients by midnight of the day they arrive at the lab. However, the guarantee is 48 hours, to account for any runs that may have control fails.

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