Look inside the University of Kentucky coronavirus testing lab. Here’s how it works.
It starts with a swab up the nose.
It’s more than just a nasal swab to find out if you have COVID-19, it’s a nasopharyngeal swab. That’s when someone takes a flexible stick, around 10 inches long, and shoves it way up into your nose.
“It should be uncomfortable,” said Dr. Morgan McCoy, assistant professor in Pathology & Laboratory Medicine in the UK College of Medicine. “If it’s uncomfortable, then that means that it was a good collection.”
The stick is collecting a sample that will be put into a red liquid called “viral transport media.” Since Friday, those samples collected in the UK HealthCare system have been going to the University of Kentucky’s clinical microbiology lab for processing.
Kentucky’s flagship university was slower to establish a testing facility than some others, including the University of Louisville, which has been conducting tests since March 13. At UK, they had to wait for an instrument to arrive, and then wait for the Food and Drug Administration’s approval of the instruments UK was using for the tests. The vendor from whom they buy testing kits also had to get approval.
“The clinical laboratory is very highly regulated, for a good reason,” McCoy said. “So we have pathways for FDA approval for all of these tests and emergency use authorization is just one of those pathways, it’s just that most of us have never really had to live through one of those situations on such a scale as this.”
How coronavirus testing works
Social distancing is difficult in the clinical microbiology lab. Scientists in white coats and goggles move back and forth through rooms crowded with machines and desks as they run the various tests demanded of a lab that services Kentucky’s largest health care system.
For the coronavirus test, it’s just one sample per person.
“We want to conserve resources,” said Dr. Amy Gewirtz, UK HealthCare’s executive vice chairwoman of clinical operations. “So it’s one patient, one swab, one viral test media.”
Once the sample arrives in the lab, it has to be entered into a computer.
From there, it goes to a sterilized hood where lab technicians vortex the samples (put them on a machine that shakes up the sample at high speeds) and then transfer them into new, labeled test tubes.
The samples are refrigerated until the next step in the process: the extraction.
The UK lab uses an Abbott m2000 — a shiny, hulking box of a machine with an automatic metal arm that moves through the extraction process. The instrument required emergency FDA approval for the test and is also the machine used to test samples for chlamydia. Scientists vortex the samples again and put them into the machine, which extracts the genome of the virus. This part of the test can take up to three and a half hours.
From there, it goes into a second machine, which examines the genome and determines if the test is positive or negative. The data is checked and then sent directly to the patient files.
The whole process allows the lab to return results within a day.
The tests are processed in batches of up to 94 tests. Gewirtz said the lab is doing multiple testing runs each day but wouldn’t say how many tests are now being conducted in a day.
“It’s more prep time obviously in getting those samples ready, but then you put them on the instrument and the results also all come out at the same time,” Gewirtz said.
Each batch might include specimens received by the lab over a six- to 10-hour period, she said.
UK is in the process of training staff members in the testing process, which will help the lab operate at maximum capacity if the volume of tests goes up
“At some point, even with all of our planning, we may become overwhelmed,” Gewirtz said. “Either because of broader testing implications or resources that we’ve talked about. But so far, in the six days that we have been live with testing, we have been able to maintain that next day service.”
A shortage of COVID-19 supplies
One of the biggest concerns for testing labs right now is the supply chain. The testing kits they use could start to be allocated for “hot spot” areas for the disease elsewhere in the country, and there is a critical shortage of the swabs necessary to perform the COVID-19 test.
Kentucky currently must bid against other states and the federal government to get the equipment it needs to deal with the coronavirus pandemic, Gov. Andy Beshear has said.
At UK, they’ve started making their own test kits with existing swabs they have in the lab and making their own viral transport media to supplement the test kits they’re getting from vendors.
McCoy said the UK lab has the equipment it currently needs, but there are restrictions on who can get tested right now. At UK, those decisions are made by the hospital, but generally tests have been limited to the most severe cases and people who are presenting symptoms of the disease and have had other illnesses ruled out.
Beshear has repeatedly said he hopes there will eventually be enough equipment that everyone who needs a test can get tested.
“I am planning and I am pushing every single day to the point where we have more widespread testing,” Beshear said Monday during his daily news conference. “Our limitations are a couple, but it mainly goes down to the personal protective equipment... the truth is there is a critical shortage across our country and there is a critical shortage here in Kentucky.”
At the beginning of those daily news conferences, Beshear starts by saying “we’ll get through this.” Faced with the burdens of testing, and knowing there may be fewer supplies and more tests to come, McCoy agreed.
“We’re definitely going to get through it,” McCoy said. “It may not be easy, but we’re going to get through it.”
This story was originally published March 25, 2020 at 5:28 PM.
