On March 19, when the COVID-19 infection rate in Arkansas had risen to 62 and the need to be able to test more people for the disease had become abundantly clear, University of Arkansas for Medical Sciences Chancellor Cam Patterson announced that the medical center would soon be able to test up to 600 people a day.
On March 30, UAMS’ lab ran 83 tests, Secretary of Health Dr. Nate Smith said at at March 31 press conference. That was up from fewer than 50 the day before, Smith said. UAMS has been able to run a total of 360, Vice Chancellor Leslie Taylor said Tuesday.
The difference in UAMS’ projected number and reality was not because Patterson was being fanciful. It was because having a system in place to be able to test specimens for infection from the novel coronavirus doesn’t mean the testing can be carried out. The test is not a discrete entity, an all-in-one unit. Like producers of personal protective gear and ventilators, American companies are struggling to keep up with demand for the ingredients needed to isolate and analyze the virus. Making things more difficult in Arkansas is the need to compete with richer and needier states for those products.
Dr. Jennifer Hunt, a molecular genetic biologist at UAMS and chair of the department of pathology, and her team used Centers for Disease Control guidance to create the medical center’s own assay to prepare specimens for novel coronavirus testing. She explained how testing works:
First, the sample is collected. A health practitioner — who must be outfitted in personal protective gear — inserts a flexible 5-inch swab, called a nasopharyngeal swab, into a patient’s nose all the way back to the nasopharynx, where the nose and throat meet. This is where viruses hang out. (President Trump made quite a big deal of his suffering at the poke of the swab.) Another swab goes in the mouth, to nearly the same point. A Q-tip is useless.
What can go wrong at this stage? The health professional must be wearing personal protective equipment, PPE; the shortage of PPE is one of the major safety issues facing health care. Too, swabs are in critically short supply.
The swab is broken off and the specimen end with the material collected from the nasal passage is put into a tube with about half a teaspoon (3 ml) of pink fluid, the viral transport medium. “This week,” Hunt said in a March 25 interview, “we were missing the transport media.” But Hunt got lucky: She gave a recipe for the medium to the chair of microbiology department at UAMS. And in 20 minutes, “we had 2 liters of gold,” to be put — manually — into 3,000 tubes, she said.
“Yesterday,” she then added, “we couldn’t buy tubes.”
At this stage in testing, lab techs — also decked out in hot and uncomfortable PPE — add reagents to the specimens to create chemical reactions necessary to prepare the material for analysis. UAMS’ lack of reagents — not an Arkansas problem, but national — was made public last week by UAMS Health CEO Dr. Stephen Mette at Little Rock’s COVID-19 task force meeting.
UAMS doesn’t have to do all its testing manually: Hunt, anticipating the need, asked for the university to purchase what machine — an ePlex analyzer — in March that automates the process.
UAMS tried to buy three. It could only get one. “Everybody in the country wants them,” Hunt said.
The ePlex uses different reagents from those used in the manual assay. Samples are fed into the machine in trays. Sometimes, the chemicals needed for the automated test aren’t available. Sometimes, the trays sometimes aren’t either. UAMS has the manual assay to fall back on.
The next step is the extraction of genetic material by adding enzymes that break down RNA cell walls. The little bits of genetic material are then amplified by the polymerase chain reaction method and then examined to confirm the presence of the novel coronavirus. “Polymerase is also in short supply,” Hunt said, sighing. “Yeah. Isn’t that fun?”
The difference between using UAMS’ lab and a private lab, Hunt explained, is time. “If you come through triage with symptoms but you’re generally healthy, and make a decision to home quarantine, whether your test is negative or positive, it’s not important that I know [the results] today,” Hunt said. The specimen can be sent to a large private lab, which will give a result more slowly than the UAMS test — but the patient’s care is the same. If someone is sick or older with a chronic health condition, doctors want the faster result from their own lab.
Everyday, needed supplies are “a moving target,” Hunt said. “It’s like playing tennis with a ball that doesn’t bounce straight.”
The lack of reagents is also slowing things down at the Department of Health’s laboratory, Secretary Smith said; a lack of reagents for its machine means the lab is having to do its tests manually. It was able to run only 94 on Monday. However, Smith said the lab is planning to operate 24/7.
In a March 30 post on Twitter, Governor Hutchinson wrote, “We need more COVID-19 data in AR, and testing is what gives us that data. Increasing testing is our immediate need right now, as well as protecting our health care workers. Our whole team, including myself, is working to procure add’l tests.”
The governor’s post came at the end of a day that he’d begun with a conference call with Trump and the nation’s governors. The New York Times reported that Trump told governors on the line that he “had not heard about testing in weeks” in response to the governor of Montana’s plea for more tests, telling the president that his state was “one day away” from running out of tests. The New York Times did not report on what Hutchinson may have told the president.
The Arkansas Department of Health, UAMS and private laboratories have run 6,482 tests in total. “We are not testing as much as we should,” Smith said at the COVID-19 update, though he disputed a point raised Monday that we are among the lowest four states in terms of tests per 100,000. National up-to-date figures on testing and confirmed cases can be found at the Covid Tracking Project.