The University of Arkansas for Medical Sciences’ Little Rock campus is shown in this file photo. ( Benjamin Krain) While a national scale-up of testing for the new coronavirus has moved at a lumbering pace, the good news is that the science behind such tests is accelerating, says the University of Arkansas for Medical Sciences’ chief pathologist.
Twenty years ago, “it used to be really difficult” to design an assay — the technical term for a test — to detect a new virus, Dr. Jennifer Hunt said. “We would spend months just identifying the [virus’s] genome.”
But modern genetic sequencing lets scientists map the building blocks of a virus, animal or person in a matter of days. Since the discovery of the coronavirus in January, about 500 sequences of it showing possible mutations have been freely shared among researchers and commercial labs, Hunt said.
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Early this week, Arkansas’ academic medical center is expected to begin running an in-house coronavirus test modeled from one developed by the federal Centers for Disease Control and Prevention. With commercial lab tests, UAMS will be set up to process about 700 tests a day — a significant boost to the state’s testing capacity.
UAMS scientists are now checking to make sure the CDC’s process works the same way in their lab using their materials, results that will later be verified by the Food and Drug Administration.
The federal agency did most of the heavy lifting, Hunt said, so researchers weren’t working “from scratch.”
“Probably the biggest and hardest complicator … is whether the test works,” she said. “It’s an art, not a science, to designing an assay. There’s a ton of science behind it — and there’s a little bit of magic.”
When they begin processing samples, UAMS lab techs will use a chemical process to separate RNA molecules from other materials, such as blood, tissue or other cells, in a sample collected from a patient.
They then add several substances, which are known in chemistry as reagents, to trigger a reaction that changes RNA into a different kind of molecule: complementary DNA, or cDNA. A third process called a polymerase chain reaction blows up a strand of the new molecule into millions of identical particles so a machine can see it, Hunt said.
She said the test designed by the CDC is somewhat labor-intensive — more of an “everyday workhorse” test rather than one designed for high throughput.
That’s why UAMS and labs around the country are incorporating both tests using the CDC model, as well as others developed by private companies, to take advantage of different processing times and varying materials.
Part of what limits daily testing capacity is simply the number of slots in the machines that do the analysis, Hunt said. Labs also have scrambled to acquire the chemicals and other supplies they need, which are in high demand.
“No one anticipated needing truckloads of these reagents months ago,” Hunt said.
Patients nationwide have been frustrated by the limited availability of tests for the new coronavirus, which some states — such as Kentucky — have reserved for the sickest or most at-risk individuals.
In Arkansas, testing is expanding in fits and starts, though screening to triage patients and determine who should be tested is more widespread at area hospitals.
The state’s network of community health centers, many of which serve rural communities such as Marianna, Clarendon and Mena, recently rolled out testing processed through commercial labs, said the group’s board chairman, Allan Nichols.
They have about 70 test kits across several clinics serving uninsured and low-income Arkansans, but will soon need materials to collect samples such as swabs, said Nichols, who also is chief executive officer of Mainline Health Systems.
“They said [the supplies are] on back order, and we have no idea when we will get them,” he said.
The group also has discussed setting up a test site at a fast-food restaurant in Monticello, but other supplies such as protective gowns and gloves are a limiting factor in that plan.
Generally, the crisis has created a resource crunch for the centers, which recently have endured uncertainty regarding their federal funding. The fast-moving nature of the outbreak has been a challenge for everyone, Nichols added.
“What is the right thing to do today will not be the right thing to do next week,” he said.
A Section on 03/23/2020
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