After several weeks’ delay caused by faulty testing kits and bureaucratic hurdles, regulatory guidelines for COVID-19 tests are rapidly loosening in the US and testing capability is ramping up on a national and local scale.
By January, many American clinicians and academic researchers had an eye on the viral outbreak in Wuhan, China, and contemplated setting up in-house testing for the new coronavirus. “We had the foresight in January to imagine that the ability to provide testing for COVID-19 would be important, and we worked hard to make that happen,” Benjamin Pinsky, an infectious disease expert at Stanford University School of Medicine, said in a press release March 16.
After the US Centers for Disease Control and Prevention (CDC) posted their official instructions for SARS-CoV-2 tests on January 28, clinical laboratories began preparing their own tests, modeled on the CDC’s instructions, in anticipation of eventual Food and Drug Administration (FDA) approval. In late February, when it became clear COVID-19 was more entrenched within the US than previously thought, public health department and academic labs began petitioning the FDA to let them start running their tests through Emergency Use Authorization (EUA).
We were basically told, ‘we’ll worry about the costs later, go build capacity as fast as you can.’—Keith Jerome, University of Washington
On February 29, the FDA issued a new policy: labs could start testing patients for SARS-CoV-2 before the FDA approved their EUA requests. Previously limited to CDC and state health departments, any laboratory certified under the Clinical Laboratory Improvement Amendments (CLIA) to perform “high complexity tests” could start screening for the coronavirus, and the number of tests dramatically increased.
According to The COVID Tracking Project, led by The Atlantic journalist Alexis Madrigal, by March 23 a total of 294,056 SARS-CoV-2 tests were run in the US. On March 16, the number was only 41,714.
One of the fastest testing facilities out the gate is based in the University of Washington (UW) School of Medicine. On March 20, UW virologist Keith Jerome told The Scientist his lab was successfully running 3,000 tests per day, and intended to ramp up capacity to 4,000 or 5,000 this week. In contrast to the back and forth negotiation in February to accelerate the federal regulatory approval process, Jerome found his university supervisors supportive from his first conversations with them in January. “We were basically told, ‘we’ll worry about the costs later, go build capacity as fast as you can.’”
The CDC test protocol uses three primer and probe sets to detect three regions in the gene for the SARS-CoV-2 nucleocapsid (N) protein.
UW Medicine has two testing protocols, one that targets two regions within the N gene, and the other that looks for the presence of two conserved regions of the SARS-CoV-2 ORF1ab gene.
In addition to large laboratories processing thousands of samples a day on behalf of hospitals, many hospitals themselves have chosen to set up in-house COVID-19 testing. NorthShore University HealthSystem in Illinois was one of the first hospital systems to set up its own in-house test after the FDA announcement, and more have followed suit.
Karen Kaul, a molecular biologist at NorthShore who led the test development and validation, says her colleagues who’d worked through the 2009 swine flu pandemic saw the potential need for a test in January. NorthShore kept its test protocols identical to the CDC’s, hoping this would streamline the regulatory approval process.
“To perform tests in large volumes, you need systems that can get the results back out to the doctors, patients, and medical records. Hospitals and academic labs are set up to get this information,” Jerome notes.
NorthShore is currently testing up to 600 patients per day, but the test is only available to patients presenting with the most severe COVID-like symptoms. This testing capacity may be lowered by the nationwide shortages of reagents and basic laboratory supplies.
“There are shortages of everything throughout the whole process.” says Kaul. These shortages include personal protective equipment, pipette tips, viral transport media, and RNA extraction reagents. Her laboratory, and others around the country, set up multiple testing platforms made by different life science companies that they can toggle between if they run out of a particular reagent.
State laboratories, academic labs, and hospitals were quick to begin rolling out small- to medium-scale assays, but shortly afterwards commercial testing companies unveiled the largest testing capabilities of all. On March 5, LabCorp began providing COVID-19 diagnostic tests, and Quest Diagnostics followed four days later. On March 19, LabCorp said in a statement it will be able to perform more than 20,000 COVID-19 tests per day beginning March 20, with a projected three- to four-day turnaround for results. Quest Diagnostics estimates it will achieve a similar throughput by the end of March.
Even though commercial testing capacity dwarfs that of hospitals and university labs, both testing options are necessary during a pandemic, says Kaul, who notes that an in-house COVID-19 test, which gives results within hours, is necessary so hospitals can triage sick patients. “If you’ve got a relatively healthy patient who is going to go home and self-isolate, they can probably wait a few days.” In that scenario, the hospital would prefer to save its limited in-house resources and send that sample out for commercial testing.
Right now, most testing laboratories are simply responding to the immediate testing shortages and gathering enough supplies to test the sickest patients for COVID-19. In the coming weeks, Jerome says, he hopes expanded capacity will allow UW to accept more healthcare clients in the Seattle area and start assisting with basic research aimed at understanding and combating the coronavirus.