Since mid-January, more than 84,000 specimens from US patients have been tested for Covid-19. That’s almost certainly a fraction of the number that would have gotten processed if the tests were easier to come by.
At first, federal agencies were slow to approve tests that laboratories would need to help diagnose patients. Now, with those approvals in effect, labs around the country are reporting shortages of some of the chemicals and other materials necessary to perform diagnostic tests.
To understand the shortages, you need to understand the testing process, which confirms the presence of coronavirus by looking for its genetic material. Every stage demands a new set of highly-specialized supplies—each of which adds a potential bottleneck in testing capacity.
To start a test, front-line healthcare workers need to collect samples by swabbing a patient’s nose or throat. They can’t just use Q-tips: These specialized swabs are long, skinny tubes that are flexible enough to get all the way to the back of the throat, called the nasopharynx. Manufacturers of these swabs are reportedly straining to keep up with demand.
Those workers also need to protect themselves with the same kinds of surgical masks and rubber gloves in short supply at hospitals. If these kinds of shortages continue, it won’t matter how efficient the diagnostic tests are. “If you can’t produce a sample, you can’t produce a test,” says Geoffrey S. Baird, a pathologist in a lab conducting tests at the University of Washington.
After swirling it around, healthcare workers stick the swab into a specialized vial with a particular kind of liquid pooled in the bottom. The cells fall off the swab and into the liquid, which becomes a sample lab techs can test.
The healthcare facilities send those samples off to a lab—one run by a state or local public health organization, university, the Centers for Disease Control and Prevention (CDC), the Department of Defense, or a for-profit company.
When the sample gets to the lab, it’s just a bunch of human cells. Lab techs need to get the virus, and its genetic material, out of those cells. Some samples require more treatment than others: Lung liquid called sputum is so sticky when it comes in that it needs to be processed with extra ingredients.
Once the sample is in a workable form, technicians extract the virus’s genetic material—in this case, RNA—using a set of chemicals that usually come in pre-assembled kits.
These types of extraction kits are commonly used in molecular biology and clinical labs around the world, but the CDC-approved kits are only made by a few companies (pdf, p. 7-8). And some, like Qiagen and Roche, have seen their global supply chains interrupted due to the virus. “The big shortage is extraction kits,” says Eric Blank, chief program officer at the Association of Public Health Laboratories, an organization with 125 member labs, 92 of which are currently doing coronavirus testing.
There are no easy replacements here: “These reagents that are used in extraction are fairly complex chemicals. They have to be very pure, and they have to be in pure solution—we’re dealing with genetic material, so you can’t be introducing things that will interfere with the test itself,” Blank says.
Though these companies say they are now ramping up their production, there’s no telling when that might result in more resources for US-based labs. Plus, since the US Food and Drug Administration approved commercial diagnostic labs, like those run by LabCorp and Quest Diagnostics, on March 17, even more facilities are now competing for those same resources.
Once the coronavirus RNA has been liberated from human cells, it’s time for the actual test part of the test: PCR, which stands for polymerase chain reaction. This process searches for small sequences of SARS-CoV-2 RNA, and makes enough copies that they can be measured. This is one of the most common ways labs test for SARS-CoV-2.
Each step in this process calls for specific chemicals. Though Baird says his lab hasn’t had trouble getting the reagents necessary to identify the coronavirus, others around the country already have.
The first is called reverse transcriptase; it converts the RNA into DNA. The second, and perhaps most crucial, is the primers—short stretches of DNA designed to match up with the viral genetic material.
If the viral RNA-turned-DNA is present, these primers will latch onto it. The CDC’s original test kit included three sets of primers (pdf), and now includes two, after one primer set introduced inconsistent results. The CDC has only approved two companies, BioSearch Technologies and Integrated DNA Technologies, to make the primers for its test.
The labs themselves are in charge of sourcing everything else needed to run the tests. This includes hardware: vortex mixers, microcentrifuges, specially-treated tubes, specially-designed racks, micropipettes to squirt tiny bits of liquid from place to place. Baird has found it difficult to find pipette tips because they must be disposed of after each use and can be bespoke to the instruments they’re used on.
Once the primers latch on, an enzyme called polymerase assembles the second strand of genetic material needed to convert single-stranded viral RNA into the double helix of DNA. And then the magic happens.
Running the tests
Using a special piece of machinery, lab technicians run the mix through a sequence of temperatures—hot, then cold, then medium. That process exponentially amplifies the amount of viral genetic material in each sample.
Lab techs count the number of cycles it takes for them to see the signal from those copies: About a dozen cycles means there were a lot of viruses in the original sample and that the patient tests positive; a few dozen cycles may mean there’s too little of the virus to say the patient is infected.
Tests can be completed in a matter of hours, usually about six to eight if demand isn’t too high. But for a country in the grips of a pandemic, demand is obviously high. As of Monday afternoon, Baird’s virology lab at the University of Washington had tested 24,507 patients. That makes up “most of the testing in the state of Washington,” he says.
“I would say that the reason why testing isn’t widespread is not because the labs didn’t want to do it. It’s just very hard to do and the supplies are really limiting right now,” Baird says. “Many hospitals that would like to be doing this testing simply cannot buy an instrument or get the supplies to do it.”