The Science Behind Coronavirus Testing, and Where the U.S. Went Wrong

America was never prepared for this

Photo: MediaNews Group/Reading Eagle/Getty Images

As has been widely reported, a major bottleneck in addressing the novel coronavirus outbreak in the U.S. is the extremely limited testing capacity. While South Korea has tested over a quarter million people, the U.S. has performed only 33,000 tests to date*, just three times South Korea’s daily testing capacity. Speculations about negligence, incompetence, and deliberate conspiracy have been floating around to explain this discrepancy. In reality, as is almost always the case, the factors impacting the U.S.’s ability to ramp up testing are incredibly complex. Complications include regulatory hurdles at the federal and local levels, shortages of supplies, equipment, and certified personnel, as well as technical challenges associated with the test itself.

Given these challenges, it may surprise you to learn that the coronavirus test is relatively simple, and operationally the same in every country. As a molecular biologist, I have run similar procedures hundreds of times. So with South Korea performing an order of magnitude more tests than the U.S., where did we go wrong? If the test is so simple that it can be performed in any molecular biology lab, why aren’t we routinely testing thousands of people every day? Why aren’t results available for days after testing? Will curbside and at-home testing help?

To detect a virus, we just have to look for its instruction manual.

How does the coronavirus test work?

To answer these questions, let’s first consider the culprit the test aims to detect: the virus itself. Viruses, at their core, are surprisingly simple entities: capsules with machinery to penetrate a cell, containing genetic information with instructions to make more viruses. Once a virus enters a cell, the instructions are read and more viral parts are made and assembled. Newly made viruses have mechanisms to escape their host cells and, in the case of coronavirus, travel further down the respiratory tract, eventually reaching the lung cells. When infected, lung cells can no longer perform their normal jobs, leading to the respiratory symptoms of Covid-19 (the disease caused by the novel coronavirus).

The novel coronavirus enters and multiplies inside our cells

There are a number of ways to detect the presence of a virus in a clinical sample. We can look for an indication that our immune system is reacting to it, or we can look for the virus itself. The latter turns out to be much more straightforward because we have a tried-and-true, easily adaptable method to detect one feature of the virus: the “how to make more virus” instructions that it carries.

These instructions are the virus’ genetic information, similar to our DNA. They are a chain of molecular building blocks — abbreviated as As, Cs, Gs, and U’s — strung together in an order we understand — they are a manual we can open and read, letter by letter. To detect a virus, we just have to look for its instruction manual.

To do so, we use a standard molecular biology technique called polymerase chain reaction, or PCR. PCR allows us to make copies of a small, specific section of DNA — say, a sentence from the instruction manual — as long as we know the first and last word of that sentence. These flanking words are called primers, and as you will see, it is important to choose them wisely. By combining primers with the patient sample and a few other components in a machine that can cycle through a few different temperature settings, we can produce millions of copies of our chosen DNA “sentence” relatively quickly (in 30–45 minutes).

The coronavirus test is relatively simple, and operationally the same in every country.

(To be totally accurate, coronavirus is actually an RNA virus. RNA is similar to DNA, but this method looks a little different in practice and is referred to as RT-PCR. The outcome is the same: Many, many copies of the DNA are made from the viral RNA instructions.)

But wait, which sentence in the instruction manual are we trying to copy…and why? The sentence itself turns out not to matter much, as long as it exists exclusively in the coronavirus’ instruction manual; it must be absent from the genetic code of other common viruses like flu. We make copies not so we can read them, but purely to see they can be made.Think of it this way: A million copies of a document are easier to see than a single sheet of paper. To “see” these copies, we use a fluorescent probe, which only emits light when it binds to DNA — the more DNA copies are made, the more light is emitted from the sample. In a sample from an uninfected individual — where no viral material exists in the first place — no copies will be made, and no light will be emitted. A sample containing viral RNA will get brighter over time. We can track the amount of light emitted by each sample in real time, as shown below.

The tests developed by the Center for Disease Control (CDC) in the U.S., the World Health Organization (WHO), and in-house at labs around the U.S., as well as those used in South Korea, all employ this basic strategy: using RT-PCR to detect viral RNA.

If the test is so simple, why is the U.S. having trouble getting it to work?

The U.S. initially mandated the use of CDC-developed test kits for all coronavirus testing, but labs reportedly had trouble getting them to work. The CDC was criticized for not using test kits developed in Germany, which were successfully detecting coronavirus around the world and were backed by WHO. U.S. labs responded by developing their own tests, and in some cases reporting quicker turnaround of results. This prompts the question: What are the differences between these tests and why do some work better than others?

The answer is relatively simple: Each test chose a different “sentence” to copy from the viral RNA. Effectively, this changes the primers (first and last word of the sentence), the fluorescent probe (corresponding to some word in the middle), and the “positive control” (a tube of DNA containing the “sentence” that is used to make sure the test is working properly). In fact, the CDC’s test kits are really just this: a few tubes containing the three components above.

Most molecular biology labs can develop such a test in a week or two, but those who have done so have come against another major hurdle: FDA regulations.

Choosing primers for any PCR experiment turns out to be tricky and sometimes unpredictable. Primers are just short pieces of DNA themselves, and some DNA has a tendency to fold in on itself, creating a “hairpin” structure which inhibits PCR. (This is a bit like the matching letters in a palindrome finding one another). These “palindrome” primers can produce a false negative — an infected patient whose sample appears to lack the virus. Alternatively, the primers can work just fine to make copies of coronavirus RNA, but might also be capable of copying some part of human DNA. Because patient samples (most often nasal swabs) contain both viral particles and human cells, these primers can produce a false positive — an uninfected individual testing positive for the virus. Other potential sources of RT-PCR failure are temperature issues, low primer or sample concentration, and contamination, among others.

How a coronavirus test can fail. A “palindrome” primer can cause a false negative. Primers which can recognize human DNA can lead to a false positive.

Whether the CDC’s primers were inferior to others’ has been debated, but U.S. labs have another critical reason to develop their own tests: The CDC’s test kits are in short supply. In principle, most molecular biology labs can develop such a test in a week or two, but those who have done so have come against another major hurdle: FDA regulations barring them from testing patient samples and returning results.

Federal regulations complicate in-house testing

Before we get into the weeds here, it is important to remind ourselves why FDA regulations exist: to protect the consumer — us — from being given incorrect medical information. Typically, there is regulatory oversight both of the laboratories where clinical tests are performed and of the tests themselves (though as this article points out, prior to this outbreak, FDA oversight of clinical tests under the current administration has been alarmingly slim).

In response to this outbreak, the FDA initially mandated use of the CDC’s tests exclusively, but loosened restrictions when it became clear that the need severely outpaced the CDC’s supply. Currently, CLIA-certified labs (those already certified to perform clinical testing) are permitted to develop and use their own tests, but must submit an Emergency Use Authorization application, which involves careful (and time-consuming) validation of in-house tests and sample collection procedures. Labs with extensive experience and infrastructure to perform viral PCR assays of clinical samples, but whose primary focus has historically been research rather than clinical diagnostics, must obtain CLIA certification as well. This added requirement temporarily prevented at least one well-equipped lab which played a central role in uncovering the extent of Seattle’s outbreak from doing further testing.

It is a complicated matter that pits individual consumer protections against the country’s immediate need to ramp up testing quickly in the face of a public health emergency. Stringent and time-consuming FDA requirements are preventing academic and clinical labs around the country, with capacity and willingness to develop and deploy testing within their communities, from being able to do so.

Though a path to certification exists, it is neither quick nor painless, and in a crisis that grows exponentially worse every day, where widespread testing has proven effective in curbing transmission, it is crucial that the federal government do everything in its power to allow willing labs to pick up the slack where it has ultimately failed: being prepared to mobilize quickly in the event of a public health crisis — a job that was formerly held by the pandemic preparedness team which Trump disbanded in 2018.

Massive supply shortages require creative solutions

Labs that manage to get proper certification to run clinical testing face another hurdle: a massive shortage of supplies. Patient samples are most commonly collected as nasal swabs, and before RT-PCR, viral RNA must be separated from mucous, human cells, and other debris. Commercially available RNA extraction kits are by far the quickest and safest way to process many samples at once, but unsurprisingly, demand has quickly outpaced supply, forcing testing labs to seek donations locally via social media.

PCR machines are another major bottleneck, as well as trained individuals needed to run them at capacity. Although some researchers argue that FDA restrictions should be lifted to allow all academic labs to fire up their idle PCR machines and start testing immediately, even they recognize this would substantially increase the rate of erroneous results, leading us into uncharted and unpredictable territory. It seems more prudent for the FDA to move quickly to certify a set of well-equipped labs, which can train volunteer scientists to perform approved in-house tests at scale. On the West Coast, it’s already all hands on deck. Both the University of Washington’s School of Medicine and UC Berkeley’s Innovative Genomics Institute are training willing academic researchers, graduate students, and postdocs to perform coronavirus testing.

Will drive-thru & at-home testing help?

First, let’s clear up some confusion here. When it comes to coronavirus testing, “drive-thru” and “at-home” do not describe the test itself, which requires training and specialized equipment. These terms refer instead to how and where nasal swabs are collected. Though these strategies may not substantially increase the speed of testing, there may be immense public health benefits to performing sample collection via mail or a drive-thru point. Why? Because those who fear they are ill need not travel to a clinic, risking infecting others while there or in transit. Plans to implement at-home sample collection are already in progress, and drive-thru testing is already available for UW Medicine patients and staff. But regulatory hurdles exist in this domain as well. To process at-home tests, labs must provide substantial evidence that these samples are reliable relative to those collected by trained individuals, further hampering labs’ ability to quickly roll out these operations.

Where do we go from here?

The challenges outlined here all converge around one conclusion: The U.S. was completely unprepared for a public health emergency of this scale. South Korea revamped its emergency preparedness plans after the MERS outbreak of 2015, recognizing that early detection and isolation were effective to mitigate an outbreak, and putting resources and procedures into place which could be mobilized quickly.

Hopefully, the U.S. government learns from this catastrophe and diverts more resources toward emergency preparedness in the future. In the meantime, scientists are heroically doing what they can to pick up the slack, and it should be the government’s immediate priority to simplify and accelerate regulatory procedures to permit qualified and well-equipped labs to scale up testing. To paraphrase Trevor Bedford, a virologist and leading voice reporting on the virus’s predicted prevalence and expected trajectory, increasing testing capacity is crucial to reduce rates of transmission and get the coronavirus outbreak under control in the U.S.

As a scientist, I feel proud and encouraged by the quick and selfless responses of fellow scientists to extend testing, communicate important information to the public, and begin developing and testing vaccines at record speed. Ultimately, we are all in this together.