COVID spit test is faster, cheaper, avoids shortages—and now greenlit by FDA

Patrick
Enlarge / A doctor wearing personal protective equipment (PPE) prepares to take a saliva swab from a patients during coronavirus symptom tests in the coronavirus outpatient clinic at the Paracelsus Clinic in Zwickau, Germany, on Thursday, April 2, 2020.

The US Food and Drug Administration this weekend authorized a saliva-based diagnostic test for COVID-19 that costs less than $5, is faster than current laboratory tests, and may dodge supply shortages plaguing the country—without losing much in accuracy, according to early data.

The test, called SalivaDirect, was developed by researchers at Yale University, who have no plans to commercialize the test and have made the test’s protocol completely open and available.

If the protocol becomes widely adopted, it could help improve the country’s COVID-19 testing, which is currently dismal. Some patients face weeks-long waits to get results. With such long delays, contact tracers have no chance of reaching out to those exposed before they have the chance to pass on the infection. The delays stem from the sheer volume of tests coming in, as well as shortages of critical supplies, such as nose swabs and chemical reagents necessary to run the tests. SalivaDirect tries to address both of those problems.

How standard testing works

The new test is basically a streamlined version of the current standard for COVID-19 diagnostic testing. Generally, these tests determine if a person is currently infected with the pandemic coronavirus, SARS-CoV-2, by detecting the genetic material of SARS-CoV-2, which is in the form of RNA rather than DNA.

The basic steps of the test start with sticking a long swab far into a person’s nose until it hits the back—a nasopharyngeal swap—to try to scrape up any SARS-CoV-2 that may be present. The swab picks up all sorts of things, of course, including snot, bits of human cells from the nose, whole viral particles, and any other germs that may be present. To clean up the starting material, most test protocols then call for performing an assay that extracts out just the genetic material, clearing away all the debris and inconsequential bits. This requires time and specific reagents, which can be in short supply.

Then, the isolated genetic material heads to a second assay called an RT-qPCR, or a quantitative reverse transcription polymerase chain reaction. In it, bits of RNA are converted into DNA, which is then probed for sequences present only in SARS-CoV-2. If those sequences are present, tiny fragments of synthetic DNA—called primers—latch onto the SARS-CoV-2 code and direct enzymes to make copies of that stretch of DNA. The copies are cleverly designed to fluoresce when they’re formed. Then, the assay repeats this step to make another set of glowing copies, and another, and another, and another in an exponential process, until enough copies of the SARS-CoV-2 DNA are present to detect a fluorescent signal above background.

Cutting corners

The faster that signal is detected—that is, the fewer cycles it takes to get it—the more SARS-CoV-2 RNA was there to begin with, hence the “quantitative” part of the name. Researchers refer to this as the “Cycle threshold,” or Ct. If the Ct is low, say below 30 cycles, it suggests there was a good amount of RNA to begin with, perhaps from a raging infection. If it’s above, say 37, it means there was little SARS-CoV-2 RNA in the sample, perhaps from a fading infection or genetic remnants of a recently ended infection.

For diagnostic tests, the Ct value isn’t necessarily useful—if you have any amount of SARS-CoV-2 RNA in your nose, you are or were very recently infected. The test doesn’t indicate infectiousness or past exposure to the virus. But comparing the Ct values between different tests for SARS-CoV-2 is helpful for comparing how sensitive any given test is.

For the SalivaDirect test, Yale researchers cut some corners without losing much in accuracy or sensitivity. First, with the global shortage of swabs, they skipped the stick and went just to spit. They verified that SARS-CoV-2 is present in saliva as it is in the nose. They took saliva and nasal swabs from 37 known-positive patients and ran a standard lab test for SARS-CoV-2 on all the samples. Between the paired nasal swabs and saliva samples, there was 83 percent agreement. Nearly all were positive, but three nasal swabs and three different saliva samples came back negative, invalid, or inconclusive. They also found that in collected saliva, the virus was stable for up to seven days at 4°C, room temperature, or 30°C without the addition of preservatives.

The researchers then skipped the RNA extraction step entirely. Instead, they warmed up the saliva samples along with an enzyme called proteinase K that hacks away at any protein debris in the sample—human cells, whole viral particles, etc—leaving the SARS-CoV-2 RNA standing. This is useful since the extraction step takes extra time and the reagents used in the assay are currently in short supply. Last, the researchers streamlined the RT-qPCR by combining a few steps and still saw similar Ct values.

Testing testing

In a head-to-head comparison with dozens of positive samples from infected people, SalivaDirect results were the same as standard nasal test results 94 percent of the time. Comparing SalivaDirect to standard lab tests on saliva, the tests agreed 97 percent of the time for positive samples and 100 percent on negative samples. The researchers didn’t see any false positive results in any of their experiments.

To do some of their validation work, Yale partnered with the National Basketball Association to test players and staff in the NBA’s bubble. The NBA partly funded the research.

Based on list prices of materials used, the researchers estimate SalivaDirect costs anywhere from $1.29 to $4.37 per sample, depending on if a lab chooses to use a saliva collection device. This is cheaper than the current standard tests, which experts estimate in the range of $15 to $50 per sample for materials. The Yale researchers suggest that labs charge $10 for a SalivaDirect test.

“Widespread testing is critical for our control efforts,” Nathan Grubaugh, one of the test developers and professor at Yale School of Public health said in a news release. “We simplified the test so that it only costs a couple of dollars for reagents, and we expect that labs will only charge about $10 per sample. If cheap alternatives like SalivaDirect can be implemented across the country, we may finally get a handle on this pandemic, even before a vaccine,” he said.

Step in the right direction

On Saturday, August 15, the FDA granted SalivaDirect at an Emergency Use Authorization. “The SalivaDirect test for rapid detection of SARS-CoV-2 is yet another testing innovation game changer that will reduce the demand for scarce testing resources,” Assistant Secretary for Health and COVID-19 Testing Coordinator Admiral Brett Giroir said in a statement. Though the FDA noted that it has approved four other COVID-19 tests that use saliva, those tests had “variable performance.”

While there has been much fanfare around the authorization of SalivaDirect, it’s important to note that it is not a rapid, at-home test that some have suggested using on a daily basis to control the pandemic. Those cheaper, less accurate tests are more akin to home pregnancy tests—though with saliva instead of pee. SalivaDirect still requires testing in a laboratory involving a specialized machine to run the RT-qPCR.



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