The U.S. 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 can deliver deficiencies that plague 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 protocol fully open and available.
If the protocol is widely adopted, it could help improve the country’s COVID-19 testing, which is currently expensive. Some patients sit for weeks waiting for results. With such long delays, contacts do not have a chance to reach the exposed person before they have a chance to pass on the infection. The delays stem from the sheer volume of tests that come in, such as lack of critical supplies, such as nasal swabs and chemical reagents needed to perform the tests. SalivaDirect attempts to address both of these issues.
How standard testing works
The new test is basically a streamlined version of the current standard for diagnostic testing of COVID-19. In general, 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 instead of DNA.
The basic steps of the test begin with placing a long pennant far in a person’s nose until it hits the back – a nasopharyngeal exchange – to try and scrape off any SARS-CoV-2 that may be present. . The swab picks up all sorts of things, of course, including snot, pieces of human cells from the nose, highly viral particles, and any other germs that may be present. To clean the starting material, most test protocols then ask for a test that simply extracts the genetic material, and removes all debris and incomprehensible bits. This requires time and specific reagents, which may be in short supply.
Then, the isolated genetic material goes to a second assay called an RT-qPCR, as a quantitative reverse transcription-polymerase chain reaction. In it, bits of RNA are converted to DNA, which is then examined for sequences present only in SARS-CoV-2. If these sequences are present, small fragments of synthetic DNA – called primers – attach to the SARS-CoV-2 code and direct enzymes to make copies of that piece of DNA. The copies are cleverly designed to fluoresce as they are 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 produce a to detect fluorescent signal above background.
Cut 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 ‘Cycled Threshold’, as Ct. If the Ct is low, say below 30 cycles, suggesting that there was a good amount of RNA to begin with, perhaps from a raging infection. If it is above, say 37, then it means that there was not much SARS-CoV-2 RNA in the sample, perhaps from a fading infection or genetic remnants of a recently terminated infection.
For diagnostic tests, the Ct value is not necessarily useful – if you have any amount of SARS-CoV-2 RNA in your nose, you are or have been recently infected. The test does not indicate any infections or exposure to the virus in the past. But comparing the Ct values between different tests for SARS-CoV-2 is useful to compare how sensitive each given test is.
For the SalivaDirect test, Yale researchers cut some corners without losing much in accuracy or sensitivity. First, with the worldwide shortage of swabs, they skipped the stick and just went to spit. They verify that SARS-CoV-2 is present in saliva because 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 samples. Between the paired nosebands and saliva samples, there was 83 percent agreement. Almost all were positive, but three nasal swabs and three different saliva samples came back negative, invalid, or incomprehensible. They also found that in collected saliva the virus was stable for up to seven days at 4 ° C, room temperature, as high as 30 ° C without the addition of preservatives.
The researchers then completely skipped the RNA extraction step. Instead, they heated the saliva samples together with an enzyme called proteinase K, which removes all the protein debris in the sample – human cells, highly viral particles, and so on. – and let the SARS-CoV-2 RNA stand. This is convenient because the extraction step takes extra time and the reagents used in the assay are currently in short supply. Finally, the researchers streamlined the RT-qPCR by combining a few steps and saw even more 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 SalivaDirekt to standard lab tests on saliva, the tests were matched 97 percent of the time for positive samples and 100 percent on negative samples. The researchers did not see any false positive results in any of their experiments.
To do some of her validation work, Yale teamed up with the National Basketball Association to test players and staff in the NBA bubble. The NBA funded the investigation in part.
Based on list prices of used materials, researchers estimate SalivaDirect costs anywhere from $ 1.29 to $ 4.37 per sample, depending on whether a lab chooses to use a saliva collection. This is cheaper than the current standard tests, which experts estimate in the range of $ 15 to $ 50 per sample for materials. Yale researchers suggest labs pay $ 10 for a SalivaDirect test.
“Widespread testing is critical to our control efforts,” Nathan Grubaugh, one of the test developers and professor at Yale School of Public Health, said in a news release. “We have simplified the test so that it only costs a few dollars for reagent, and we expect labs to pay only about $ 10 per sample. If cheap alternatives like SalivaDirect can be implemented across the country, we can finally get a grip on this pandemic, even for a vaccine, ”he said.
Step in the right direction
On Saturday, August 15, the FDA granted SalivaDirect an authorization for emergency use. “The SalivaDirect rapid detection test of SARS-CoV-2 is yet another innovation game changer that will reduce the demand for scarce test resources,” said Assistant Secretary to Health and COVID-19 Test Coordinator Admiral Brett Giroir in a statement. . Although the FDA noted that it approved four other COVID-19 tests that use saliva, those tests had “variable performance.”
Although there has been a lot of fanfare around the authorization of SalivaDirect, it is important to note that it is so net a rapid, home test that some have suggested using on a daily basis to control the pandemic. Those cheaper, less accurate tests are more akin to tests for pregnancy at home – albeit with saliva instead of piss. SalivaDirect still requires testing in a laboratory with a specialized machine to perform the RT-qPCR.
