Since mid-March, when the World Health Organization declared that the outbreak of a pneumonia-like disease called COVID-19 had reached pandemic status, determining exactly how widespread the disease is has been an ongoing challenge. Many areas of the country hit hard by the disease still have not had adequate testing capacity, so properly quantifying the number of people in an area with the disease has been difficult.
And the testing we have currently is a bit unwieldy. Until now, testing has required that a health care worker insert a long stick with a small bit of cotton on the end — a tool called a nasopharyngeal swab — deep into the nose to reach the back of the nose and throat. Then, the health care worker gently scrapes the back of the nose and throat to collect a sample of nasal secretions that may contain viral particles that would indicate that the person is infected with the SARS-CoV-2 virus that causes COVID-19.
This swab is then taken to a lab where it’s processed and tested using an established protocol. A few hours, days or, in many cases, a week or two later, a test result comes back, and the patient is told whether they’re positive or negative for the virus. It’s a laborious and time- and resource-intensive process that requires a steady stream of supplies and health care workers who are potentially in harm’s way when collecting the samples from patients.
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The Importance of Testing
Testing is a critical piece of controlling this pandemic, especially for colleges and other institutions that are trying to reopen safely. Knowing who has the virus can help organizations isolate infected individuals to prevent onward spread within the community. But this requires widespread and consistent access to fast and reliable testing options, which has been a major stumbling block in this country.
As such, there’s been an urgent need to speed up, simplify and expand testing to better get a grip on where and how quickly the virus is moving through communities. Researchers and companies have responded by developing new technologies, tools, methods and options for better quantifying the prevalence of the disease in communities across the country.
On Aug. 15, one such new method, called SalivaDirect, received an emergency use authorization from the Food and Drug Administration — the first EUA awarded to a protocol for testing — to permit the wider use of this method. It’s currently available in some labs and will be expanding to other locations as the team that developed the test assesses and approves additional laboratories to use the protocol.
SalivaDirect is a method, not a testing kit, explains Anne Wyllie, an associate research scientist at Yale School of Public Health. Wyllie is part of the project team at Yale that developed the method, which stemmed from the group’s research over the past decade with saliva in other contexts. Suddenly, with the coronavirus pandemic, their work had a new urgency and relevance to the national conversation.
“There was a lot of discrepancy at the start of the pandemic about whether saliva was any good and how does it compare to (samples collected with) swabs,” because many labs and researchers just didn’t have that much experience working with it. But for the Yale team, “I think what has worked for us is that we have experience working with saliva,” Wyllie says.
“Up to now, the nasopharyngeal swab has been the gold standard” for testing says Adriana Rosato, executive director of molecular microbiology diagnostics-research at Riverside University Health System in Riverside, California.
“With the swabs there’s one standard protocol and standard approach that have been refined over the years for processing nucleic acids,” the genetic materials that can indicate the presence of a virus “from swabs, but no one was using saliva,” Wyllie says.
The Yale team’s work, however, suggests that saliva might actually be a better option for screening for the novel coronavirus in this pandemic situation. Because it’s lower-tech, cheaper and less invasive to collect, saliva may well be the superior option, but because few labs had experience with using it, it was passed over for the tried-and-true swab sample approach early on.
So, the team got to work and came up with a new method for authorized labs to use saliva as the sample rather than nasal secretions using a nasopharyngeal swab. The team is now working on authorizing labs across the country to use this protocol under the EUA issued by the FDA.
How it Works
A primary difference between this approach and methods that have been in use for the past several months is that the SalivaDirect approach eliminates the need for nasopharyngeal swabs. Instead, with this approach the patient spits into a sterile collection tube.
The tube is sent to a lab where it’s processed, using a similar method to what’s used for nasopharyngeal swab samples. However, the team have eliminated a step in the process that can be time-consuming and expensive, making it more accessible to a wider number of labs and a little faster to run.
Rather than extracting RNA, the sample is mixed with a reagent chemical and is heated, which releases the viral particles. Plus, there are several different reagents that can be used, reducing the risk of supply chain shortages or lack of availability with a single chemical — which can be an issue with nasal swab testing.
Advantages of SalivaDirect
This new protocol for COVID-19 testing offers several advantages:
— Easier collection.
— Cost savings.
— Flexibility and efficiency.
Easier Sample Collection
Having the swab inserted all the way into the nasal cavity can be an uncomfortable process for many folks, so the hope is that more people will be willing to take a COVID-19 test if that discomfort can be eliminated. This more comfortable collection process means the frequent testing needed to gain the upper hand on transmission will be easier to conduct.
In addition, when a health care worker collects a sample using a nasopharyngeal swab, they must come into close contact with a patient who’s potentially infected with COVID-19, putting that worker at increased risk of contracting the virus. Removing the swab from the equation also removes the need for a health care worker to collect the sample. The patient can simply spit in the tube, seal it and hand it over, keeping health care workers safer from infection.
The American Society for Microbiology, however, does note that saliva isn’t as readily collectable from some patients, and there’s a risk of aerosolizing the virus when spitting. It’s also possible to contaminate the outside of the container, so care still needs to be taken when collecting samples. Currently, SalivaDirect is not being used as a take-home test and requires a qualified health care professional for sample collection, but it’s possible that in the future this method may be applied to at-home sample collection.
Current testing methods typically cost anywhere from $60 to $150 per test. The group reports that it expects most labs to charge about $10 per sample for a SalivaDirect test. Wyllie notes that “we removed the RNA extraction step from the more standard PCR assay, and that’s what can bring the cost down by so much.” They also found that for this particular test, there’s no need for preservatives or specialized tubes for saliva collection, which also lowers costs. Plus, eliminating the need for swabs — which are in short supply in many areas — also eliminates a source of cost.
Flexibility and Efficiency
Because there are options for using different reagents in the testing process, that eliminates some of the supply chain issues that have plagued the standard testing protocol. Similarly, there’s no specific container that must be used to collect the sample, meaning that any tube or vessel can work and, with proper disinfection, could be reused.
There’s also no proprietary equipment required to process the samples. What would normally be found in an a lab that’s authorized and capable of running PCR testing can run this protocol.
Rosato notes that results won’t necessarily be available faster, as speed of receiving results can be dependent on a number of factors, including how many tests a particular lab has to run, but this method can eliminate some issues surrounding shortages of test collection equipment that can delay testing or limit its availability. The hope is that this alternate method of testing will increase speed of reporting because eliminating the RNA extraction step can make for faster test processing.
Rosato notes that while the sample is more accessible and less traumatic to collect than when using a nasopharyngeal swab, “the accuracy is not 100%. Studies show accuracy between 85% and 95%,” when compared to the standard nasal swab approach. It seems, however, that “the concentration of COVID virus may be higher in saliva than at the back of throat and nose,” Rosato says, which might make this approach better at detecting positive results for individuals with a low viral load or few or no symptoms.
According to a study done at Yale, saliva samples taken from just inside the mouth were more accurate and consistent than deep nasal swabs taken from 44 patients and 98 health care workers. This higher prevalence of viral particles in saliva makes it a “promising candidate” for COVID-detection, the study noted. Additionally, there was less variability in results with the self-sample collection of saliva.
The Yale team has also been conducting a study to detect whether SalivaDirect can accurately detect asymptomatic cases through a partnership with the National Basketball Association and the National Basketball Players Association called Surveillance with Improved Screening and Health or SWISH. That involves collecting samples from players and staff using both the standard test approach and Saliva Direct and comparing the outcomes. Results are expected soon.
Testing = Knowledge = Power
Wyllie reiterates that SalivaDirect is a protocol, not a kit. There’s no product or company involved, and this isn’t an at-home test that will be made available to the public or that you can pick up at the store. There’s no commercial interest for the group at stake here.
Rather, this is a method that authorized labs around the country can use to run more COVID-19 tests more efficiently and at lower cost. The team is continuing to work on additional advances and innovations that may further increase the number of tests that can be run across the country every day.
The Yale group notes that their method “won’t solve everything,” but it can improve the efficiency of testing for population screening. The hope is that this method may lead to other innovations that make testing even easier, cheaper and more widely available to help bring this pandemic to a halt. As such, this may be one piece to solving some of the testing issues currently plaguing the U.S. in the quest to control the coronavirus pandemic.
“We are hopeful that the new test will help us increase testing capacity with cheaper and simpler options,” Rosato says.
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