NEW YORK – Researchers from the University of California, Santa Barbara have developed an isothermal amplification-based SARS-CoV-2 and influenza test that could retail for as little as $2 while addressing a key problem with loop-mediated isothermal amplification tests — false positive results.
In a paper published on Friday in JAMA Network Open, its developers described using their method to detect and differentiate SARS-CoV-2 from the flu, and according to one of its developers the test can be used for a variety of infectious diseases and sample types.
Because LAMP tests are so sensitive, primer-dimer amplification can occur, where the primers and dimers of a test react with each other, leading to false positive results. But the new test has been developed with the ideal conditions to avoid this reactivity problem, said Michael Mahan, a professor at UCSB and one of the developers of the test.
It took his team 500 attempts and more than a year to create the exact conditions to avoid the primer-dimer problem, but now that it's been cracked, their LAMP test can deliver rapid, highly sensitive results for a fraction of the cost of PCR, he said, going "mano a mano" with the gold standard technology.
Developing those ideal conditions was like working with a "giant Rubik's cube," Mahan said, with the team trying out a variety of different things to get to the final master mix for the test — including changing the pH, the magnesium concentrations, the enzyme concentrations, and the dilution of the saliva sample.
During its development, Mahan said they realized that it is not only the composition of the mix but also the sequence of adding the different components that makes the difference to eliminate the primer-dimer problem. The "recipe" for this mix is included in the JAMA paper, allowing other researchers to replicate it and create their own LAMP tests, Mahan said.
The goal of making the recipe available to anyone is to reduce inequities around the world and promote low-cost, accurate SARS-CoV-2 tests to help nations with less access to testing, he said. And now that the primer-dimer problem has been solved, the recipe allows LAMP technology to be used for a variety of disease applications, he said.
Mahan's smartphone-based test specifically detects and distinguishes between SARS-CoV-2 and influenza A/B from saliva. The only requirements to run the test are a smartphone, which includes an app developed by Mahan's team, LED lights, the master mix, a hot plate, and a cardboard box. Those materials — excluding the master mix — Mahan said, could eventually be eliminated for an all-in-one device when the test is commercialized.
To perform the test, a user spits into a sterile cup and pipettes the saliva sample into a tube containing the optimized master mix. The tube is then placed onto the heat block and covered with the cardboard box, which has a small hole poked into it. The smartphone camera is placed over the hole to take photos of the mix, which will glow if any of the viruses are detected. The phone camera is used because it's better able to detect the fluorescence and the box is used to ensure there's no light interference, Mahan said.
As time passes, the mix amplifies the virus and glows, he said. The more virus that is present in the sample, the more the mix glows, which also allows the test to quantify the amount of virus, he said.
Once the sample has been placed into the tube and covered with the box, Mahan said the phone app developed by his team does all the work — a user doesn't have to manually take the photos but can just put the camera on the box and press a button. The app will then take a photo every 10 seconds to measure the change in the fluorescence, he said.
The app analyzes the photos taken by the camera, measuring the glow rate and returns a positive or negative result — a positive result can be returned within 15 minutes, with 25 minutes as the cutoff to receiving a result. The time to result can also depend on the saliva sample and whether it's been degraded by food or drink, he added.
Mahan's team tested the assay with five different variants and found it was able to detect all of them, he noted. While it hasn't been tested with Omicron and there are currently no plans to do so, the researchers used a bioinformatics tool to predict the likelihood of the test detecting Omicron and found that it was "highly likely," he said. When developing the test, Mahan said the team stayed away from using the spike protein, since they knew it was "highly mutable." And if a variant arises that the test can't detect, only the primer would need to be changed, which wouldn't be hard, he added.
The primer change would also be necessary to detect other viruses, which Mahan's team has shown can be done, he said. The test has been used to detect urinary tract infections, Escherichia coli, and Staphylococcus in humans, as well as Streptococcus in mice, he said. It can also use different sample types, including blood, urine, and feces, he said.
"It's just a matter of primer design," he said.
Although the JAMA study found 100 percent concordance with PCR and sensitivity and specificity of 95 percent, Mahan noted that it was limited to only 50 patients due to difficulty getting samples. When performing the study, the team followed the guidelines laid out by the US Food and Drug Administration for a test to receive Emergency Use Authorization, for which the researchers plan to submit.
He added that they have had some minor discussions with potential partners for commercialization, but nothing has been formalized yet. To be commercialized, the test would likely need to come with a device that would include a way to heat the sample, as well as a box and light to capture the glow of the mix, he said. For the JAMA study, his team spent less than $100 on the device needed for the test. Right now, supplies are $7 per test, but Mahan said that it could eventually get down to between $2 and $3 per test. About 90 percent of the $7 price is enzymes, which Mahan said could "be easily cut in half with a large quantity purchase," reducing the price significantly.
Mahan emphasized that he doesn't want to patent the test and leave it on a shelf for only people with disposable income to buy — the "driving force" was to "get something to developing countries" to help with the pandemic, although he also sees "real applications" for the test in the US as well as a cheaper and more accurate at-home product than currently available rapid antigen tests.
"Until we get the world's population 90 percent vaccinated … these tests are going to be very important," he said.