Jason Botten and Emily Bruce, who developed an optimized COVID-19 test with no scarce chemicals in their research lab at the University of Vermont's Larner College of Medicine. The machine between them is used to measure the presence and amount of viral RNA in patient samples. Photo credit: Brian Jenkins
A major obstacle to large-scale testing for coronavirus infection in developing countries is the lack of key chemicals or reagents needed for the test, especially those used to extract the genetic material or RNA of the virus.
A team of scientists from the University of Vermont, working with a group from the University of Washington, has developed a test method for the COVID-19 virus that does not use these chemicals but still gives an accurate result. Paving the way for low-cost, widespread testing in both developing and industrialized countries such as the United States, where reagent supplies are again scarce.
The method for the test, published October 2 in PLOS Biology, skips the step of the widely used reverse transcription polymerase chain reaction (RT-PCR) test, which requires the scarce reagents.
92% accuracy, only the slightest viral load is missing
The accuracy of the new test was assessed by a team of researchers at the University of Washington, led by Keith Jerome, director of the University's Molecular Virology Lab, using 215 COVID-19 samples that RT-PCR tests had shown they were positive with a range of viral loads and 30 that were negative.
92% of the positive and 100% of the negative samples were correctly identified.
The positive samples that the new test failed to catch had very low levels of virus. Public health experts increasingly believe that highly sensitive tests that identify people with even the lowest viral load are not needed to slow the spread of the disease.
"It was a very positive result," said Jason Botten, an expert on RNA pathogenic viruses at the University of Vermont's Larner College of Medicine and senior author of the PLOS Biology Paper. Bottens colleague Emily A. Bruce is the newspaper's lead author.
"You can take the perfect test or you can use the test that the vast majority of people pick up and stop transmission," said Botten. "With the game now focused on finding people who are contagious, there is no reason why this test shouldn't be a priority, especially in developing countries where there are often limited testing programs due to reagent and other supply shortages . "
Skip a step
The standard PCR test consists of three steps, while this simpler version of the standard test only has two steps, Botten said.
"In step 1 of the RT-PCR test, take the swab with the nasal specimen, clamp the end, and place it in a vial of liquid or medium. Any virus on the swab will be transferred from the swab to the medium." he said. "In Step 2, you take a small sample of the virus-containing media and use chemical reagents, which are often in short supply, to extract the viral RNA. In Step 3, you use different chemicals to highly amplify any viral gene material that may be present If a virus was present, you will get a positive signal. "
The new test skips the second step.
"It takes a sample of the medium containing the nasal swab and goes straight to the third amplification step," said Botten, which eliminates the need for scarce RNA extraction reagents and significantly reduces the time, effort, and cost of extracting viruses RNA from the medium in step 2.
Botten said the test is ideal for screening programs in developed and developing countries because it is inexpensive, requires much less processing time, and reliably identifies those likely to spread the disease.
The low cost and efficiency could expand testing capacity to groups not currently being tested, Botten said, including asymptomatic nursing home residents, essential workers and school children. The standard RT-PCR test could be reserved for groups such as health care workers where near 100% accuracy is essential.
An influential form indicates widespread acceptance of the test
The two-step test developed by the University of Vermont team first caught the attention of the scientific community in March when preliminary results, accurately identifying six positive and three negative Vermont samples, were pre-printed in bioRxiv, an open access repository for the biological Sciences. The preprint was downloaded 18,000 times – in the first week it was ranked 17th out of 15 million articles published by the website – and the abstract was viewed 40,000 times.
Botten heard from laboratories around the world who had seen the preprint and wanted to learn more about the new test.
"They said, 'I'm from Nigeria or the West Indies. We can't test and people's lives are at stake. Can you help us?'"
Botten also heard from Syril Pettit, director of HESI, the Institute for Health and Environmental Sciences, a nonprofit that is gathering scientific expertise and methodology for addressing a range of global health challenges, who also saw the preprint.
Pettit asked Botten to join a think tank of like-minded scientists whose goal was to increase global testing capacity for COVID-19. The test developed by the University of Vermont and University of Washington teams would serve as the centerpiece. To catalyze a global response, the group published a call to action in EMBO Molecular Medicine.
And action has been taken to reach 10 laboratories in seven countries including Brazil, Chile, Malawi, Nigeria, and Trinidad / Tobago, and the US and France, to see if they would be interested in doing the two-step test a trial run. "Generally the answer was yes," said Pettit.
Public relations led to a new HESI program called PROPAGATE. Each of the laboratories on the PROPAGATE network use the two-step test on a series of positive and negative samples sent to them by the University of Washington to see if they can replicate the results obtained by the university.
The study has already shown promising results. One of the laboratories in Chile also used the test on its own samples from the community and achieved precise results.
Assuming all goes well, Pettit and her colleagues at the University of Vermont and the University of Washington, as well as scientists from the 10 partner locations, plan to release the results.
"The goal is to make the two-step test available to any laboratory in the world that is facing these hurdles and to achieve broad acceptance," she said.
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The new COVID test does not use scarce reagents and catches all but the least infectious (2020, October 2nd).
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