Clinicians using the Novel Coronavirus screening test can not only diagnose COVID-19 in minutes with a portable device, but also simultaneously test for other viruses, such as influenza — which could be mistaken for the Novel Coronavirus, according to the report. At the same time, they can sequence the virus, providing valuable information on COVID-19 mutations and the spread of mutations. The new test, called NIRVANA, was described online March 31, 2021, in the Journal Medicine by a team of scientists from multiple institutions.
“This is an approach to virus detection and surveillance that does not require the use of expensive infrastructure as other methods,” said Juan Carlos Izpisua Belmonte, study co-corresponding author and professor in Salk’s Gene Expression Laboratory. “We can use one portable test to do the same thing that people do with two or three different tests with different machines.”
Around the world, more than 100 million people have been infected with SARS-CoV-2, the virus that causes COVID-19. To date, more than half a million Americans have died from COVID-19 — a staggering number. Testing people is key to stopping the spread of the virus. In addition, it is crucial to track the spread of new SARS-CoV-2 variants — some of which may respond differently to treatment or vaccines.
The current standard method for determining whether a nasal swab is positive for COVID-19 is a polymerase chain reaction (PCR) test to detect the genetic material of the SARS-CoV-2 virus. However, if the sample is negative, the patient and clinician don’t get any information that could lead to the Novel Coronavirus-like symptoms — unless they use separate PCR tests for other viruses using a different swab sample. And if the sample is positive for SARS-CoV-2, they won’t know which variant of COVID-19 the patient has unless they run another set of tests; The tests require a large and expensive next-generation gene-sequencing machine.
Last summer, Li Mo, an associate professor of biological sciences at King Abdullah University of Science and Technology in Saudi Arabia, was thinking about how his expertise in genetic engineering and nanopore sequencing could be used to fight the COVID-19 pandemic. Lemer, who previously spent six years as a Salk Postdoctoral fellow in Izpisua Belmonte’s lab, wondered whether a genetic test called isothermal recombinase polymerase amplification (RPA), combined with real-time nanopore sequencing, would be more useful than current COVID-19 tests, as well as being faster, cheaper and more portable. He teamed up with Izpisua Belmonte to find out.
Unlike PCR, which uses lower and higher temperature cycles to separate DNA strands and replicate them, RPA uses proteins to do the same thing in as little as 20 minutes, rather than temperature changes. The technique allows researchers to copy longer segments of DNA and detect multiple genes simultaneously.
“We quickly realized that we could use this technique not only to detect SARS-CoV-2, but also to detect other viruses,” Lemer said.
In the new paper, Lemer and Izpisua Belmonte describe a small, portable device that can simultaneously screen 96 samples using the RPA assay. They call the method NIRVANA for “Nanopore sequencing for isothermal rapid viral amplification for near real-time analysis.”
The scientists designed NIRVANA to simultaneously test samples for COVID-19, influenza A, human adenovirus and non-SARS-CoV-2 coronavirus. Within as little as 15 minutes, the device began reporting positive and negative results, the researchers reported. Within three hours, the device would finally determine the results for all 96 samples — including the sequence of five regions of SARS-CoV-2 that are particularly prone to accumulating mutations that lead to new ones, such as the B.1.1.7 mutation found in Britain.
Li Mo and Izpisua Belmonte tested NIRVANA on 10 samples known to be SARS-CoV-2 positive, 60 samples with unknown SARS-CoV-2 status, and samples of municipal wastewater that harbors SARS-CoV-2 virus. In all cases, the test correctly identified which viruses were present. The sequencing data also allowed them to narrow down the source of SARS-CoV-2 in positive samples; For example, distinguish between strains from China and Europe.
“The design of this test is really flexible, so it’s not limited to the example we showed,” Lemer said. “We can easily tweak it to deal with another pathogen, or even something that’s new.”