Rapid, Portable COVID-19 Test Could Help Track Variants

A new viral screening test could not only diagnose COVID-19 in a matter of minutes, but new research suggests it could simultaneously test for other viruses that might be mistaken for COVID-19, according to the study authors. In addition, the test can sequence the virus, providing information on the spread of COVID-19 variants.

The test, called nanopore sequencing of isothermal rapid viral amplification for near real-time analysis (NIRVANA), was described by a team of researchers in the journal Med. According to a press release, one of the test’s major benefits is its small, pocket-sized portability.

“This is a virus detection and surveillance method that doesn’t require an expensive infrastructure like other approaches,” said co-corresponding author Juan Carlos Izpisua, in the press release. “We can accomplish with 1 portable test the same thing that others are using 2 or 3 different tests, with different machines, to do.”

The current standard approach for COVID-19 testing is to use a nasal swab and run a polymerase chain reaction (PCR) test to detect genetic material from the SARS-CoV-2 virus. If the sample is negative, however, the researchers said clinicians have no information on what could be causing the patient’s symptoms, unless they run separate PCR tests for other viruses. On the other hand, if the sample is positive for SARS-CoV-2, clinicians still do not know which COVID-19 variant a patient is infected with.

To address these problems, researchers at King Abdullah University of Science and Technology in Saudi Arabia developed an isothermal recombinase polymerase amplification (RPA) testing approach and combined it with real-time nanopore sequencing. The resulting test is faster, cheaper, and more portable than the current COVID-19 testing approach, according to the press release.

Unlike PCR tests, which cycle through lower and higher temperatures to separate DNA strands and copy them, RPA uses proteins to accomplish the same thing in just 20 minutes. The technology allows researchers to copy longer stretches of DNA and probe for multiple genes at the same time.

“We quickly realized that we could use this technique to not only detect SARS-CoV-2, but other viruses at the same time,” said developer Mo Li, an assistant professor of bioscience at King Abdullah University of Science and Technology, in a press release.

The investigators designed NIRVANA to simultaneously test samples for COVID-19, influenza A, human adenovirus, and non-SARS-CoV-2 human coronavirus, according to the press release. In their article, the researchers said the device begins to report positive and negative results in just 15 minutes, and it finalized results on all 96 samples within 3 hours. This includes the sequencing of 5 regions of SARS-CoV-2 that are particularly prone to accumulate mutations leading to new variants, according to the press release.

Researchers tested NIRVANA on 10 samples known to be positive for SARS-CoV-2, 60 samples of unknown SARS-CoV-2 status, and samples of municipal wastewater harboring the SARS-CoV-2 virus and others. In all cases, the assay correctly identified which viruses were present, according to the press release. The data also allowed the investigators to narrow down the origin of SARS-CoV-2 in positive samples, such as differentiating strains from China and Europe.

“The design of this assay is really flexible, so it’s not just limited to the examples we’ve shown,” Li said in the press release. “We can easily adapt it to tackle another pathogen, even something new and emergent.”

Based on their findings and considering the small size and portability of the test, the investigators said it could be used for fast virus detection in schools, airports, or ports, and it could also be used to monitor wastewater or streams for the presence of new viruses.

“The pandemic has provided 2 important lessons: first, test widely and quickly, and second, know your variants,” explained Izpisua Belmonte, a researcher at Salk, in the press release. “Our NIRVANA method provides a promising solution to these 2 challenges not only for the current pandemic, but also for possible future ones.”

REFERENCE

Fast, Portable Test Can Diagnose COVID-19 and Track Variants [news release]. Salk; March 31, 2021. https://www.salk.edu/news-release/fast-portable-test-can-diagnose-covid-19-and-track-variants/. Accessed April 5, 2021.