Fast, Portable Test Can Diagnose COVID-19 and Track Variants

If the sample is negative, however, patients and clinicians don’t get any information on what might be causing the coronavirus-like symptoms - nless they run separate PCR tests, using different swab samples, for other viruses. And if the sample is positive for SARS-CoV-2, they don’t learn which COVID-19 variant a patient is infected with unless another set of tests is run; those require a large and expensive next-generation gene-sequencing machine.

Researchers at The Salk Institute attempted to find out whether a gene-detection approach called isothermal recombinase polymerase amplification (RPA) coupled with real-time nanopore sequencing might be more useful—and faster, cheaper and more portable - than the current COVID-19 testing approach. Unlike PCR, which cycles through lower and higher temperatures to separate DNA strands and copy them, RPA uses proteins—rather than temperature changes—to accomplish the same thing in only 20 minutes. The technology lets researchers copy longer stretches of DNA, and probe for multiple genes at the same time.

The researchers have developed a small, portable device that can screen 96 samples at the same time using the RPA assay. They call the method NIRVANA, for “nanopore sequencing of 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 human coronavirus. In just 15 minutes, the researchers report, the device begins to report positive and negative results. And within three hours, the device finalizes results on all 96 samples—including the sequences of five regions of SARS-CoV-2 that are particularly prone to accumulate mutations leading to new variants such as the B.1.1.7 variant identified in the UK.

The researchers tested NIRVANA on 10 samples known to be positive for SARS-CoV-2, 60 samples of unknown SARS-CoV-2 status, as well as samples of municipal wastewater harboring the SARS-COV-2 virus and others. In all cases, the assay was able to correctly identify which viruses were present. The sequencing data also allowed them to narrow down the origin of SARS-CoV-2 in positive samples; differentiating strains from China and Europe, for instance. With the small size and portability of the NIRVANA workflow, it could be used for fast virus detection at schools, airports or ports, the researchers say. It also could be used to monitor wastewater or streams for the presence of new viruses.

“This is a virus detection and surveillance method that doesn’t require an expensive infrastructure like other approaches,” said Juan Carlos Izpisua Belmonte, co-corresponding author and a professor in Salk’s Gene Expression Laboratory. “We can accomplish with one portable test the same thing that others are using two or three different tests, with different machines, to do.”

Related Links:
The Salk Institute for Biological Studies