Researchers at the Salk Institute in California, working with outside collaborators, have developed a COVID-19 test that can rapidly identify and sequence the causative virus, helping to track new variants. The test, called “nanopore sequencing of isothermal rapid viral amplification for near real-time analysis,” (NIRVANA), can also simultaneously test for other viruses, such as influenza, that may cause similar symptoms.
As SARS-CoV-2 continues to mutate, health authorities are increasingly concerned about new variants being more dangerous, more transmissible, and more difficult to treat or vaccinate against. At present, a PCR test is required to spot SARS-CoV-2 and then additional genetic sequencing is needed to identify the viral variant, which requires bulky and expensive lab equipment. This new technology aims to combine these results in just one test, which is small and portable.
“This is a virus detection and surveillance method that doesn’t require an expensive infrastructure like other approaches,” said Juan Carlos Izpisua Belmonte, a researcher involved in the study, via a Salk press release. “We can accomplish with one portable test the same thing that others are using two or three different tests, with different machines, to do.”
The approach is called isothermal recombinase polymerase amplification (RPA). It uses proteins to separate and copy DNA strands in as little as 20 minutes, which is different from PCR, which requires temperature cycling to achieve the same thing. The technology also involves a technique called real-time nanopore sequencing, and it allows the researchers to sequence regions of the virus that are prone to mutation, helping them to track variants. Additionally, the test can assess samples for other viruses, such as influenza.
“We quickly realized that we could use this technique to not only detect SARS-CoV-2, but other viruses at the same time,” said Mo Li, another researcher involved in the study. “We can easily adapt it to tackle another pathogen, even something new and emergent.”
A small portable field test incorporates the technology, and can analyze 96 samples at a time. It could be useful for rapid screening in airports or schools. “The pandemic has provided two important lessons: first, test widely and quickly, and second, know your variants. Our NIRVANA method provides a promising solution to these two challenges not only for the current pandemic but also for possible future ones,” added Izpisua Belmonte.
Study in journal Med: Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing
Via: Salk Institute