Skip to main content
Premium Trial:

Request an Annual Quote

Princeton-Led Group Develops Cas13 SARS-CoV-2 Assay for Point-of-Care Use


NEW YORK – A research group led by Princeton University scientists has developed a new Cas13-based approach for SARS-CoV-2 testing that allows for visual discrimination of the virus's most common variants.

The test can be prepared in a lateral flow format, requires no additional instruments, and can be run in at-home settings. The authors detailed the approach, dubbed SHINEv.2, in a Nature Biomedical Engineering paper published online on Monday.

Along with Princeton researchers, investigators from the Broad Institute, Harvard, the US National Institute of Allergy and Infectious Diseases, the US Centers for Disease Control and Prevention, Howard Hughes Medical Institute, and the African Center of Excellence for Genomics of Infectious Diseases also contributed to the work.

Cameron Myhrvold, an assistant professor of molecular biology at Princeton and corresponding author on the study, and his colleagues in November 2020 published a method called Streamlined Highlighting of Infections to Navigate Epidemics (SHINE) in Nature Communications, describing a diagnostics approach to detect SARS-CoV-2 from unextracted samples. This first generation, RNA-extraction-free method relies on recombinase polymerase amplification and Cas13-based detection and can be run on both nasopharyngeal swabs and saliva with an in-tube fluorescent readout, and interpreted via a smartphone application.

According to Myhrvold, the researchers wanted to improve on SHINEv.1 for several reasons. One was the emergence of new SARS-CoV-2 variants over the course of 2021, and thus a desire to produce a multiplex version of the SHINE assay that could cover the most important emerging variants. Another reason was to produce a version of the assay that could work at the point of care, as well as in lower-resource settings, and at ambient temperatures. Indeed, the SHINEv.2 method provides an underarm incubation step for the lateral flow version of the assay, where one holds the test cartridge under their arm to maintain the right temperature.

"We were working on some aspects of SHINEv.2, to make the assay easier to run and simpler, when the variants emerged," said Myhrvold in an interview.

As noted in the paper, the researchers sought to craft an approach that would have advantages over other tried-and-true SARS-CoV-2 diagnostic approaches, such as real-time PCR and antigen testing, as well as other CRISPR diagnostics.

The goal was to produce a sensitive, specific, multiplex method that could be run without cold storage for reagents and auxiliary equipment for heating steps. Such conditions, the authors wrote, had made other CRISPR diagnostics "not well poised for widespread deployment."

The authors' response to these needs was to employ lyophilized reagents, in this case the FastAmp lysis reagent purchased from Intact Genomics, which allowed them to eliminate the heating steps and a need for cold storage. In the paper, they benchmarked the approach by running it against PCR on nasopharyngeal samples and reported 90.5 percent sensitivity and 100 percent specificity in a lateral flow format, when used together with a heat block at 37 degrees Celsius. SHINEv.2 also supported the visual discrimination of the Alpha, Beta, Gamma, Delta, and Omicron variants, and could also be run using body heat instead of the heat block.

"To me, the most exciting thing about SHINEv.2 is the simplicity of the method," commented Myhrvold. "We really try to make it as easy as possible for the user to perform a test," he said, citing the underarm incubation method. He noted that SHINEv.2 compared favorably with PCR when tested on patient samples, and noted it was "a lot more sensitive" than antigen tests, which he said had a level of detection about 50 times lower. In the study, the investigators tested their approach against Abbott's BinaxNow and Access Bio's CareStart COVID-19 antigen tests.

But it's the ability to detect different variants in a lateral flow format that Myhrvold said was particularly compelling. "Rapid antigen tests can do simple testing, but SHINE is more sensitive, and antigen tests cannot tell you what variant you have," he said.

The obvious use case for SHINEv.2 is point-of-care and at-home settings, but rugged environments could also benefit from the introduction of such a test. For this reason, the researchers liaised with partners in Nigeria to trial SHINEv.2. As part of this, they worked with Christian Happi, director of the World Bank-funded African Center of Excellence for Genomics of Infectious Diseases at Redeemer's University in Ede. Happi, as well as paper coauthor Pardis Sabeti, are also involved with Sentinel, a large-scale pandemic prevention effort in West Africa.

"We sent them SHINE pallets, and they have implemented SHINE there and got it to work," said Myhrvold of the collaboration. "They confirmed this approach could be translated around the world."

In the paper, the authors note that the approach could be used to inform public health responses, by helping to prioritize testing and vaccine rollout in highly affected communities, or to select subsets of samples for further viral sequencing. SHINEv.2 could also be used to select therapies for COVID-19 patients.

"We believe that SHINEv.2 will be especially valuable for community surveillance testing," the authors wrote.

"We are focused mostly on lower resource, or point-of-need, point-of-care settings," confirmed Myhrvold. "Ultimately, we think the technology could be used for self-testing, like antigen tests. We like that it is visual, you can take a photo of it with a smartphone, like a rapid antigen test."

But how such a test would reach the market is unclear. "The commercial path is complicated," Myhrvold acknowledged, as there are multiple CRISPR diagnostics companies that could potentially license SHINEv.2.

One of those is Sherlock Biosciences, based in Cambridge, Massachusetts, which was founded in part to commercialize the SHERLOCK CRISPR platform that Myhrvold, Sabeti, and others helped to develop while at the Broad. Sabeti is also a cofounder of Sherlock, and serves on the board of Danaher. Sherlock has also worked to deploy SARS-CoV-2 detection assays based on its technology.

Myhrvold said it was "hard to say" how SHINEv.2 could be commercialized, as various CRISPR diagnostic companies have their own internal diagnostics efforts. "It is not clear if they would use what they have already developed," he said, "or use specific improvements we made."

The subject of cost is also "tricky," he noted, as it would depend on the scale of production.

Myhrvold and fellow researchers will continue to innovate on SHINEv.2 though. One goal is to reduce the assay time (currently about 90 minutes), which is faster than PCR but trails antigen testing. And if it could lose the need for a heating block or underarm incubation too, that would also be an improvement. "We would love to see a version of the test in the future where you don't need any of that."

Myhrvold is also keen to see SHINEv.2 be adopted more broadly for infectious disease testing for other pathogens aside from SARS-CoV-2, though he declined to name any potential indications of interest at this time.

"There are lots of pathogens you'd want to detect easily," he said.