Imagine it’s flu season and that tickle in the back of your throat has turned into symptoms bad enough to drive you to visit your doctor. Your physician would ideally run some tests to diagnose what pathogen is afflicting you, but unless they are at a large hospital, they may not have access to the complicated, costly tests they need. That’s the conundrum Princeton University researcher Cameron Myhrvold  and his collaborators at the Broad Institute, Yibin Zhang, Jon Arizti-Sanz, and Pardis Sabeti, aim to solve in their paper appearing June 18th in The Journal of Molecular Diagnostics.

To treat an illness, a doctor needs an accurate diagnosis. For example, it would be helpful to know whether a patient does in fact have flu or if they might instead have one of the myriad other respiratory illnesses. If the patient has flu, is it a seasonal influenza A virus such as H1N1, or could it be a less common influenza B virus that carries greater risk of hospitalization? Is the patient’s infection resistant to available antiviral medications?

Currently, none of these questions can be answered without undertaking expensive and technically demanding molecular tests. But what if doctors or patients could take a simple nasal swab, drop it in a tube, and answer all of these questions without needing any special equipment or training? That’s the promise of SHINE, a new diagnostic technology being pioneered by researchers at Princeton University and the Broad Institute of MIT and Harvard.

“Our ultimate goal is to make SHINE as easy to perform as a rapid antigen test, so that it will be easy for people to do self-testing at home,” said Cameron Myhrvold, Assistant Professor in the Department of Molecular Biology at Princeton.

SHINE, short for Streamlined Highlighting of Infections to Navigate Epidemics, delivers the  accuracy and versatility of CRISPR-based diagnostics in a fast and convenient format usable by clinics and medical offices that lack access to well-equipped molecular biology laboratories and the personnel needed to run them. It works by using CRISPR-Cas complexes that can accurately zero in on genetic sequences unique to a particular type of pathogen with the help of “CRISPR RNAs” complementary to those sequences. Upon locating a target sequence, the modified CRISPR-Cas complexes activate an enzyme that produces a fluorescent signal in the test solution or a color change on a strip of paper to flag up the presence of the target pathogen in laboratory or clinical samples.

“We originally developed SHINE for SARS-CoV-2 detection,” said Myhrvold.

Later, Myhrvold and colleagues developed a version of SHINE that could accurately distinguish between different SARS-CoV2 Variants of Concern, but the researchers knew they could do even more with SHINE. In their current work, the team developed versions of SHINE that can detect influenza A or influenza B virus infections in clinical samples, with accuracy comparable to gold-standard molecular tests but in a fraction of the time. The team also generated SHINE tests that can discern between the common H1N1 and H3N2 subtypes of seasonal influenza virus, as well as a version that can determine whether the virus has a mutation that confers resistance to the drug Oseltamivir (better known as Tamiflu). Knowing that a drug-resistant strain is present would let physicians change treatments.

Importantly, SHINE achieves all this in a convenient format; the test is easy to use and multiple samples can be processed in under 20 minutes. Larger organizations that conduct lots of tests can evaluate many SHINE tests at once using an inexpensive machine to monitor color changes in the test solution. For smaller clinics, doctors’ offices, or home users, the researchers developed a version of the test that delivers results on a paper strip (similar to at-home Covid tests) and can be stored at room temperature for long periods of time. Having already demonstrated several applications for SHINE, Myhrvold and his collaborators are now working to turn it into an even more versatile diagnostic platform. 

“We are developing assays for avian and swine flu strains, such as H5N1,” said Myhrvold. This virus has been making headlines and causing consternation among scientists and doctors due to its extreme contagiousness and lethality in animal populations, and fears that it could someday spread to humans.

“[We are also] developing assays for additional flu mutations so that we can track the virus as it evolves,” said Myhrvold. The benefits of rapid, inexpensive, and easy-to-use diagnostics cannot be overstated, especially as new pathogens emerge to assail us.

Citation: Yibin B. Zhang, Jon Arizti-Sanz, A’Doriann Bradley, Yujia Huang, Tinna-Solveig F. Kosoko-Thoroddsen, Pardis C. Sabeti, and Cameron Myhrvold. CRISPR-based assays for point of need detection and subtyping of influenza. Journal of Molecular Diagnostics. 2020. DOI: 10.1016/j.jmoldx.2024.04.004

Funding: Support for the work described in this story was provided by the Defense Advanced Research Projects Agency (D18AC00006); the Centers for Disease Control and Prevention (75D30122C15113); the Flu Laboratory;  the ELMA Foundation; MacKenzie Scott; Skoll Foundation; Open Philanthropy; and the Merck KGaA Future Insight Prize. 

Grant Numbers: D18AC00006, 75D30122C15113

Funders: Defense Advanced Research Projects Agency, Centers for Disease Control and Prevention, Flu Laboratory, ELMA Foundation, MacKenzie Scott, Skoll Foundation, Open Philanthropy, Merck KGaA Future Insight Prize