Researchers from UC Berkeley and Gladstone Institutes have developed a technology that could detect the coronavirus in five minutes based on Nobel Prize-winning CRISPR technology.
Last month, UC Berkeley professor Jennifer Doudna was awarded the 2020 Nobel Prize in chemistry for her codeveloping of CRISPR, a gene-editing technology. Researchers have been developing a novel CRISPR-based diagnostic that is fast, portable and inexpensive.
“COVID-19 has made it clear that we urgently need better options to rapidly diagnose infections,” Doudna said in an email. “CRISPR is normally discussed as a way to find and edit specific DNA sequences, but it can also be used as a precision diagnostic tool.”
The research began at the start of the COVID-19 pandemic as a collaboration between Doudna, Melanie Ott of the Gladstone Institute of Virology at UCSF and Dan Fletcher of UC Berkeley. The research brings together concepts from Doudna’s work in CRISPR, Fletcher’s work in mobile phone cameras and Ott’s experience with biology labs.
To detect the virus, the CRISPR test recognizes a sequence of RNA in the SARS-CoV-2, the coronavirus that leads to the disease COVID-19. It does this by making a “guide” RNA that is complementary to the target RNA.
Once the guide binds to the target, the CRISPR-Cas13a enzyme, an RNA-editing technique and detection assay, is activated and starts cutting any nearby single-stranded RNA, according to Ott. These cuts then release a separate fluorescent particle into the test solution that can be detected with a laser light if the virus is present.
What makes this test novel, according to Ott, is the use of a mobile phone reader instead of the usual $30,000 plate readers used in labs.
In addition to being fast and mobile, the test is quantitative, which is different from all other tests currently on the market, according to Ott.
“The main advantages of the CRISPR-based diagnostic tests we’re developing are that they can be done quickly at the point of need (no laboratory necessary), and they can be easily tailored to a specific pathogen,” Doudna said in an email. “This is especially helpful in places with limited access to testing, and in cases like the current pandemic where frequent, rapid testing is needed.”
According to Ott, the idea for the portable mobile camera came from the scarcity of resources during the lockdown, something that she described as a “nightmare.” With the high availability of mobile phones, researchers just needed additional optics and a small laser to illuminate the fluorescence.
Another advantage of the test is that no amplification is required.
Typically, most tests for viral diagnostics involve amplification, meaning that small amounts of RNA are reverse transcribed into DNA and then amplified, according to Ott. She added that many CRISPR tests also involve some sort of amplification prior to using CRISPR for detection.
However, this diagnostic does not amplify the coronavirus RNA to make it “abundant enough” to be detectable. Rather, this assay is a one-step process, which can directly detect the RNA, according to Ott.
“We have a ways to go before CRISPR-based diagnostics reach widespread use, but I believe we’ll see an impact during the current pandemic,” Doudna said in an email. “Because it is simple to adjust these tests to detect other targets, the platform we’re developing now is laying the groundwork to deploy CRISPR for rapid diagnosis during future outbreaks.”