The experimental CRISPR-based test, with further development, could potentially be used outside of labs.
Rapid COVID-19 test delivers accurate results with minimal equipment
Researchers at the Broad Institute of MIT and Harvard have developed a new COVID-19 test called SHINE that can identify 90 percent of samples with the SARS-CoV-2 virus and 100 percent of negative samples compared to the gold-standard RT-qPCR test. The test, still in the research stage, doesn’t require bulky and expensive equipment and could one day enable SARS-CoV-2 testing outside of hospitals and labs.
“It requires so much less infrastructure and lab space that you could imagine workers could get tested in the morning and get results back within an hour,” said Cameron Myhrvold, co-senior author of the new study published in Nature Communications. He is the Diagnostics Group Lead in the lab of Pardis Sabeti, a Broad institute member, a Harvard University professor, and co-senior author of the paper. “I could imagine that being done in a mobile testing truck that pulls up outside of a workplace to test employees,” said Myhrvold.
The standard qPCR-based SARS-CoV-2 test is accurate but requires multiple steps to inactivate the virus in samples, amplify the viral RNA, and then detect its presence. Each step takes time and equipment typically only available in specialized lab environments.
SHINE improves this process in multiple ways. First, it reduces the virus inactivation step to just 10 minutes. Second, it amplifies the RNA in the samples at a stable temperature, eliminating the need for some equipment. Third, it amplifies RNA and detects the presence of the virus in one step, further saving time and resources.
“SHINE makes the whole process simpler,” said Jon Arizti Sanz, a graduate student in the Sabeti lab and co-first author of the study. “You don't need to make the different mixes or change temperatures and you don't need to be transferring samples and reagents between steps, which reduces the risk of contamination.”
To detect the virus, SHINE uses the RNA-cutting CRISPR enzyme Cas13, which the researchers programmed to home in on SARS-CoV-2 RNA. When Cas13 finds its target in a sample test tube, it makes a series of cuts in the amplified viral RNA, triggering another molecule that’s part of the SHINE system to fluoresce. Shining a low-cost, specialized light on the test tube allows the fluorescent signal to be read and interpreted by a smartphone application the team developed.
In the 50 patient samples analyzed in the new study, SHINE returned the same result as the control qPCR test 94 percent of the time when using in-tube fluorescence. The team also incorporated SHINE into paper test strips, which generated the same results as the qPCR test 100 percent of the time.
The researchers say SHINE very rarely misidentifies other viruses as SARS-CoV-2, because the CRISPR-Cas13 system is programmed to specifically target only SARS-CoV-2 RNA. “It doesn't hit any other respiratory pathogens or other related coronaviruses that infect humans,” said Catherine Freije, co-first author of the study who recently was a research scientist in the Sabeti lab and is now a postdoctoral researcher at Rockefeller University.
The team hopes to bring SHINE to testing sites soon. They have partnered with a lab in Nigeria, which has been running a pilot of SHINE. They are also working on the next version of the technology to improve ease of use. The team recently entered SHINE into XPrize Rapid Covid Testing, a competition that will award $6 million to winning teams to develop and deploy rapid, scalable, and affordable COVID-19 tests.
“The pandemic has really helped us refocus our efforts on what really matters,” said Myhrvold.
Support for this research was provided in part by DARPA and the Open Philanthropy Project.