The revolutionary genetic technique better known for its potential to
cure thousands of inherited diseases could also solve the challenge of
Covid-19 diagnostic testing, scientists announced on Tuesday. A team
headed by biologist Feng Zhang of the McGovern Institute at MIT and the
Broad Institute has repurposed the genome-editing tool CRISPR into a
test able to quickly detect as few as 100 coronavirus particles in a
swab or saliva sample.
Crucially, the technique, dubbed a “one pot” protocol, works in a
single test tube and does not require the many specialty chemicals, or
reagents, whose shortage has hampered the rollout of widespread Covid-19
testing in the U.S. It takes about an hour to get results, requires
minimal handling, and in preliminary studies has been highly accurate,
Zhang told STAT. He and his colleagues, led by the McGovern’s Jonathan
Gootenberg and Omar Abudayyeh, released the protocol on their
STOPCovid.science website.
Because the test has not been approved by the Food and Drug
Administration, it is only for research purposes for now. But minutes
before speaking to STAT on Monday, Zhang and his colleagues were on a
conference call with FDA officials about what they needed to do to
receive an “emergency use authorization” that would allow clinical use
of the test. The FDA has used EUAs to fast-track Covid-19 diagnostics as
well as experimental therapies, including
remdesivir, after less extensive testing than usually required.
For an EUA, Zhang said, the agency will require his lab to validate
the test, which they call STOPCovid, on several samples. Although “it is
still early in the process,” Zhang said, he and his colleagues are
confident enough in its accuracy that they are conferring with potential
commercial partners who could turn the test into a cartridge-like
device, similar to a pregnancy test, enabling Covid-19 testing at doctor
offices and other point-of-care sites.
“It could potentially even be used at home or at workplaces,” Zhang
said. “It’s inexpensive, does not require a lab, and can return results
within an hour using a paper strip, not unlike a pregnancy test. This
helps address the urgent need for widespread, accurate, inexpensive, and
accessible Covid-19 testing.” Public health experts say the
availability of such a test is one of the keys to safely reopening
society, which will require widespread testing, and then tracing and
possibly isolating the contacts of those who test positive.
The scientists are also in discussions with the Gates Foundation
about distributing the testing kits. “It could be especially valuable in
places where there is not the capacity for centralized testing,”
Gootenberg said.
Other labs are also developing CRISPR-based Covid-19 tests. Last
month scientists at the University of California, San Francisco, and
Mammoth Biosciences
reported
that theirs takes roughly 40 minutes, compared with four to six hours
for the traditional swab tests (which use a biochemical reaction called
PCR and require numerous reagents). But that test appears to produce
false negatives slightly more often than the PCR test. It also requires
two steps, similar to one that Zhang developed in February; that adds
complexity and increases the chances that samples will
cross-contaminate.
Zhang’s February test is being used by hospitals in Thailand. But
with his colleagues, he has spent the last two months creating the
one-step version.
“The key advance for STOP is the simplification into a single-step
reaction, which prevents cross contamination during step-to-step liquid
transfers,” he said. “That makes it suitable for point-of-care use.”
Existing “home” Covid-19 diagnostic tests such as that from
LabCorp allow
people to collect the sample — that is, swab themselves — at home. The
actual test must be done at a lab. Currently approved point-of-care
Covid-19 diagnostic tests, such as Abbott ID NOW and Cepheid GeneXpert,
require specialized and expensive instrumentation and technical
expertise, limiting widespread use. Abbott’s has also been plagued by
false negatives, meaning it sometimes fails to detect the coronavirus.
STOP stands for “Sherlock Testing in One Pot.” It builds on Zhang’s 2017 CRISPR invention, called
Sherlock.
Like the better-known, genome-editing versions of CRISPR, Sherlock
starts with a guide molecule that homes in on a specific stretch of DNA —
or RNA, which constitutes the genome of the new coronavirus. An enzyme
called AapCas12b, from the bacterium Alicyclobacillus acidophilus, cuts
the RNA in a way that generates a fluorescent signal detectable much as
home pregnancy tests detect the presence of a pregnancy-related hormone.
For STOP, the scientists targeted their guide molecule at the
coronavirus’s N gene, which codes for the nucleocapsid, or shell, that
encloses its genome. The
PCR test developed by the Centers for Disease Control and Prevention also targets the N gene.
The MIT scientists tested STOP on nasopharyngeal swabs from Covid-19
patients and on saliva samples from healthy people to which the new
coronavirus was added. STOP had 100% specificity — it never “found” the
coronavirus if the microbe wasn’t really there — and 97% sensitivity,
meaning if the virus was present, the test missed it only 3% of the
time. The existing PCR test misses up to
30% of cases, scientists have said.
The scientists have prepared enough material so far for 10,000 tests,
and are making it free to researchers who want to evaluate its
potential diagnostic use.
New CRISPR-based test for Covid-19 could be a simple, cheap at-home diagnostic, scientists say
