Rapid, One-Step Mobile Test for COVID-19 Developed
Imagine swabbing your
nostrils, putting the swab in a device, and getting a read-out on your
phone in 15 to 30 minutes that tells you if you are infected with the
COVID-19 virus. This has been the vision for a team of scientists at
Gladstone Institutes, University of California, Berkeley (UC Berkeley),
and University of California, San Francisco (UCSF). And now, they report
a scientific breakthrough that brings them closer to making this vision
a reality.
One of the major hurdles to combating the COVID-19
pandemic and fully reopening communities across the country is the
availability of mass rapid testing. Knowing who is infected would
provide valuable insights about the potential spread and threat of the
virus for policymakers and citizens alike.
Yet, people must often
wait several days for their results, or even longer when there is a
backlog in processing lab tests. And, the situation is worsened by the
fact that most infected people have mild or no symptoms, yet still carry
and spread the virus.
In a new study published in the scientific journal Cell,
the team from Gladstone, UC Berkeley, and UCSF has outlined the
technology for a CRISPR-based test for COVID-19 that uses a smartphone
camera to provide accurate results in under 30 minutes.
"It has
been an urgent task for the scientific community to not only increase
testing, but also to provide new testing options," says Melanie Ott, MD,
PhD, director of the Gladstone Institute of Virology and one of the
leaders of the study. "The assay we developed could provide rapid,
low-cost testing to help control the spread of COVID-19."
The
technique was designed in collaboration with UC Berkeley bioengineer
Daniel Fletcher, PhD, as well as Jennifer Doudna, PhD, who is a senior
investigator at Gladstone, a professor at UC Berkeley, president of the
Innovative Genomics Institute, and an investigator of the Howard Hughes
Medical Institute. Doudna recently won the 2020 Nobel Prize in Chemistry
for co-discovering CRISPR-Cas genome editing, the technology that
underlies this work.
Not only can their new diagnostic test
generate a positive or negative result, it also measures the viral load
(or the concentration of SARS-CoV-2, the virus that causes COVID-19) in a
given sample.
"When coupled with repeated testing, measuring
viral load could help determine whether an infection is increasing or
decreasing," says Fletcher, who is also a Chan Zuckerberg Biohub
Investigator. "Monitoring the course of a patient's infection could help
health care professionals estimate the stage of infection and predict,
in real time, how long is likely needed for recovery."
A Simpler Test through Direct Detection
Current
COVID-19 tests use a method called quantitative PCR--the gold standard
of testing. However, one of the issues with using this technique to test
for SARS-CoV-2 is that it requires DNA. Coronavirus is an RNA virus,
which means that to use the PCR approach, the viral RNA must first be
converted to DNA. In addition, this technique relies on a two-step
chemical reaction, including an amplification step to provide enough of
the DNA to make it detectable. So, current tests typically need trained
users, specialized reagents, and cumbersome lab equipment, which
severely limits where testing can occur and causes delays in receiving
results.
As an alternative to PCR, scientists are developing
testing strategies based on the gene-editing echnology CRISPR, which
excels at specifically identifying genetic material.
All CRISPR
diagnostics to date have required that the viral RNA be converted to DNA
and amplified before it can be detected, adding time and complexity. In
contrast, the novel approach described in this recent study skips all
the conversion and amplification steps, using CRISPR to directly detect
the viral RNA.
"One reason we're excited about CRISPR-based
diagnostics is the potential for quick, accurate results at the point of
need," says Doudna. "This is especially helpful in places with limited
access to testing, or when frequent, rapid testing is needed. It could
eliminate a lot of the bottlenecks we've seen with COVID-19."
Parinaz
Fozouni, a UCSF graduate student working in Ott's lab at Gladstone, had
been working on an RNA detection system for HIV for the past few years.
But in January 2020, when it became clear that the coronavirus was
becoming a bigger issue globally and that testing was a potential
pitfall, she and her colleagues decided to shift their focus to
COVID-19.
"We knew the assay we were developing would be a
logical fit to help the crisis by allowing rapid testing with minimal
resources," says Fozouni, who is co-first author of the paper, along
with Sungmin Son and María Díaz de León Derby from Fletcher's team at UC
Berkeley. "Instead of the well-known CRISPR protein called Cas9, which
recognizes and cleaves DNA, we used Cas13, which cleaves RNA."
In
the new test, the Cas13 protein is combined with a reporter molecule
that becomes fluorescent when cut, and then mixed with a patient sample
from a nasal swab. The sample is placed in a device that attaches to a
smartphone. If the sample contains RNA from SARS-CoV-2, Cas13 will be
activated and will cut the reporter molecule, causing the emission of a
fluorescent signal. Then, the smartphone camera, essentially converted
into a microscope, can detect the fluorescence and report that a swab
tested positive for the virus.
"What really makes this test
unique is that it uses a one-step reaction to directly test the viral
RNA, as opposed to the two-step process in traditional PCR tests," says
Ott, who is also a professor in the Department of Medicine at UCSF. "The
simpler chemistry, paired with the smartphone camera, cuts down
detection time and doesn't require complex lab equipment. It also allows
the test to yield quantitative measurements rather than simply a
positive or negative result."
The researchers also say that their
assay could be adapted to a variety of mobile phones, making the
technology easily accessible.
"We chose to use mobile phones as
the basis for our detection device since they have intuitive user
interfaces and highly sensitive cameras that we can use to detect
fluorescence," explains Fletcher. "Mobile phones are also mass-produced
and cost-effective, demonstrating that specialized lab instruments
aren't necessary for this assay."
Accurate and Quick Results to Limit the Pandemic
When
the scientists tested their device using patient samples, they
confirmed that it could provide a very fast turnaround time of results
for samples with clinically relevant viral loads. In fact, the device
accurately detected a set of positive samples in under 5 minutes. For
samples with a low viral load, the device required up to 30 minutes to
distinguish it from a negative test.
"Recent models of SARS-CoV-2
suggest that frequent testing with a fast turnaround time is what we
need to overcome the current pandemic," says Ott. "We hope that with
increased testing, we can avoid lockdowns and protect the most
vulnerable populations."
Not only does the new CRISPR-based test
offer a promising option for rapid testing, but by using a smartphone
and avoiding the need for bulky lab equipment, it has the potential to
become portable and eventually be made available for point-of-care or
even at-home use. And, it could also be expanded to diagnose other
respiratory viruses beyond SARS-CoV-2.
In addition, the high
sensitivity of smartphone cameras, together with their connectivity,
GPS, and data-processing capabilities, have made them attractive tools
for diagnosing disease in low-resource regions.
"We hope to
develop our test into a device that could instantly upload results into
cloud-based systems while maintaining patient privacy, which would be
important for contact tracing and epidemiologic studies," Ott says.
"This type of smartphone-based diagnostic test could play a crucial role
in controlling the current and future pandemics."