New rapid CRISPR-based test for sensitive SARS-CoV-2 detection

By Dr. Liji Thomas, MDMay 13 2020

A new study reports the approval of a new CRISPR-based coronavirus test that is both sensitive and rapid and intended to help reduce the time required to test symptomatic or potentially contagious cases.

The new diagnostic kit comes from Sherlock Biosciences, a Cambridge-based biotechnology company.

The technology programs a CRISPR molecule to detect the presence of the genetic signature for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recovered from slivers of genetic material from the nose, throat swab, mouth swab or alveolar lavage fluid.

The U.S. Food and Drug Administration (FDA) has issued emergency-use authorization for the new test.

Observer Mitchell O’Connell of New York’s University of Rochester says this kind of testing will help reduce backlogs and improve the testing ratio. However, real-world performance in clinics and hospitals is still to be evaluated compared to laboratory testing in standard conditions.

CRISPR DNA Editing. Image Credit: Nathan Devery / Shutterstock

The Scientists

The approach on which the new test has been built is called STOP (SHERLOCK Testing in One Pot). It is based on a CRISPR approach, developed by Feng Zhang and his colleagues. They come from five institutions: the McGovern Institute for Brain Research at MIT, the Broad Institute of MIT and Harvard, the Ragon Institute, and the Howard Hughes Medical Institute (HHMI).

Zhang is the scientist who pioneered the field of CRISPR, along with MIT’s James Collins, in 2017. Their work continued with some of the same researchers to demonstrate its ability to pick up Zika and Dengue viruses at low levels, in 2017.

In January 2020, they began to develop tests to diagnose COVID-19, and the earliest version of the current test to be rolled out is now in use in Thai hospitals for screening purposes. The current test is called STOPCovid and shows rapid, sensitive, and accurate detection of SARS-CoV-2.

“While it has only been a little over a year since the launch of Sherlock Biosciences, today we have made history with the very first FDA-authorized use of CRISPR technology, which will be used to rapidly identify the virus that causes COVID-19,” said Rahul Dhanda, co-founder, president and CEO of Sherlock Biosciences. “We are committed to providing this initial wave of testing kits to physicians, laboratory experts, and researchers worldwide to enable them to assist frontline workers leading the charge against this pandemic.”

“When our lab collaborated with Dr. Feng Zhang’s team to develop SHERLOCK, we believed that this CRISPR-based diagnostic method would have a significant impact on global health,” said James J. Collins, co-founder and board member of Sherlock Biosciences and Termeer Professor of Medical Engineering and Science for MIT’s Institute for Medical Engineering and Science (IMES) and Department of Biological Engineering. “During what is a major healthcare crisis across the globe, we are heartened that the first FDA-authorized use of CRISPR will aid in the fight against this global COVID-19 pandemic.”

How STOPCovid Works

The new test uses CRISPR enzymes that are modified to detect the genetic signature of the virus, and suitable amplification reagents to increase the number of matching sequences to large amounts, allowing virus detection even when as few as 100 copies of the virus are present in the sample – an incredibly low detection limit.

The test strip is easy to read, designed like a pregnancy kit. To achieve this one-step format, they hunted for CRISPR enzymes to find one which is active at the same temperature as the amplification enzymes. They finally decided to use one from the bacterium Alicyclobacillus acidophilus that causes spoiled orange juice to have its characteristic taste.

The enzyme, called AapCas12b, allows the whole test to be done at a single temperature. This avoids the opening of test tubes midway, and thus boosts the reliability of the test by preventing sample contamination.

Another significant advantage of the diagnostic platform is its ‘one-pot’ approach, which means it requires minimal handling and has only one step. The equipment required, such as test tubes and water baths, are inexpensive and readily available.  

When the test returns positive, it shows that the CRISPR machinery has homed in on the target sequence, generating fluorescence by an attached enzyme. The results are available in an hour, say company sources.

A third outstanding advantage is the high sensitivity, accuracy, and speed of reaction that makes it suitable for point-of-care and home testing.

Towards Widespread Simplified Testing

While coronavirus testing is the backbone of any successful containment strategy, along with the interruption of transmission by measures that restrict mobility at a population level, testing shortages have proven to be a headache in even the most developed countries. For instance, the U.S. has increased testing to the current level of almost 250,000 a day but is still not able to meet the demand in some places, according to the nonprofit The Covid Tracking Project.

Extensive and reliable testing for COVID-19 is essential and should ideally be available without sophisticated laboratory facilities, to drive contact tracing measures and thus facilitate the control of new outbreaks. Most current tests are limited by their need for expensive or advanced tools and unavailability of supplies.

However, researchers have already shown that many steps can be bypassed or simplified without much reduction in quality, such as RNA extraction. Eventually, the elimination of nasopharyngeal swabs as test material could make the tests still more broadly available.

Zhang comments, “The ability to test for COVID-19 at home, or even in pharmacies or places of employment, could be a game-changer for getting people safely back to work and into their communities.”

Using Technology to Broaden Diagnostic Access

The company has validated the test using nasopharyngeal swabs from COVID-19 patients. The results show the test to have 97% sensitivity and 100% specificity. In other words, 97% of positive samples will be picked up, and if the test reads negative, the individual can be sure the infection is not present.

The test has also been performed using saliva contaminated with SARS-CoV-2 RNA, to demonstrate the feasibility of detecting the infection in saliva with high sensitivity. This means swabs could be on their way out, making the test far easier and reducing the need for such equipment.

Rahul Dhanda, who is the Sherlock CEO, says that the company is now designing a single cartridge for the test to allow home use, without the need for laboratory facilities. This would, however, need to be validated in additional rounds of clinical trials, and another FDA authorization will be needed. None of the over 60 tests for the detection of SARS-CoV-2 that have so far received emergency-use authorizations have been cleared for home use.

Open Platform, Faster Results

Similarly, designed tests are being reported from San Francisco, California, that take about 40 minutes to report the result. A preprint publication from Argentinian researchers and another Californian team of scientists also describe the same test approach in their work.

The open protocol for the STOPCovid test has been made available online in keeping with the COVID-19 Technology Access Framework organized by Harvard, MIT, and Stanford. This aims to model the deployment of technologies that are vitally important in the diagnosis, treatment, or prevention of COVID-19, on the broadest possible scale, for the maximum benefit in the shortest possible time.