Stanford develops CRISPR test for detecting COVID-19 in 30 minutes

Last Updated 20 November, 2020. Cellspect Co., Ltd.

Researchers at Stanford University have developed a CRISPR-based “lab on a chip” to detect COVID-19 and are working with automakers at Ford to develop their prototype into a market-ready product. This could provide an automated, hand-held device designed to deliver a coronavirus test result anywhere within 30 minutes. [1, 2]

CRISPR (clustered regularly interspaced short palindromic repeats) was honored by Chemistry Nobel this year and is called the revolutionary genetic ‘scissors.' Therefore, CRISPR-based diagnostic methods, including diagnostic assays for the COVID-19 pandemic have sparked great interest due to their versatility, sensitivity, and specificity. CRISPR tests work by identifying a sequence of RNA—about 20 RNA bases long—that is unique to SARS-CoV-2. They do so by creating a “guide” RNA that is complementary to the target RNA sequence and, thus, will bind to it in solution. When the guide binds to its target, the “scissors” enzyme turns on and cuts apart any nearby single-stranded RNA. These cuts release a separately introduced fluorescent particle in the test solution. When the sample is then hit with a burst of laser light, the released fluorescent particles light up, signaling the presence of the virus.

On May 6, Sherlock Biosciences was the first company to gain emergency use approval (EUA) for a CRISPR-based kit for detection of coronavirus genetic material. Mammoth Biosciences was second, receiving its EUA for a CRISPR-based protocol and set of reagents on August 31. [3, 4] CRISPR-based assays are said to be as accurate as PCR genetic tests, which are the gold standard for accuracy in COVID-19 diagnostics. However, existing CRISPR diagnostic methods suffer from the requirements of up-front nucleic acid extraction, large reagent volumes, and several manual steps—factors which prolong the process and impede use in low-resource settings. [4]

In the current study published recently in PNAS, the test spotted active infections quickly and cheaply on a microfluidic chip which is just half the size of a credit card containing a complex network of channels. They use electric fields to purify fluids from a nasal swab sample and drive DNA-cutting reagents within the system’s tiny passages. By using the CRISPR enzyme Cas12, a sibling of the highly celebrated CRISPR-Cas9, the test triggers a fluorescent molecular probe that causes samples to glow when genetic material derived from the coronavirus is found. The researchers said the test approach could also be modified to spot the signs of other infections, by recalibrating the CRISPR enzyme for a different genetic marker. "If we want to look for a different disease, we simply design the appropriate nucleic acid sequence on a computer and send it over email to a commercial maker of synthetic RNA,” said Ramachandran, the study's first author. “They mail back a vial with the molecule that completely reconfigures our assay for a new disease.” [1, 2]

The new test has another key advantage that can quantify a sample’s amount of virus. When standard coronavirus tests amplify the virus’ genetic material to detect it, this changes the amount of genetic material present—and thus wipes out any chance of precisely quantifying just how much virus is in the sample. In other words, the fluorescent signal will be proportional to the amount of virus in the sample, revealing not just whether a sample was positive, but also how much virus a patient had. That information can help doctors tailor treatment decisions to each patient’s condition. [5]

 References:

  1. Conor Hale, 06 Nov 2020. “Stanford develops CRISPR 'lab on a chip' for detecting COVID-19” FIERCE Biotech news.

  2. Ashwin Ramachandran et al., 04 Nov 2020. “Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2” PNAS.

  3. Julia Joung et al. 08 Oct 2020 “Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing” N Engl J Med. 383(15):1492-1494

  4. Anjani Shah et al. 05 Oct 2020 “COVID-19 Testing Gets Crisper with CRISPR-Based Diagnostics” Future Lab press.

  5. Robert F. Service 08 Oct 2020 “New test detects coronavirus in just 5 minutes” Science daily newsletter.

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