The role of CRISPR in viral diagnostics

A comprehensive new review paper, published in the journal Virsues, explains in depth how CRISPR can be utilized as a reliable tool to investigate the viral life cycles – and especially how many new CRISPR systems can be repurposed for diagnostics.

Study: CRISPR Tackles Emerging Viral Pathogens. Image Credit: Nathan Devery/ Shutterstock

Understanding all the complex facets of dynamic association between viral agents and cellular host factors is pivotal to advancing our knowledge of viral entry, replication, and disease mechanisms. Still, these findings may also inform the development of antivirals.

A Nobel Prize award-winning CRISPR genome editing technology has enhanced our understanding of this topic significantly by pinpointing both proviral and antiviral cellular host factors for a myriad of viruses – and most recently for the severe respiratory syndrome coronavirus 2 (SARS-CoV-2), a causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic.

One of the most pertinent questions is: can it be of even better use in curbing this pandemic? Even though we have rather powerful methods of SARS-CoV-2 detection, there are certain issues regarding cost, equipment, turnaround time, and reagent availability. Moreover, can CRISPR be of use for viral diagnostics in general?

What is CRISPR?

This technology represents a defense mechanism of bacteria against invading viruses known as bacteriophages. One of the most known combinations is CRISPR/Cas9 (consisting of enzyme Cas9 and a guide RNA), which can edit genes by accurately cutting DNA and allowing natural DNA repair events to take over.

However, unlike Cas9 (which is a hallmark of CRISPR gene editing), there is also a Cas13 enzyme that can cut the genetic sequence in accordance with targeting information, which then instigates indiscriminate slicing of RNA.

Although this type of behavior can be a big issue when gene editing is concerned, it is a huge advantage in diagnostics since all that cutting can be utilized as a signal that can indicate designated genetic sequences using CRISPR.

CRISPR as a diagnostic tool in virology

This is why CRISPR tests are seen as a way to diagnose infections with the same accuracy as conventional methods, and basically in the same manner as at-home pregnancy tests. In other words, this method holds the potential of increasing our yield in tracking and detecting viral diseases; however, it has not yet been officially approved for this use.

Still, CRISPR has significant advantages, primarily as it yields rapid results in a much more time-sensitive and cost-effective manner. Furthermore, this technology can be easily field-deployable, which is particularly important for low- and middle-income countries.

For now, two main platforms are currently in the development phase: SHERLOCK and DETECTR. In a nutshell, SHERLOCK functions by adding RNA molecules that produce a signal when sliced by Cas13, while DETECTR is similar but uses Cas12 that is activated after it recognizes target DNA.

Both of these platforms have been successfully validated to detect SARS‐CoV‐2 and other (potentially deadly) viruses of human importance, such as influenza A virus, Ebola virus, and lymphocytic choriomeningitis virus, and vesicular stomatitis virus.

From identification to antiviral therapeutics

Such wide adaptation and implementation of CRISPR has revolutionized gene editing and opened a door for the whole new field of screening and viral diagnostic. And naturally, our understanding of the dynamic virus-host relationship, disease mechanisms, and immune response increased in an unprecedented manner.

Hence, this could enable the development of antiviral treatment options in years to come, as further developments in CRISPR technology will reduce undesired off-target effects and allow much easier RNA editing.

And although they are still considered emerging technologies, SHERLOCK and DETECTR are very promising candidates for rapid identification of various infectious disease agents, as these are ultrasensitive tests without the need for complicated processing. We will find out very soon whether they will play a certain role in the COVID-19 pandemic.

Written by

Dr. Tomislav Meštrović

Dr. Tomislav Meštrović is a medical doctor (MD) with a Ph.D. in biomedical and health sciences, specialist in the field of clinical microbiology, and an Assistant Professor at Croatia's youngest university – University North. In addition to his interest in clinical, research and lecturing activities, his immense passion for medical writing and scientific communication goes back to his student days. He enjoys contributing back to the community. In his spare time, Tomislav is a movie buff and an avid traveler.