How the CRISPR- technology can help set up a faster and cheaper COVID-19 testing strategy
By: Trisha Bose
Tags: Research, Biotechnology, Health, Covid 19, Science

The year 2020 witnessed a pandemic, crashing economies, depressing lockdowns, loss in all forms and figures, hospitals and healthcare centers stacked with the diseased and their helpless loved ones, unsung heroes working relentlessly in the depths of such facilities, and widespread chaos. We were hit by an enemy we weren’t prepared for. Now, everyone knows how that played out. It’s hard not to miss the jostling streets, the jammed high roads, grabbing a quick bite in a restaurant, or even the Monday morning dread of rushing to work.

While some are trying to cope up with the disease itself, the rest try to acknowledge the mental and economical damage unearthed by this pandemic. In summation, everyone seems to be going through a tough time. The best of times only took a year to culminate into the worst of times.

However, when the world was toiling away into the abyss of uncertainties, Science was the only guy holding the cards. This might be a sorry state, but the progress made by the researchers is unparalleled. Just when we all thought that there’s no more going around this impending disease, Research revealed another trick up its sleeve.

Can CRISPR-technology diagnose COVID-19?

There was a time when CRISPR technology was a fancy term only known to the Biotechnologists, Biologists, and a few Biology enthusiasts. The fancy gene-editing technology rose to fame during 2013 and has ever since been on a journey uphill. Over time there came about designer babies, transparent squids, and whatnot. CRISPR now has become a household name. Who knew CRISPR could do more than that? You ask What? Well, before jumping on to the answer, it is important to speculate on the relationship between CRISPR technology and COVID-19.

Coronaviruses or CoVs are not new to the game. They have been cohabiting with our kind for a long time now. The newly mutated strain SARS-CoV-2 is the one with enhanced pathogenic powers and spells trouble. This new strain was detected in the first place by nucleic-acid based tests (metagenomic next-generation sequencing or mNGS) that suggested a 79% difference from the six members of the existing SARS-CoV family. Besides, a CRISPR based assay namely, the GeneXpert assay was suggested only last year to detect Mycobacterium tuberculosis with enhanced sensitivity. This indicated the potential of the CRISPR/Cas complex in assay development for other pathogenic diseases as well.

Furthermore, in a recent study, CRISPR technology happened to show the potential for in vitro diagnosis of COVID-19 with 100% accuracy. On the contrary, the best part of this discovery remains the estimated manufacturing cost of 70 cents.

What does that mean?

As of now, over five million individuals have been identified with SARS-CoV-2 infection. It means that COVID-19 tests can be made available to a larger mass of people, especially in the developing and under-developed countries. This comes as a milestone for places where healthcare comes at a great cost and the citizens have been failing till now to get themselves tested. Besides, as the world grows desperate to get back on its feet and run into the dear dear arms of a normal life, the demand for rapid, sensitive, and inexpensive diagnostics has increased.

COVID-19 testing

In the past few months, countless debates have been aired and promoted concerning the efficiency of COVID-19 testing. However, the lack of 100% accuracy had always left a window open for doubt and speculation. Currently, metagenomics next-generation sequencing and reverse transcription PCR (RT-PCR) are commonly being used to diagnose COVID-19. While sequencing is costly and time-consuming, RT-PCR requires specialized equipment (thermocycler) which is difficult to use. Therefore, the deficiency of precision and a higher time consumption lands us in a weak spot.

“A tool kit of rapid diagnostics faster than typical RT-PCR is in great demand to circumvent the bottlenecks in assay turn-around time and reagent supply for COVID-19 testing,” the researchers write. “To address the expanding clinical needs, we developed CRISPR-COVID, a rapid assay for SARS-CoV-2 detection based on Cas13a.”

Into the Experiment Chambers

Scientists used genome sequencing to determine two unique regions of Sars-Cov-2 that sets it apart from other pathogens including other coronaviruses. Therefore, having two such targets coupled with the sensitivity of CRISPR/Cas13a, the situation turned out to be advantageous. They were now finally able to develop an assay combining the two to create an isothermal-based assay that eliminated the need for sophisticated analytical instruments.

Hard to believe, but the study progresses to show a single-copy sensitivity of the assay. When examined against human cells infected with a variety of pathogens as interference samples, the newly developed assay did not have one false positive on record.

The study has been published in Plos Pathogens.

Trust comes with Evidence

When talking about scientific discovery, it is difficult to obliterate the technical aspects. And when talking about COVID-9, the evidence is the Holy Grail.

The scientists used 114 RNA samples to conduct the diagnosis among which 61 were suspected COVID-19 cases (52 confirmed, 9 ruled-out by mNGS), 17 SARS-CoV-2-/hCoV+ cases, and 36 samples were of healthy individuals. CRISPR-COVID (as the researchers named the assay) demonstrated a sensitivity of 100% by detecting all 52 COVID-19 cases. No false positives were found in all 62 negative cases, including the hCoV-infected samples. On the contrary, PCR methods showed 90% accuracy on records. Besides, it took 1.5 hours for a complete run. mNGS on the other hand took 20 hours to generate any results. In comparison to these data, CRISPR-COVID took 40 minutes in total to give the result. Precisely, the reaction turn-around time (TAT) of the CRISPR-COVID assay was much lower than that of the other molecular biology-based methods.

“The current discovery of the collateral activity of certain Cas family members, provides a great opportunity to take advantage of both the sensitivity of an isothermal assay and the specificity of the CRISPR system, suggesting CRISPR-COVID as a competitive alternative not only technologically but also financially.”

When it comes to healthcare, it is better to be safe than sorry. Besides, studies like these call for much more research and experimentation to ascertain that the medical advances being made are for the people, and of the people. However, this recent discovery can evolve to be a successful endeavor only if more diagnostic studies show equally accurate results. It has the potential of not only becoming an excellent diagnosis strategy but also an economical one. Needless to say that this pandemic is a medical challenge coupled with a financial one, and we need to use the resources at our disposal to the best of our abilities to make the most out of the situation.