New strategy to contain COVID-19 disease

By Paduano Francesco

CRISPR gene-editing technology to identify SARS-CoV-2 infected patients: a new strategy to contain COVID-19 disease

Today, the coronavirus disease called COVID-19 caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is causing a massive pandemic worldwide, compromising the public health systems around the world. Due to the high transmissibility of this coronavirus, millions of people need to be tested every day to prevent and contain the virus’s spread.

Thus, the early detection of SARS-CoV-2 plays an essential role in the controlling of COVID-19 disease. In this context, the absence of rapid and accurate molecular diagnostic tests for the SARS-CoV-2 detection has delayed the public health response [1,2].

covid-19 testingIn the fight against the SARS-CoV-2, the current testing method for the detection of SARS-CoV-2 is the quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR), which is the gold standard molecular detection method approved by US Centres for World Health Organization (WHO) and Disease Control and Prevention (CDC).

Although this method is considered as the gold standard for the recognition of COVID-19 disease due to its high specificity and sensitivity, the test is expensive, complicated and needs expensive tools, reagents and well-trained personnel with adequate expertise. In addition, this test protocol requires a long detection time (4 to 6 hours) with a 24h turnaround time for detecting patients having suspected infection. In addition, insufficient access to reagents and equipment has reduced disease recognition, decreasing the possibility to control this pandemic virus [1,3]. Therefore, the development of a high-speed test for diagnosing the SARS-CoV-2 virus based on alternative technologies is needed for public health. In fact, the National Institutes of Health (NIH) has recently announced around $120 million in funding for the discovery of new technologies that are able to identify the SARS-CoV-2 virus.

covid-19In this context, some scientists have used the CRISPR/Cas9 system, a biotechnological tool for editing genomes, to rapidly and accurately detect the genetic signature of the SARS-CoV-2 virus. In general, the CRISPR genome editing system can be used to insert, delete, or alter any form of human DNA/RNA. Since CRISPR/cas9 can be manipulated to target any genetic sequence, the scientists programmed it to detect a specific region of the SARS-CoV-2 virus. Importantly, CRISPR/Cas-based nucleic acid detection technology does not require sophisticated equipment or procedures of a clinical laboratory. Therefore, the use of CRISPR/Cas systems for the diagnosis of SARS-CoV-2 virus has opened new frontiers in the field of clinical virology.

In this context, the two biotech company Sherlock Biosciences and Mammoth Biosciences, have discovered a novel CRISPR technology for COVID-19 diagnosis, simplifying the virus detection. Particular enzymes such as Cas9 and Cas12 work as a type of molecular scissors and thus by using one of these enzymes combined with a specific CRISPR target sequence, scientists can detect predefined coronavirus sequences. The ultimate goal of CRISPR gene editing techniques is to make the detection of SARS-CoV-2 virus faster, cheaper, and more accessible without the requirement of specialized equipment. It has been observed that by using CRISPR technology, it is possible a fast detection of SARS-CoV-2 RNA in saliva within 1 hour at home without requiring any costly equipment.

The Massachusetts-based biotech called Sherlock Biosciences was the first company that acquired an emergency use authorization (EUA) from the US Food and Drug Administration (FDA) for the CRISPR-based diagnostic tool for detecting SARS-CoV2 virus [3].

The sherlock CRISPR SARS-CoV-2 method is centered on a CRISPR molecule that is able to detect a specific SARS-CoV-2 genetic sequence in specimens such as oropharyngeal, nasal, and nasopharyngeal swabs. When the genetic material of SARS-Cov-2 is detected in the sample, the CRISPR protein is activated and releases a visible signal, giving results in about 1 hour. Since this method is able to detect Covid-19 patients in only 20 minutes, it has become an exciting strategy to detect and control this virus.

The start-up Mammoth Biosciences was the second EUA granted to a CRISPR-based SARS-CoV-2 detection method called RNA DETECTR [1]. Also, the DETECTR platform does not need a sophisticated laboratory and is able to detect specific sequences of the coronavirus’ RNA in less than 20 minutes, starting from a nasal swab. Both Sherlock’s and Mammoth’s Covid-19 tests are based on the research of two pioneer scientists of CRISPR gene-editing technology, Feng Zhang and Jennifer Doudna, respectively. Both testing methods offer similar levels of sensitivity and specificity to qRT-PCR, and thus today, they are very promising methods for SARS-CoV-2 detection.

Actually, some biotech company such as Mammoth is creating a specific test for COVID-19 detection based on the CRISPR technology in a format similar to a pregnancy test that can be executed at home. In conclusion, the CRISPR technology could give an answer to the increasing request for a quick screening test for the identification of COVID-19 infected patients around the world. 


Take home message

To reduce the number of COVID-19 infected patients around the world and to control the second wave of infections, it is necessary to use a quick diagnostic tool able to detect who is currently infected with SARS-CoV-2. The existing method for detecting the SARS-CoV-2 virus in suspected patients with Covid-19 is the qRT-PCR. This old method needs several passages, such as the isolation of viral RNA from a patient followed by the reverse transcription of RNA into cDNA and subsequent PCR to amplify the specific viral sequence. Therefore, this method requires a turnaround time of more than 24 hours, which is not actually optimal to control the SARS-CoV-2 virus diffusion around the world. Thus, for a successful public health response, there is a strict necessity for a rapid and accessible detecting method of the SARS-CoV-2 virus. In this context, scientists adapted the CRISPR technology approaches to detect SARS-CoV-2 nucleic acids, making diagnostics of COVID-19 more affordable and accessible. In the near future, CRISPR technology will be used to quickly detect COVID-19 infected patients, a crucial step in the successful coronavirus containment strategy.



  1. Broughton, J.P.; Deng, X.; Yu, G.; Fasching, C.L.; Servellita, V.; Singh, J.; Miao, X.; Streithorst, J.A.; Granados, A.; Sotomayor-Gonzalez, A. CRISPR–Cas12-based detection of SARS-CoV-2. Nature Biotechnology 2020, 1-5.
  2. Hou, T.; Zeng, W.; Yang, M.; Chen, W.; Ren, L.; Ai, J.; Wu, J.; Liao, Y.; Gou, X.; Li, Y. Development and evaluation of a rapid CRISPR-based diagnostic for COVID-19. PLoS Pathogens 2020, 16, e1008705.
  3. Zhang, F.; Abudayyeh, O.O.; Gootenberg, J.S. A protocol for detection of COVID-19 using CRISPR diagnostics. A protocol for detection of COVID-19 using CRISPR diagnostics 2020, 8.


NIH continues to boost national COVID-19 testing capacity. Retrieved from


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