CRISPR-based tools for Coronavirus Disease 2019 (COVID-19) test
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Author:
Huajun Bai1 Xiaolong Cai1, 2* Xiaoyan Zhang1
1. R&D Center, GeneMedi Co.Ltd., Shanghai, P.R. China (www.genemedi.net)
2. Hanbio Research Center, Hanbio Tech Co. Ltd., Shanghai, P.R. China (www.hanbio.net)
Abstract:
The outbreak of COVID-19, caused by 2019 novel coronavirus (2019-nCoV), has been a global public health threat and caught the worldwide concern. Scientists throughout the world are sparing all efforts to explore strategies for the determination of the 2019-nCoV virus and diagnosis of COVID-19 rapidly. Several assays are developed for COVID-19 test , including RT-PCR, coronavirus antigens-based immunoassays, and CRISPR-based strategies (Cas13a or Cas12a), etc. Different assays have their advantages and drawbacks, and people should choose the most suitable assay according to their demands. Here, we make a brief introduction about these assays and give a simple overview of them, hoping to help doctors and researchers to select the most suitable assay for the Coronavirus Disease 2019 test (COVID-19 test) .
CRISPR-based tools for Coronavirus Disease 2019 (COVID-19) test
1) Principles for Diagnostics
As RT-PCR assay for COVID-19 requires several reagents, specific instruments and complicated processes, CRISPR-based tools have been developed to test COVID-19 within 30 minutes, which is really easy and simple to operated and saves a lot of time.
A. CRISPR-Cas13a (SHERLOCK)
Based on CRISPR (clustered regularly interspaced short palindromic repeats) technology, single-effector RNA-guided ribonucleases (RNases), such as Cas13a (previously known as C2c2) [12, 13], can be activated to engage in “collateral” cleavage of nearby nontargeted RNAs once recognizing its RNA targets. Recombinase polymerase amplification (RPA) can efficiently amplify DNA from single-molecule to 1012 level at a low isothermal state with no need to break the double-stranded structure of DNA [14]. Combined with RPA and T7 RNA polymerase, the CRISPR-Cas13a system can detect RNA rapidly with attomolar (10-18) sensitivity. This technology can be applied for real-time detection of the presence of target RNAs in vitro with signal amplification by non-specific collateral cleavage of nearby nontargeted reporter RNA (Fig. 4) [15]. Therefore, this system is called Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) based on the amplification of nucleic acid and Cas13a-mediated collateral cleavage of a reporter RNA.
Figure 4. General principle of SHERLOCK tool. dsDNA, double-stranded DNA; RPA, recombinase polymerase amplification, RT-RPA, reverse transcriptase–RPA [15].
For COVID-19 determination, two specific gRNAs targeting Orf1ab and S gene are used and the sequences are as follows. The SHERLOCK COVID-19 detection protocol only requires 3 steps: ① 25min incubation for isothermal amplification of the extracted nucleic acid sample with RPA kit; ② 30 min incubation for the determination of pre-amplified viral RNA sequence using Cas13 protein; ③ 2 min incubation for visual read out of the detection result with a commercially-available paper dipstick.
| S gene crRNA | 5’-GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAACGCAGCACCAGCUGUCCAACCUGAAGAAG-3’ |
| Orf1ab-crRNA | 5’-GAUUUAGACUACCCCAAAAACGAAGGGGACUAAAACCCAACCUCUUCUGUAAUUUUUAAACUAU-3’ |
| Reporter RNA | 5’-/56-FAM/mArArUrGrGrCmAmArArUrGrGrCmA/3Bio/-3’ |
Table 2. crRNA for SHERLOCK COVID-19 detection
B. CRISPR-based DETECT Lateral Flow Assay
Similarly, another diagnostic tool based on CRISPR is DETECTR (DNA endonuclease-targeted CRISPR trans reporter) system [16, 17]. DETECTR system carry out reverse transcription as well as DNA amplification simultaneously with loop-mediated amplification (RT-LAMP) [18]. The gRNAs are designed to target E gene and N gene of SARS-CoV-2 with the protospacer adjacent motif (PAM) sequence for Cas12 (also known as Cpf1) enzyme [19]. When Cas12 specifically recognizes and binds to the target single-stranded DNA (ssDNA), it will be activated to completely degrade ssDNA molecules non-specifically. DETECTR system is based on the isothermal amplification of target DNA and Cas12-mediated to collateral cleavage the ssDNA probe. The detailed workflow of DETECTR system-based COVID-19 test is shown in Fig. 6 [20], similarly to SHERLOCK system.
Figure 5. Flow diagram of COVID-19 test based on DETECTR system [20].
| N gene crRNA | 5'-CACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGG-3' |
| E gene crRNA | 5'-CTTGCTTTCGTGGTATTCTTGCTAGTTACACTAG-3' |
| Reporter | 5’-/56-FAM/TTATTATT/3Bio/-3’, IDT |
Table 3. crRNA for DETECTR system COVID-19 detection
2) Advantages and disadvantages
Advantages:
① Easy to use and operate in a large scale.
② No requirement of additional equipment.
③ High specificity and sensitivity. Both of the two molecular diagnostic technologies, SHERLOCK and DETECTR, can be used to detect specific RNA/DNA at the attomolar level [16, 17].
④ Cost little time, within 1h.
⑤ Can detect early infection of SARS-CoV-2.
Disadvantages:
There may exist some off-target effects.
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