CRISPR-cas13 enzymology rapidly detects SARS-CoV-2 fragments in a clinical setting

Khan, Wahab; Barney, Rachael E.; Tsongalis, Gregory J.

doi:10.1016/j.jcv.2021.105019

Cited by 19 publications

(22 citation statements)

References 24 publications

(33 reference statements)

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“…The 15 articles included consist of studies from different countries around the world ( Figure 2 ). It was observed that 40% of the studies were conducted in the USA only [ 14 , 15 , 25–28 ], 13% in Canada [ 29 , 17 ] and China [ 2 , 30 ] each. Apart from this, some studies have been conducted in Germany [ 31 ], Singapore (Ooi et al, 2021[ 32 ]), Netherlands [ 18 ], Japan [ 33 ], and Saudi Arabia [ 34 ], representing 7% each from included studies ( Figure 2 ).…”

Section: Resultsmentioning

confidence: 99%

“…Apart from this, some studies have been conducted in Germany [ 31 ], Singapore (Ooi et al, 2021[ 32 ]), Netherlands [ 18 ], Japan [ 33 ], and Saudi Arabia [ 34 ], representing 7% each from included studies ( Figure 2 ). Patient’s details have not been specified in any of the articles, although the type of specimen taken for most of the studies was nasopharyngeal swab (n = 10) [ 14 , 25 , 26 , 2 , 13 , 17 , 18 , 27 , 28 , 31 ]. Some studies have tested on both nasopharyngeal and oropharyngeal swab (n = 3) [ 15 , 33 , 34 ] and only a few studies (n = 2) [ 29 , 30 ] have used the respiratory throat swab samples for their experiments ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“… Fluorescence 75% 100% 10 copies/ul quantitative RT-PCR assay 12 26 USA Nasopharyngeal swabs N& E 62 30 1 30 1 Yes 50 min. Fluorescence & lateral flow readouts 96.70% 100% 200 copies /ul quantitative RT-PCR assay 13 14 USA Nasopharyngeal swabs N & ORF1a 50 33 0 17 0 Yes 50 min. Fluorescence 100% 100% 6.75 copies/ul quantitative RT-PCR assay 14 33 Japan Orophrayngeal and nasopharyngeal swabs N 31 9 1 20 1 Yes 40 min.…”

Section: Resultsmentioning

confidence: 99%

“…N gene was most commonly used in 86.67% of included studies followed by E-gene (53.33%), ORF1 (20.00%), and S-gene (13.33%) ( Figure 3 ). Additionally, from the perspective of the type of detection method used for these 15 studies, the fluorescence method (n = 7) [ 2 , 14 , 17 , 18 , 27 , 28 , 30 ] was most frequently used while gold nano-particle (n = 1) based detection method was used in one study [ 29 ]. In five studies, the combination of fluorescence and lateral flow assay was used for the viral detection [ 13 , 15 , 25 , 26 , 34 ] while the lateral flow assay was used in two studies [ 31 , 33 ] ( Figure 4 ).…”

Section: Resultsmentioning

confidence: 99%

“…Simple amplification-based assay (SAMBA) uses DNA-dependent RNA polymerase and RNA-dependent DNA polymerase to alternately transcribe and reverse transcribe RNA target. CRISPR diagnosis combines isothermal amplification techniques (such as RT-LAMP and RT-RPA) with specific DNA or RNA targeting ability of crRNA and Cas12 [ 12 , 13 ] or Cas13 [ 14 , [ 5 ]Schermer et al, 2020] enzymes. The outputs of these detection techniques can be coupled with fluorescent or colorimetric reporters as well as lateral flow strip platforms to facilitate readout processes.…”

Section: Introductionmentioning

confidence: 99%

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Diagnostic efficiency of RT-LAMP integrated CRISPR-Cas technique for COVID-19: A systematic review and meta-analysis

Bhatt

Bumbrah

Ruwali

et al. 2022

Pathogens and Global Health

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To address the challenges associated with COVID-19 diagnosis, we need a faster, direct, and more versatile detection method for efficient epidemiological management of the COVID-19 pandemic. RT-qPCR (reverse transcription quantitative real-time Polymerase Chain Reaction) although the most popular diagnostic method suffers from a major drawback of equipment dependency and trained molecular biologists that limits rapid and large-scale screening, particularly in low resource regions. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a feasible alternative for RT-qPCR; however, it also suffers from the drawback of false-positive issues. Recently, RT-LAMP has been integrated with the CRISPR-Cas technique to take care of the problems associated with RT-LAMP for COVID-19 diagnosis. In this study, a meta-analysis was conducted using three scientific databases considering the PRISMA guidelines to assess the diagnostic efficiency of RT-LAMP integrated CRISPR-Cas technology. Out of a total of 1286 studies on COVID-19, we identified 15 articles that met our eligibility criteria of using simultaneous RT-LAMP and CRISPR-Cas technique. Our meta-analysis of the included studies revealed that most of the studies were conducted in the USA with the N gene as the most common target and fluorescence-based detection method. The meta-analysis results of all included studies have further revealed a pooled sensitivity value of higher than 85% and a pooled specificity value of 80% with the confidence interval of 95%, respectively, as revealed from the forest plot and SROC curve. The accuracy rate of included studies was also calculated which varied from 77.4% to 100%. Furthermore, the precision of included studies varied from 75% to 100%. Lastly, a quality assessment of bias and applicability was performed based on QUADAS-2. Taken together, combined RT-LAMP and CRISPR-Cas technique could be a potential alternative to RT-qPCR particularly in low resource regions having a high demand for rapid testing.

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