CRISPR-based detection of SARS-CoV-2: A review from sample to result

Nouri, Reza; Tang, Zifan; Dong, Ming; Liu, Tianyi; Kshirsagar, Aneesh; Guan, Weihua

doi:10.1016/j.bios.2021.113012

Cited by 113 publications

(91 citation statements)

References 107 publications

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“…(Bruce et al, 2020;Deka and Kalita, 2020;Hasan et al, 2020;Kriegova et al, 2020;Graham et al, 2021;Vogels et al, 2021). Molecular test methods with alternative chemistry and detection methods such as isothermal amplification or CRISPRbased test methods were developed, and their performance characteristics were compared to the standard test methods (Broughton et al, 2020;Yan et al, 2020;Fozouni et al, 2021;Nouri et al, 2021). These alternative test approaches were designed to be inexpensive, rapid and suitable for point-of-care (POC) applications.…”

Section: Introductionmentioning

confidence: 99%

Metabolomics in the Diagnosis and Prognosis of COVID-19

2021

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Coronavirus disease 2019 (COVID-19) pandemic triggered an unprecedented global effort in developing rapid and inexpensive diagnostic and prognostic tools. Since the genome of SARS-CoV-2 was uncovered, detection of viral RNA by RT-qPCR has played the most significant role in preventing the spread of the virus through early detection and tracing of suspected COVID-19 cases and through screening of at-risk population. However, a large number of alternative test methods based on SARS-CoV-2 RNA or proteins or host factors associated with SARS-CoV-2 infection have been developed and evaluated. The application of metabolomics in infectious disease diagnostics is an evolving area of science that was boosted by the urgency of COVID-19 pandemic. Metabolomics approaches that rely on the analysis of volatile organic compounds exhaled by COVID-19 patients hold promise for applications in a large-scale screening of population in point-of-care (POC) setting. On the other hand, successful application of mass-spectrometry to detect specific spectral signatures associated with COVID-19 in nasopharyngeal swab specimens may significantly save the cost and turnaround time of COVID-19 testing in the diagnostic microbiology and virology laboratories. Active research is also ongoing on the discovery of potential metabolomics-based prognostic markers for the disease that can be applied to serum or plasma specimens. Several metabolic pathways related to amino acid, lipid and energy metabolism were found to be affected by severe disease with COVID-19. In particular, tryptophan metabolism via the kynurenine pathway were persistently dysregulated in several independent studies, suggesting the roles of several metabolites of this pathway such as tryptophan, kynurenine and 3-hydroxykynurenine as potential prognostic markers of the disease. However, standardization of the test methods and large-scale clinical validation are necessary before these tests can be applied in a clinical setting. With rapidly expanding data on the metabolic profiles of COVID-19 patients with varying degrees of severity, it is likely that metabolomics will play an important role in near future in predicting the outcome of the disease with a greater degree of certainty.

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Section: Introductionmentioning

confidence: 99%

Metabolomics in the Diagnosis and Prognosis of COVID-19

2021

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“…Very recently, new innovative technologies have been reported, with reliable efficiency in decreasing the overall time of the analysis and in pushing the limits of detection. Some of them are RT-PCR-like such as nano-PCR 25 , multiplex RT-PCR 26 , isothermal amplification 27 ; and others rely on the integration of interesting CRISPR-based detection 28 – 30 .…”

Section: Introductionmentioning

confidence: 99%

A simple and fast spectroscopy-based technique for Covid-19 diagnosis

Kitane

LOUKMAN²,

Marchoudi³

et al. 2021

Sci Rep

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The coronavirus pandemic, which appeared in Wuhan, China, in December 2019, rapidly spread all over the world in only a few weeks. Faster testing techniques requiring less resources are key in managing the pandemic, either to enable larger scale testing or even just provide developing countries with limited resources, particularly in Africa, means to perform tests to manage the crisis. Here, we report an unprecedented, rapid, reagent-free and easy-to-use screening spectroscopic method for the detection of SARS-CoV-2 on RNA extracts. This method, validated on clinical samples collected from 280 patients with quantitative predictive scores on both positive and negative samples, is based on a multivariate analysis of FTIR spectra of RNA extracts. This technique, in agreement with RT-PCR, achieves 97.8% accuracy, 97% sensitivity and 98.3% specificity while reducing the testing time post RNA extraction from hours to minutes. Furthermore, this technique can be used in several laboratories with limited resources.

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“…A new SHERLOCK assay called STOPCovid.v2 ( Joung et al, 2020 ) aims to address sample preparation by coupling one-step CRISPR-Cas12b-assisted reverse transcription loop-mediated isothermal amplification ( Notomi, 2000 ) (RT-LAMP) to benchtop magnetic-based RNA extraction, but the multiple manual steps in this assay present challenges for POC use. Thus, there has not yet to see a CRISPR-Cas-assisted SARS-CoV-2 detection assay that satisfies the requirements for POC use ( Nouri et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Point-of-care CRISPR-Cas-assisted SARS-CoV-2 detection in an automated and portable droplet magnetofluidic device

Chen

Lee

Trick

et al. 2021

Biosensors and Bioelectronics

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In the fight against COVID-19, there remains an unmet need for point-of-care (POC) diagnostic testing tools that can rapidly and sensitively detect the causative SARS-CoV-2 virus to control disease transmission and improve patient management. Emerging CRISPR-Cas-assisted SARS-CoV-2 detection assays are viewed as transformative solutions for POC diagnostic testing, but lack of streamlined sample preparation and full integration within an automated and portable device hamper their potential for POC use. We report herein POC-CRISPR – a single-step CRISPR-Cas-assisted assay that leverages facile magnetic concentration and transport of nucleic acid-binding magnetic beads to incorporate sample preparation with minimal manual operation. Moreover, POC-CRISPR has been adapted into a compact thermoplastic cartridge within a palm-sized yet fully-integrated and automated device. During analytical evaluation, POC-CRISPR was able detect 1 genome equivalent/μL SARS-CoV-2 RNA from a sample volume of 100 μL in < 30 min. Finally, when evaluated with 27 unprocessed clinical nasopharyngeal swab eluates that were pre-typed by standard RT-qPCR (C q values ranged from 18.3 to 30.2 for the positive samples), POC-CRISPR achieved 27 out of 27 concordance and could detect positive samples with high SARS-CoV-2 loads (C q < 25) in 20 min.

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CRISPR-based detection of SARS-CoV-2: A review from sample to result

Cited by 113 publications

References 107 publications

Metabolomics in the Diagnosis and Prognosis of COVID-19

Metabolomics in the Diagnosis and Prognosis of COVID-19

A simple and fast spectroscopy-based technique for Covid-19 diagnosis

Point-of-care CRISPR-Cas-assisted SARS-CoV-2 detection in an automated and portable droplet magnetofluidic device

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