Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus

Hou, Tieying; Zeng, Weiqi; Yang, Minling; Chen, Wenjing; Ren, Lili; Ai, Jingwen; Wu, Ji; Liao, Yalong; Gou, Xuejing; Li, Yongjun; Wang, Xiaorui; Su, Hang; Gu, Bing; Wang, Jianwei; Teng, Xu

doi:10.1101/2020.02.22.20025460

Cited by 47 publications

(64 citation statements)

References 21 publications

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“…In the case of the SARS-CoV-2 outbreak, genomes have been generated and shared at a remarkable pace, and we thank those who have contributed their data through GISAID [13]. We and others, relying on this data [14], have shown that it is possible to rapidly design CRISPR-based tools for detection and surveillance during an outbreak.…”

Section: Discussionmentioning

confidence: 99%

CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design

Metsky

Freije

Kosoko-Thoroddsen

et al. 2020

Preprint

137

138

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The emergence and outbreak of SARS-CoV-2, the causative agent of COVID-19, has rapidly become a global concern and has highlighted the need for fast, sensitive, and specific tools to surveil circulating viruses. Here we provide assay designs and experimental resources, for use with CRISPR-based nucleic acid detection, that could be valuable for ongoing surveillance. We provide assay designs for detection of 67 viral species and subspecies, including: SARS-CoV-2, phylogenetically-related viruses, and viruses with similar clinical presentation. The designs are outputs of algorithms that we are developing for rapidly designing nucleic acid detection assays that are comprehensive across genomic diversity and predicted to be highly sensitive and specific. Of our design set, we experimentally screened 4 SARS-CoV-2 designs with a CRISPR-Cas13 detection system and then extensively tested the highest-performing SARS-CoV-2 assay. We demonstrate the sensitivity and speed of this assay using synthetic targets with fluorescent and lateral flow detection. Moreover, our provided protocol can be extended for testing the other 66 provided designs. Assay designs are available at https://adapt.sabetilab.org/ .

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Section: Discussionmentioning

confidence: 99%

CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design

Metsky

Freije

Kosoko-Thoroddsen

et al. 2020

Preprint

137

138

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“…The amplified product RNA activates Cas13a, which in turn cleaves a reporter RNA, liberating a fluorescent dye from a quencher. This method consistently detects synthetic SARS-CoV-2 viral RNA in the range between 10 and 100 copies per L of input, only requires a lateral flow dipstick for visual readout of the detection result, and can be completed in 40 minutes (Hou et al 2020) or 57 minutes Metsky et al 2020) after the RNA extraction step. SHERLOCK (termed "CRISPR-nCoV" in Hou et al 2020) also demonstrated its diagnostic potential by detecting SARS-CoV-2 RNA with 100% sensitivity in 52 patient samples (Hou et al 2020).…”

Section: Crispr-based Detectionmentioning

confidence: 99%

Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection

Esbin

Whitney

Chong

et al. 2020

RNA

454

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The current COVID-19 pandemic presents a serious public health crisis, and a better understanding of the scope and spread of the virus would be aided by more widespread testing. Nucleicacid based tests currently offer the most sensitive and early detection of COVID-19. However, the "gold standard" test pioneered by the United States Center for Disease Control & Prevention, takes several hours to complete and requires extensive human labor, materials such as RNA extraction kits that could become in short supply and relatively scarce qPCR machines. It is clear that a huge effort needs to be made to scale up current COVID-19 testing by orders of magnitude. There is thus a pressing need to evaluate alternative protocols, reagents, and approaches to allow nucleic-acid testing to continue in the face of these potential shortages. There has been a tremendous explosion in the number of papers written within the first weeks of the pandemic evaluating potential advances, comparable reagents, and alternatives to the "gold-standard" CDC RT-PCR test. Here we present a collection of these recent advances in COVID-19 nucleic acid testing, including both peer-reviewed and preprint articles. Due to the rapid developments during this crisis, we have included as many publications as possible, but many of the cited sources have not yet been peer-reviewed, so we urge researchers to further validate results in their own labs. We hope that this review can urgently consolidate and disseminate information to aid researchers in designing and implementing optimized COVID-19 testing protocols to increase the availability, accuracy, and speed of widespread COVID-19 testing.

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“…70 A SHERLOCK protocol for detecting SARS-CoV-2 has been released, 71 and another Cas13a-based detection system has been tested with SARS-CoV-2 clinical isolates. 72 Protein Testing. Viral protein antigens and antibodies that are created in response to a SARS-CoV-2 infection can be used for diagnosing COVID-19.…”

mentioning

confidence: 99%

Diagnosing COVID-19: The Disease and Tools for Detection

et al. 2020

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COVID-19 has spread globally since its discovery in Hubei province, China in December 2019. A combination of computed tomography imaging, whole genome sequencing, and electron microscopy were initially used to screen and identify SARS-CoV-2, the viral etiology of COVID-19. The aim of this review article is to inform the audience of diagnostic and surveillance technologies for SARS-CoV-2 and their performance characteristics. We describe point-of-care diagnostics that are on the horizon and encourage academics to advance their technologies beyond conception. Developing plug-and-play diagnostics to manage the SARS-CoV-2 outbreak would be useful in preventing future epidemics.

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Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus

Cited by 47 publications

References 21 publications

CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design

CRISPR-based surveillance for COVID-19 using genomically-comprehensive machine learning design

Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection

Diagnosing COVID-19: The Disease and Tools for Detection

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