4.6 Review

Advances in the application of CRISPR-Cas technology in rapid detection of pathogen nucleic acid

Related references

Note: Only part of the references are listed.
Review Genetics & Heredity

The CRISPR/Cas System: A Customizable Toolbox for Molecular Detection

Yuxuan He et al.

Summary: CRISPR/Cas system is a promising molecular diagnostic tool for elucidating the structure and function of genomes due to its high specificity, programmability, and multi-system compatibility in nucleic acid recognition. However, its ability to detect DNA or RNA is limited by multiple parameters, and it needs to be used in conjunction with other nucleic acid amplification techniques or signal detection techniques. The design of a molecular detection platform employing the CRISPR/Cas system focuses on performance optimization, enhancement of detection signal, and compatibility with multiple reaction systems.

GENES (2023)

Review Biotechnology & Applied Microbiology

Advances in the application of recombinase-aided amplification combined with CRISPR-Cas technology in quick detection of pathogenic microbes

Xiaoping Li et al.

Summary: The rapid diagnosis of pathogenic infections is crucial for disease prevention and public health safety. Recombinase-aided amplification (RAA) is an innovative technology that allows fast DNA or RNA amplification at low temperatures. Researchers have combined RAA with the CRISPR-Cas system to improve convenience and accuracy in pathogen detection, expanding the application of RAA in this field.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2023)

Article Multidisciplinary Sciences

CRISPR-Cas3-based diagnostics for SARS-CoV-2 and influenza virus

Kazuto Yoshimi et al.

Summary: This article introduces CRISPR-based diagnostics, including Cas12-based DETECTR and Cas13-based SHERLOCK Class 2 CRISPRs, which have been used to detect DNA or RNA from pathogens. A new method called CONAN, using Cas3, is described for rapid, low-cost detection of SARS-CoV-2 and single-base-pair mutations in IAV variants.

ISCIENCE (2022)

Article Biophysics

Electrochemical biosensor for nucleic acid amplification-free and sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA via CRISPR/Cas13a trans-cleavage reaction

Woong Heo et al.

Summary: A electrochemical biosensor based on CRISPR/Cas13a was developed for the rapid and sensitive detection of SARS-CoV-2 without the need for nucleic acid amplification. The biosensor showed high sensitivity and a wide detection range, making it suitable for on-site rapid diagnostic testing.

BIOSENSORS & BIOELECTRONICS (2022)

Article Biochemical Research Methods

Paired dCas9 design as a nucleic acid detection platform for pathogenic strains

Yihao Zhang et al.

Summary: A novel in vitro DNA detection system, named Paired dCas9 (PC) reporter, has been developed for specific DNA detection. The system utilizes a pair of dCas9 proteins linked to split halves of luciferase, enabling rapid prototyping of pathogen DNA detection kits.

METHODS (2022)

Article Microbiology

Development of a Rapid and Efficient RPA-CRISPR/Cas12a Assay for Mycoplasma pneumoniae Detection

Feina Li et al.

Summary: In this study, a rapid and efficient method utilizing RPA-CRISPR/Cas12a technology was proposed for the diagnosis of Mycoplasma pneumoniae. This method eliminates the need for expensive instruments and specialized personnel. The entire process, including sample extraction, RPA reaction, CRISPR/Cas12a detection, and visual observation, can be completed within 1 hour with high sensitivity and specificity.

FRONTIERS IN MICROBIOLOGY (2022)

Review Microbiology

Adaptation by Type III CRISPR-Cas Systems: Breakthrough Findings and Open Questions

Xinfu Zhang et al.

Summary: This review summarizes our knowledge regarding CRISPR-Cas adaptation, with a focus on type III systems, and discusses open questions in type III adaptation studies.

FRONTIERS IN MICROBIOLOGY (2022)

Article Engineering, Biomedical

Theragnostic application of nanoparticle and CRISPR against food-borne multi-drug resistant pathogens

Rahul Bhattacharjee et al.

Summary: Foodborne infection is a major source of infections worldwide, especially from multidrug-resistant (MDR) pathogens in the food industry. The use of CRISPR-Cas system and nanoparticles has gained interest as enhanced microbial detection tools. Nanoparticles can overcome the diagnostic limitations of the CRISPR-Cas system by acting as vehicles. The application of CRISPR-Cas technologies includes phage resistance, phage vaccination, strain typing, genome editing, and antimicrobial, while nanoparticles are effective in detecting and combating MDR pathogens in food.

MATERIALS TODAY BIO (2022)

Article Chemistry, Analytical

Photoactivatable CRISPR/Cas12a Strategy for One-Pot DETECTR Molecular Diagnosis

Yong Chen et al.

Summary: A photoactivated CRISPR/Cas12a strategy was proposed in this study to achieve high-sensitivity nucleic acid detection in one pot, avoiding amplicon contamination and lowering the threshold for molecular diagnostics in POC.

ANALYTICAL CHEMISTRY (2022)

Article Biochemistry & Molecular Biology

CRISPR/Cas12a-based electrochemical biosensor for highly sensitive detection of cTnI

Hao Chen et al.

Summary: The successful fabrication of the cTnI detection platform is of great significance for instant diagnosis of myocardial injury and related cardiovascular diseases. This electrochemical biosensor, utilizing magnetic nanoparticles, aptamer, and the Cas12a/crRNA system, demonstrates high specificity and sensitivity in detecting cTnI.

BIOELECTROCHEMISTRY (2022)

Review Biochemistry & Molecular Biology

Application of the CRISPR/Cas System in Pathogen Detection: A Review

Bowei Yuan et al.

Summary: This article reviews the application of the CRISPR/Cas system in pathogen detection, focusing on the Type II (cas9), Type V (cas12a, cas12b, cas14a), and Type VI (cas13a) systems. The CRISPR/Cas system offers strong specificity, high sensitivity, and convenience for detection, making it suitable for practical applications.

MOLECULES (2022)

Article Cell Biology

Overlapping gene dependencies for PARP inhibitors and carboplatin response identified by functional CRISPR-Cas9 screening in ovarian cancer

Ricardo Coelho et al.

Summary: PARP inhibitors have shown outstanding benefits in the treatment of epithelial ovarian cancer, especially in patients with BRCA1/2 mutations or defects in the homologous recombination repair system. This study identified ATM, MUS81, NBN, BRCA2, and RAD51B as predictive markers for olaparib response and highlighted CDK12 as a potential therapeutic target in EOC.

CELL DEATH & DISEASE (2022)

Article Multidisciplinary Sciences

Comprehensive assessment of miniature CRISPR-Cas12f nucleases for gene disruption

Changchang Xin et al.

Summary: This study compared the editing efficiency, specificity, and safety of four Cas12f proteins with Cas9 and two Cas12a proteins at multiple genomic sites using a high-throughput sequencing method. The results showed that Cas12f nucleases exhibit robust cleavage at most sites, mainly producing deletional fragments. In comparison, Cas9 and Cas12a showed higher editing efficiency at more sites. Furthermore, the off-target hotspots identified in Cas9- and Cas12a-edited cells were rarely detected in Cas12f-edited cells. Compared to Cas9 and Cas12a nucleases, Cas12f nucleases reduced the levels of chromosomal translocations, large deletions, and integrated vectors. Therefore, Cas12f nucleases have the ability to preserve genome integrity during genome editing.

NATURE COMMUNICATIONS (2022)

Article Biophysics

A CRISPR-based and post-amplification coupled SARS-CoV-2 detection with a portable evanescent wave biosensor

Yihan Yang et al.

Summary: This study presents a rapid, easy-to-implement, and accurate biosensing platform for detecting SARS-CoV-2 using CRISPR technology. By combining Cas13a collateral effect with HCR reaction, the method shows good discrimination capability when target RNA of SARS-CoV-2 is added to negative oropharyngeal swabs, demonstrating its promising potential for point-of-care diagnosis of COVID-19.

BIOSENSORS & BIOELECTRONICS (2021)

Article Virology

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

Wahab A. Khan et al.

Summary: The well-established genome editing technology of the CRISPR-Cas system has facilitated significant advancements in CRISPR diagnostics, which has led to interest in developing new biosensing applications for nucleic acid detection, particularly in the realm of SARS-CoV-2 detection. The novel fluorescence-based assay using SHERLOCK CRISPR technology showed 100% accuracy in diagnosing COVID-19 patient samples across a range of viral loads, demonstrating promising results for clinical diagnosis in the ongoing COVID-19 pandemic.

JOURNAL OF CLINICAL VIROLOGY (2021)

Article Chemistry, Analytical

Reverse Transcription Recombinase Polymerase Amplification Coupled with CRISPR-Cas12a for Facile and Highly Sensitive Colorimetric SARS-CoV-2 Detection

Wei S. Zhang et al.

Summary: The proposed method combines RT-RPA with CRISPR-Cas12a colorimetric assay for SARS-CoV-2 detection, utilizing DNA-modified gold nanoparticles to achieve high sensitivity and specificity. This novel approach can effectively avoid false positive results from other beta coronavirus members, improving the practical testing availability of SARS-CoV-2.

ANALYTICAL CHEMISTRY (2021)

Article Virology

CRISPR-Cas12a combined with reverse transcription recombinase polymerase amplification for sensitive and specific detection of human norovirus genotype GII.4

Weidong Qian et al.

Summary: This study developed a rapid, reliable, and portable detection system by combining RT-RPA with CRISPR-Cas12a for diagnosing NOV genotype GII.4. The method can be completed within 40 minutes, with a detection limit of up to 9.65 x 10(2)copies/mL and no cross-reactivity with other viruses.

VIROLOGY (2021)

Article Virology

Visual detection of human metapneumovirus using CRISPR-Cas12a diagnostics

Weidong Qian et al.

Summary: The study developed a detection technique using RT-RPA combined with CRISPR-Cas12a for clinical diagnosis of HmPV. The RT-RPA-Cas12a based fluorescence or LF assay showed high sensitivity and specificity with a detection limit of 6.97 x 10(2) copies/mL, and no cross reaction with other common viruses.

VIRUS RESEARCH (2021)

Review Pathology

Applications of the CRISPR-Cas system for infectious disease diagnostics

Peipei Li et al.

Summary: This review summarizes the progress and applications of CRISPR-associated (Cas) systems in the diagnosis of infectious diseases, focusing on their early detection capabilities in different infectious diseases. Future development should focus on improving the specificity, sensitivity, and stability of diagnostic tools. The CRISPR-Cas approaches are expected to emerge as more promising and robust tools for infectious disease diagnosis in the future.

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS (2021)

Article Biochemistry & Molecular Biology

CRISPR/Cas12-Based Ultra-Sensitive and Specific Point-of-Care Detection of HBV

Ronghua Ding et al.

Summary: The study developed a rapid and accurate point-of-care assay for HBV based on LAMP-Cas12a, addressing the challenge of nucleic acid extraction and providing visualization of the assay results. The method showed high sensitivity and specificity, with results comparable to qPCR.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Multidisciplinary Sciences

Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9

Chunlei Jiao et al.

Summary: The study found that tracrRNA hybridizing with cellular RNAs can lead to the formation of new crRNAs capable of guiding DNA targeting by Cas9. Reprogrammed tracrRNAs linking the presence of RNA of interest to DNA targeting were used in the LEOPARD diagnostic platform, allowing simultaneous detection of RNAs from different viruses in one test.

SCIENCE (2021)

Article Chemistry, Analytical

CRISPR/Cas14a-Based Isothermal Amplification for Profiling Plant MicroRNAs

Hao Yang et al.

Summary: The new method Cas14R enables detection of plant miRNAs without the need for reverse transcription and demethylation, providing a convenient tool for studying the biological processes in plants.

ANALYTICAL CHEMISTRY (2021)

Article Multidisciplinary Sciences

The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases

Han Altae-Tran et al.

Summary: IscB and TnpB, proteins encoded in the IS200/IS605 transposons, are likely ancestors of RNA-guided endonucleases Cas9 and Cas12, respectively, using RNA for DNA cleavage. This study unveils a widespread class of transposon-encoded RNA-guided nucleases, OMEGA, with great potential for biotechnological applications.

SCIENCE (2021)

Review Engineering, Biomedical

CRISPR-based diagnostics

Michael M. Kaminski et al.

Summary: This Review summarizes the rapidly expanding toolbox of CRISPR-based diagnostics, highlighting their applications in real-time diagnosis. It mentions that nucleic acid-based diagnostics are sensitive and specific, but most require expensive equipment and trained personnel.

NATURE BIOMEDICAL ENGINEERING (2021)

Review Biochemistry & Molecular Biology

Isothermal Nucleic Acid Amplification Techniques and Their Use in Bioanalysis

O. L. Bodulev et al.

BIOCHEMISTRY-MOSCOW (2020)

Review Microbiology

Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants

Kira S. Makarova et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Biochemistry & Molecular Biology

Type IV CRISPR Cas systems are highly diverse and involved in competition between plasmids

Rafael Pinilla-Redondo et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Biotechnology & Applied Microbiology

Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering

Zheng Yanli et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

Article Multidisciplinary Sciences

Massively multiplexed nucleic acid detection with Cas13

Cheri M. Ackerman et al.

NATURE (2020)

Article Biotechnology & Applied Microbiology

CRISPR-Cas12-based detection of SARS-CoV-2

James P. Broughton et al.

NATURE BIOTECHNOLOGY (2020)

Letter Cell Biology

SARS-CoV-2 detection with CRISPR diagnostics

Lu Guo et al.

CELL DISCOVERY (2020)

Article Cell Biology

COVID-19 diagnostics in context

Ralph Weissleder et al.

SCIENCE TRANSLATIONAL MEDICINE (2020)

Article Multidisciplinary Sciences

Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

Kayla G. Barnes et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay

Xiong Ding et al.

NATURE COMMUNICATIONS (2020)

Article Microbiology

Development and evaluation of a rapid CRISPR-based diagnostic for COVID-19

Tieying Hou et al.

PLOS PATHOGENS (2020)

Article Chemistry, Multidisciplinary

MeCas12a, a Highly Sensitive and Specific System for COVID-19 Detection

Peixiang Ma et al.

ADVANCED SCIENCE (2020)

Article Engineering, Biomedical

Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA

Maturada Patchsung et al.

NATURE BIOMEDICAL ENGINEERING (2020)

Review Biochemistry & Molecular Biology

Molecular Mechanisms of RNA Targeting by Cas13-containing Type VI CRISPR-Cas Systems

Mitchell R. O'Connell

JOURNAL OF MOLECULAR BIOLOGY (2019)

Article Chemistry, Multidisciplinary

An RNA-Guided Cas9 Nickase-Based Method for Universal Isothermal DNA Amplification

Ting Wang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Article Biotechnology & Applied Microbiology

Design of a generic CRISPR-Cas9 approach using the same sgRNA to perform gene editing at distinct loci

Soumaya Najah et al.

BMC BIOTECHNOLOGY (2019)

Article Engineering, Biomedical

Detection of unamplified target genes via CRISPR-Cas9 immobilized on a graphene field-effect transistor

Reza Hajian et al.

NATURE BIOMEDICAL ENGINEERING (2019)

Article Nanoscience & Nanotechnology

CRISPR-Cas14 is now part of the artillery for gene editing and molecular diagnostic

Guillermo Aquino-Jarquin

NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE (2019)

Review Cell Biology

The next generation of CRISPR-Cas technologies and applications

Adrian Pickar-Oliver et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences

Jenai Quan et al.

NUCLEIC ACIDS RESEARCH (2019)

Editorial Material Biotechnology & Applied Microbiology

Targeting Plant ssDNA Viruses with Engineered Miniature CRISPR-Cas14a

Muhammad Zuhaib Khan et al.

TRENDS IN BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

A cytosine deaminase for programmable single-base RNA editing

Omar O. Abudayyeh et al.

SCIENCE (2019)

Article Chemistry, Analytical

Cas12aVDet: A CRISPR/Cas12a-Based Platform for Rapid and Visual Nucleic Acid Detection

Bei Wang et al.

ANALYTICAL CHEMISTRY (2019)

Article Biochemical Research Methods

SHERLOCK: nucleic acid detection with CRISPR nucleases

Max J. Kellner et al.

NATURE PROTOCOLS (2019)

Article Biochemical Research Methods

HOLMESv2: A CRISPR-Cas12b-Assisted Platform for Nucleic Acid Detection and DNA Methylation Quantitation

Linxian Li et al.

ACS SYNTHETIC BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a

Daan C. Swarts et al.

MOLECULAR CELL (2019)

Article Immunology

CRISPR-based rapid and ultra-sensitive diagnostic test for Mycobacterium tuberculosis

Jing-Wen Ai et al.

EMERGING MICROBES & INFECTIONS (2019)

Review Biochemistry & Molecular Biology

The Biology of CRISPR-Cas: Backward and Forward

Frank Hille et al.

Editorial Material Biochemistry & Molecular Biology

CRISPR-based diagnostics

Hannah Stower

NATURE MEDICINE (2018)

Article Multidisciplinary Sciences

Field-deployable viral diagnostics using CRISPR-Cas13

Cameron Myhrvold et al.

SCIENCE (2018)

Article Multidisciplinary Sciences

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

Janice S. Chen et al.

SCIENCE (2018)

Article Multidisciplinary Sciences

Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6

Jonathan S. Gootenberg et al.

SCIENCE (2018)

Letter Cell Biology

CRISPR-Cas12a-assisted nucleic acid detection

Shi-Yuan Li et al.

CELL DISCOVERY (2018)

Article Multidisciplinary Sciences

Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

Lucas B. Harrington et al.

SCIENCE (2018)

Review Genetics & Heredity

Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

Kira S. Makarova et al.

CRISPR JOURNAL (2018)

Review Biotechnology & Applied Microbiology

CRISPR-Cas9/Cas12a biotechnology and application in bacteria

Ruilian Yao et al.

SYNTHETIC AND SYSTEMS BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

RNA targeting with CRISPR-Cas13

Omar O. Abudayyeh et al.

NATURE (2017)

Review Microbiology

Diversity and evolution of class 2 CRISPR-Cas systems

Sergey Shmakov et al.

NATURE REVIEWS MICROBIOLOGY (2017)

Article Multidisciplinary Sciences

RNA editing with CRISPR-Cas13

David B. T. Cox et al.

SCIENCE (2017)

Review Multidisciplinary Sciences

CRISPR-Cas: Adapting to change

Simon A. Jackson et al.

SCIENCE (2017)

Article Multidisciplinary Sciences

A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems

Migle Kazlauskiene et al.

SCIENCE (2017)

Article Biochemistry & Molecular Biology

Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components

Keith Pardee et al.

Article Multidisciplinary Sciences

Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli

Robert P. Hayes et al.

NATURE (2016)

Correction Biotechnology & Applied Microbiology

Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells (vol 34, pg 863, 2016)

Daesik Kim et al.

NATURE BIOTECHNOLOGY (2016)

Article Multidisciplinary Sciences

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

Omar O. Abudayyeh et al.

SCIENCE (2016)

Article Biochemistry & Molecular Biology

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

Bernd Zetsche et al.

Article Biochemistry & Molecular Biology

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

Sergey Shmakov et al.

MOLECULAR CELL (2015)

Article Biotechnology & Applied Microbiology

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

Isaac B. Hilton et al.

NATURE BIOTECHNOLOGY (2015)

Review Microbiology

An updated evolutionary classification of CRISPR-Cas systems

Kira S. Makarova et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Multidisciplinary Sciences

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

Samuel H. Sternberg et al.

NATURE (2014)

Article Biotechnology & Applied Microbiology

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

Wenyan Jiang et al.

NATURE BIOTECHNOLOGY (2013)

Article Multidisciplinary Sciences

Multiplex Genome Engineering Using CRISPR/Cas Systems

Le Cong et al.

SCIENCE (2013)

Article Multidisciplinary Sciences

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

Martin Jinek et al.

SCIENCE (2012)

Article Multidisciplinary Sciences

Small CRISPR RNAs guide antiviral defense in prokaryotes

Stan J. J. Brouns et al.

SCIENCE (2008)

Article Biochemistry & Molecular Biology

Identification of genes that are associated with DNA repeats in prokaryotes

R Jansen et al.

MOLECULAR MICROBIOLOGY (2002)