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Wei L, Wang Z, She Y, Fu H. CRISPR/Cas Multiplexed Biosensing: Advances, Challenges, and Perspectives. Anal Chem 2025. [PMID: 40424009 DOI: 10.1021/acs.analchem.4c04428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2025]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein systems are renowned for their high sensitivity and specificity, enabling them as a powerful diagnostic toolbox. Multiplexed detection of panels of targets, as opposed to single targets, is imperative for reliable and conclusive disease diagnostics. However, multiplex application of the CRISPR/Cas system has long been hindered by indistinguishable signals from specific targets due to nonspecific chaotic trans-cleavage. To make a breakthrough, substantial efforts have been devoted to CRISPR/Cas-powered multiplexed biosensing strategies, which consequently experienced rapid development over the past five years. This review systematically summarizes recent advances in CRISPR/Cas multiplexed detection encompassing Cas9, Cas12, and Cas13. Key focus issues include multiplex biosensing strategies and their respective advantages and limitations, sensing mechanisms, and detection performance of novel validated examples. Finally, the status and challenges of CRISPR/Cas multiplexed biosensing are critically discussed, and future outlooks are proposed for their potential practical application. This Perspective aims to inspire significant research and promote the development of the next generation of CRISPR/Cas multiplexed biosensing.
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Affiliation(s)
- Luyu Wei
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Zhilong Wang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuanbin She
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haiyan Fu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
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2
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Youngquist BM, Saliba J, Kim Y, Cutro TJ, Lyon CJ, Olivo J, Ha N, Fine J, Colman R, Vergara C, Robinson J, LaCourse S, Garfein RS, Catanzaro DG, Lange C, Perez-Then E, Graviss EA, Mitchell CD, Rodwell T, Ning B, Hu TY. Rapid tuberculosis diagnosis from respiratory or blood samples by a low cost, portable lab-in-tube assay. Sci Transl Med 2025; 17:eadp6411. [PMID: 40203083 DOI: 10.1126/scitranslmed.adp6411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 12/28/2024] [Accepted: 03/19/2025] [Indexed: 04/11/2025]
Abstract
Rapid portable assays are needed to improve diagnosis, treatment, and reduce transmission of tuberculosis (TB), but current tests are not suitable for patients in resource-limited settings with high TB burden. Here we report a low complexity, lab-in-tube system that is read by an integrated handheld device that detects Mycobacterium tuberculosis (Mtb) DNA in blood and respiratory samples from a variety of clinical settings. This microprocessor-controlled device uses an LCD user interface to control assay performance, automate assay analysis, and provide results in a simple readout. This point-of-care single-tube assay uses a DNA enrichment membrane and a low-cost cellulose disc containing lyophilized recombinase polymerase amplification and CRISPR-Cas12a reagents to attain single-nucleotide specificity and high sensitivity within 1 hour of sample application, without a conventional DNA isolation procedure. Assay results obtained with serum cell-free DNA isolated from a cohort of children aged 1 to 16 years detected pulmonary and extrapulmonary TB with high sensitivity versus culture and GeneXpert MTB/RIF results (81% versus 55% and 68%) and good specificity (94%), meeting the World Health Organization target product profile criteria for new nonsputum TB diagnostics. Changes in assay results for serum isolated during treatment were also highly predictive of clinical response. Results obtained with noninvasive sputum and saliva specimens from adults with bacteriologically confirmed pulmonary TB were also comparable to those reported for reference methods. This rapid and inexpensive lab-in-tube assay approach thus represents one means to address the need for point-of-care TB diagnostics useable in low-resource settings.
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Affiliation(s)
- Brady M Youngquist
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Julian Saliba
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Yelim Kim
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Thomas J Cutro
- School of Science and Engineering, Tulane University, New Orleans, LA 70112, USA
| | - Christopher J Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Juan Olivo
- O&M Medical School (O&Med), Santo Domingo, 10204, Dominican Republic
| | - Ngan Ha
- Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Janelle Fine
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Rebecca Colman
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Carlos Vergara
- O&M Medical School (O&Med), Santo Domingo, 10204, Dominican Republic
| | - James Robinson
- Section of Pediatric Infectious Disease, Department of Pediatrics, Tulane University, New Orleans, LA 70112, USA
| | - Sylvia LaCourse
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Richard S Garfein
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Christoph Lange
- Department of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, 23845, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, 23845, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, 23562, Germany
- Baylor College of Medicine and Texas Children's Hospital, Global Tuberculosis Program, Houston, TX 77030, USA
| | - Eddy Perez-Then
- O&M Medical School (O&Med), Santo Domingo, 10204, Dominican Republic
| | | | - Charles D Mitchell
- Department of Pediatrics, Division of Infectious Diseases and Immunology, University of Miami Miller School of Medicine, Batchelor Children's Research Institute, Miami, FL 33136, USA
| | - Timothy Rodwell
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Bo Ning
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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3
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Xue B, Qiao B, Jia L, Chi J, Su M, Song Y, Du J. A Sensitive and Fast microRNA Detection Platform Based on CRlSPR-Cas12a Coupled with Hybridization Chain Reaction and Photonic Crystal Microarray. BIOSENSORS 2025; 15:233. [PMID: 40277547 PMCID: PMC12024684 DOI: 10.3390/bios15040233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 03/25/2025] [Accepted: 03/31/2025] [Indexed: 04/26/2025]
Abstract
Changes in microRNA (miRNA) levels are closely associated with the pathological processes of many diseases. The sensitive and fast detection of miRNAs is critical for diagnosis and prognosis. Here, we report a platform employing CRISPR/Cas12a to recognize and report changes in miRNA levels while avoiding complex multi-thermal cycling procedures. A non-enzyme-dependent hybridization chain reaction (HCR) was used to convert the miRNA signal into double-stranded DNA, which contained a Cas12a activation sequence. The target sequence was amplified simply and isothermally, enabling the test to be executed at a constant temperature of 37 °C. The detection platform had the capacity to measure concentrations down to the picomolar level, and the target miRNA could be distinguished at the nanomolar level. By using photonic crystal microarrays with a stopband-matched emission spectrum of the fluorescent-quencher modified reporter, the fluorescence signal was moderately enhanced to increase the sensitivity. With this enhancement, analyzable fluorescence results were obtained in 15 min. The HCR and Cas12a cleavage processes could be conducted in a single tube by separating the two procedures into the bottom and the cap. We verified the sensitivity and specificity of this one-pot system, and both were comparable to those of the two-step method. Overall, our study produced a fast and sensitive miRNA detection platform based on a CRISPR/Cas12a system and enzyme-free HCR amplification. This platform may serve as a potential solution for miRNA detection in clinical practice.
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Affiliation(s)
- Bingjie Xue
- Beijing Anzhen Hospital, Capital Medical University, Key Laboratory of Remodeling-Related Cardio-Vascular Diseases, Ministry of Education, Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Disease, No. 2 Anzhen Road, Chaoyang District, Beijing 100029, China; (B.X.); (B.Q.); (L.J.)
| | - Bokang Qiao
- Beijing Anzhen Hospital, Capital Medical University, Key Laboratory of Remodeling-Related Cardio-Vascular Diseases, Ministry of Education, Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Disease, No. 2 Anzhen Road, Chaoyang District, Beijing 100029, China; (B.X.); (B.Q.); (L.J.)
| | - Lixin Jia
- Beijing Anzhen Hospital, Capital Medical University, Key Laboratory of Remodeling-Related Cardio-Vascular Diseases, Ministry of Education, Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Disease, No. 2 Anzhen Road, Chaoyang District, Beijing 100029, China; (B.X.); (B.Q.); (L.J.)
- Institute for Biological Therapy, Henan Academy of Innovations in Medical Science, Zhengzhou, 451163, China
| | - Jimei Chi
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing 100190, China; (J.C.); (M.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Su
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing 100190, China; (J.C.); (M.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanlin Song
- Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences (ICCAS)/Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing 100190, China; (J.C.); (M.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Du
- Beijing Anzhen Hospital, Capital Medical University, Key Laboratory of Remodeling-Related Cardio-Vascular Diseases, Ministry of Education, Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Disease, No. 2 Anzhen Road, Chaoyang District, Beijing 100029, China; (B.X.); (B.Q.); (L.J.)
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Miceli F, Bracaglia S, Sorrentino D, Porchetta A, Ranallo S, Ricci F. MAIGRET: a CRISPR-based immunoassay that employs antibody-induced cell-free transcription of CRISPR guide RNA strands. Nucleic Acids Res 2025; 53:gkaf238. [PMID: 40156855 PMCID: PMC11952961 DOI: 10.1093/nar/gkaf238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 03/08/2025] [Accepted: 03/17/2025] [Indexed: 04/01/2025] Open
Abstract
Here we report on the development of a CRISPR-based assay for the sensitive and specific detection of antibodies and antigens directly in complex sample matrices. The assay, called Molecular Assay based on antibody-Induced Guide-RNA Enzymatic Transcription (MAIGRET), is based on the use of a responsive synthetic DNA template that triggers the cell-free in vitro transcription of a guide RNA strand upon recognition of a specific target antibody. Such transcribed guide RNA activates the DNA collateral activity of the Cas12a enzyme, leading to the downstream cleavage of a fluorophore/quencher-labeled reporter and thus resulting in an increase in the measured fluorescence signal. We have used MAIGRET for the detection of six different antibodies with high sensitivity (detection limit in the picomolar range) and specificity (no signal in the presence of non-target antibodies). MAIGRET can also be adapted to a competitive approach for the detection of specific antigens. With MAIGRET, we significantly expand the scope and applicability of CRISPR-based sensing approaches to potentially enable the measurement of any molecular target for which an antibody is available.
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Affiliation(s)
- Francesca Miceli
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Sara Bracaglia
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Daniela Sorrentino
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, United States
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi, INBB, Via dei Carpegna, 00165 Rome, Italy
| | - Simona Ranallo
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi, INBB, Via dei Carpegna, 00165 Rome, Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi, INBB, Via dei Carpegna, 00165 Rome, Italy
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Modi NH, Dunkley ORS, Bell AG, Hennig E, Wats A, Huang Y, Daivaa N, Myhrvold C, Xie YL, Banada P. Simplified Co-extraction of total Nucleic Acids from Respiratory Samples for detection of Mycobacterium tuberculosis and SARS-CoV-2 optimized for compatibility across Diagnostic Platforms. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.02.27.25322880. [PMID: 40093238 PMCID: PMC11908299 DOI: 10.1101/2025.02.27.25322880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Tuberculosis (TB) and COVID-19 are leading infectious diseases with high mortality, caused by Mycobacterium tuberculosis (Mtb) and SARS-CoV-2 (SC2), respectively. Co-infection is common but is often undiagnosed as it is challenging to process both pathogens from a single sample. In this study, we present a simple and efficient method for co-extracting nucleic acids (NA) from these two distinct respiratory pathogens for downstream diagnostic testing. We evaluated three different nucleic acid amplification (NAA)-based platforms, LightCycler480 (LC480) qPCR, Qiacuity digital PCR (dPCR), and Cytation3 for CRISPR-Cas13a-based SHINE-TB/SC2 detection assays. Chelex-100 chelating resin-based boiling preparation method was optimized for Mtb NA extraction from saliva and sputum. Saliva showed compatibility with all three platforms, with sensitivity as low as 100 CFU/ml (or 2 genomic copies/μl). This method worked well for sputum using dPCR at 100% (21/21) positivity, though the CRISPR-based SHINE-TB assay showed more variability and sensitivity to sputum inhibitor carry-over, resulting in an 81% positive rate (17/21). Diluting sputum with TE buffer (1:1) improved the detection (2/4). Extraction efficiency of our method was 48%, 62.2%, 86.4% and 99.3% for concentrations 105, 104, 103 and 10 CFU/ml, respectively. The dynamic range for Mtb spiked in pooled sputum showed 100% detection (N=8) at ≥103 CFU/ml with all three methods. Dual-pathogen co-extraction and detection of SC2 (105 PFU/ml) and Mtb (105 CFU/ml) in salivary sputum was successful using CRISPR-Cas13a assays. We have developed a rapid and efficient co-extraction method for multi-pathogen testing across diagnostic platforms and believe this is the first protocol optimized to co-extract Mtb and SARS-CoV-2 from a single sample.
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Affiliation(s)
- Nisha H Modi
- Department of Medicine, International Center for Public Health, Rutgers University, Newark, NJ, 07103
| | - Owen R S Dunkley
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544
| | - Alexandra G Bell
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544
| | - Emily Hennig
- Department of Medicine, International Center for Public Health, Rutgers University, Newark, NJ, 07103
| | - Aanchal Wats
- Department of Medicine, International Center for Public Health, Rutgers University, Newark, NJ, 07103
| | - Yujia Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544
| | - Naranjargal Daivaa
- Department of Medicine, International Center for Public Health, Rutgers University, Newark, NJ, 07103
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Yingda L Xie
- Department of Medicine, International Center for Public Health, Rutgers University, Newark, NJ, 07103
| | - Padmapriya Banada
- Department of Medicine, International Center for Public Health, Rutgers University, Newark, NJ, 07103
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Zou Y, Liu M, Gao Z, Xue Y, Qiu J, Zhang H, Li X, Zhang C, Shu B. Facile and Ultrafast Microfluidic Photothermal PCR for Autonomous and Quantitative Point-of-Care Pathogen Detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025; 21:e2411417. [PMID: 39945080 DOI: 10.1002/smll.202411417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 01/21/2025] [Indexed: 03/28/2025]
Abstract
Point-of-care (POC) pathogen detection is highly desirable in diverse fields such as infectious disease diagnosis, food safety testing, and environmental monitoring. Herein, the study seeks to address this critical need by developing an automated microfluidic photothermal quantitative polymerase chain reaction (AMP-qPCR) system in a greatly simplified format. A key element of AMP-qPCR is an architecture that combines the design of a clockwork-like, magnetically-driven multi-chamber cartridge with the use of a cheap black tape beneath the PCR chamber as a fast photothermal-responsive engine. This not only enables the unprocessed sample to be lysed, purified, and subjected to real-time fluorescence PCR in an ultracompact and autonomous manner but also eliminates the need for sophisticated photonic material/device fabrication that is frequently required for performing ultrafast photothermal PCR. It is shown that AMP-qPCR can accomplish high-efficient bacterial DNA extraction and quantitative PCR within 18.5 min, enabling accurate quantification of bacteria concentration from 108 to 102 CFU·mL-1. Furthermore, its practical applicability is demonstrated in detecting Neisseria gonorrhoeae from sexually transmitted infection-suspected patients by using clinical urine and cervical swab specimens, exhibiting matched performance to the benchtop automated machine. The presented platform enhances the availability of POC molecular diagnostics for on-site and in-home testing.
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Affiliation(s)
- Yaowei Zou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science & College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Mingxu Liu
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Zixi Gao
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science & College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Yaohua Xue
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Jieyu Qiu
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Huizhen Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Xinying Li
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Chunsun Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science & College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Bowen Shu
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
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Hershan AA. Virology, epidemiology, transmissions, diagnostic tests, prophylaxis and treatments of human Mpox: Saudi Arabia perspective. Front Cell Infect Microbiol 2025; 15:1530900. [PMID: 40093536 PMCID: PMC11906441 DOI: 10.3389/fcimb.2025.1530900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 02/13/2025] [Indexed: 03/19/2025] Open
Abstract
Mpox (Monkeypox) is a highly contagious viral disease that can be transmitted from animal-to-human or human-to-human through intimate contact, Mpox is caused by the monkeypox virus (MPXV), which is an enveloped double-stranded DNA that belongs to the genus Orthopoxvirus, Poxviridae family, and subfamily Chordopoxvirinae. Mpox cases were previously only reported in West and Central Africa, however in recent times non-endemic countries including Saudi Arabia (SA) also reported confirmed Mpox cases. The first laboratory-confirmed human Mpox case in SA was reported on 14 July 2022, since then a number of confirmed Mpox cases have been reported by WHO in SA. These confirmed Mpox cases in SA were observed among individuals with a history of visiting European Union countries. SA is not only at risk of importation of Mpox cases owing to travel to such countries, but also there are various other risk factors including geographic proximity to the African continent, trade in exotic animals, and massive inflow of tourists. Therefore, government health authorities of SA should continue to collaborate with various international health organizations including WHO to prevent, manage or monitor potential health risks at most of the entry points in SA including highways, seaports, and airports by ensuring adherence to hygiene protocols, vaccinations, and health screenings. There are a range of diagnostic tests are currently available that can be used in SA to confirm Mpox infections, including real-time PCR, loop-mediated isothermal amplification, serological testing, clustered regularly interspaced short palindromic repeat-CRISPR-associated protein (CRISPR-Cas)-based systems, whole-genome sequencing, electron microscopy, and virus isolation and culture. There is no approved treatment specifically for Mpox, however multiple approved antiviral agents for smallpox treatment were found to be useful in Mpox treatment and in the management of Mpox outbreaks, such as- trifluridine, brincidofovir, tecovirimat, and cidofovir. The aim of this review is to provide valuable insights regarding virology, pathogenesis, epidemiology, transmissions, clinical presentation, diagnostic tests, prophylactic measures and therapeutic options of Mpox from SA perspective. Moreover, a side-by-side discussion on the global trend and scenarios of Mpox has been provided for comparison and further improvement in measures against Mpox in SA.
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Affiliation(s)
- Almonther Abdullah Hershan
- Department of Basic Medical Sciences, College of Medicine, The University of Jeddah, Jeddah, Saudi Arabia
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8
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Baker DV, Bernal-Escalante J, Traaseth C, Wang Y, Tran MV, Keenan S, Algar WR. Smartphones as a platform for molecular analysis: concepts, methods, devices and future potential. LAB ON A CHIP 2025; 25:884-955. [PMID: 39918205 DOI: 10.1039/d4lc00966e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2025]
Abstract
Over the past 15 years, smartphones have had a transformative effect on everyday life. These devices also have the potential to transform molecular analysis over the next 15 years. The cameras of a smartphone, and its many additional onboard features, support optical detection and other aspects of engineering an analytical device. This article reviews the development of smartphones as platforms for portable chemical and biological analysis. It is equal parts conceptual overview, technical tutorial, critical summary of the state of the art, and outlook on how to advance smartphones as a tool for analysis. It further discusses the motivations for adopting smartphones as a portable platform, summarizes their enabling features and relevant optical detection methods, then highlights complementary technologies and materials such as 3D printing, microfluidics, optoelectronics, microelectronics, and nanoparticles. The broad scope of research and key advances from the past 7 years are reviewed as a prelude to a perspective on the challenges and opportunities for translating smartphone-based lab-on-a-chip devices from prototypes to authentic applications in health, food and water safety, environmental monitoring, and beyond. The convergence of smartphones with smart assays and smart apps powered by machine learning and artificial intelligence holds immense promise for realizing a future for molecular analysis that is powerful, versatile, democratized, and no longer just the stuff of science fiction.
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Affiliation(s)
- Daina V Baker
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - Jasmine Bernal-Escalante
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - Christine Traaseth
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - Yihao Wang
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - Michael V Tran
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - Seth Keenan
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
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9
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van Dongen JE, Segerink LI. Building the Future of Clinical Diagnostics: An Analysis of Potential Benefits and Current Barriers in CRISPR/Cas Diagnostics. ACS Synth Biol 2025; 14:323-331. [PMID: 39880685 PMCID: PMC11854988 DOI: 10.1021/acssynbio.4c00816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/15/2025] [Accepted: 01/17/2025] [Indexed: 01/31/2025]
Abstract
Advancements in molecular diagnostics, such as polymerase chain reaction and next-generation sequencing, have revolutionized disease management and prognosis. Despite these advancements in molecular diagnostics, the field faces challenges due to high operational costs and the need for sophisticated equipment and highly trained personnel besides having several technical limitations. The emergent field of CRISPR/Cas sensing technology is showing promise as a new paradigm in clinical diagnostics, although widespread clinical adoption remains limited. This perspective paper discusses specific cases where CRISPR/Cas technology can surmount the challenges of existing diagnostic methods by stressing the significant role that CRISPR/Cas technology can play in revolutionizing clinical diagnostics. It underscores the urgency and importance of addressing the technological and regulatory hurdles that must be overcome to harness this technology effectively in clinical laboratories.
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Affiliation(s)
- Jeanne E. van Dongen
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical
Medical Centre, Max Planck Institute for Complex Fluid Dynamics, University
of Twente, P.O. Box 217, 7500 AE Enschede, The
Netherlands
| | - Loes I. Segerink
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical
Medical Centre, Max Planck Institute for Complex Fluid Dynamics, University
of Twente, P.O. Box 217, 7500 AE Enschede, The
Netherlands
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10
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Mai Z, Zhou T, Lin Z. Detecting CYP2C19 genes through an integrated CRISPR/Cas13a-assisted system. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2025; 17:1382-1388. [PMID: 39836103 DOI: 10.1039/d4ay01930j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
CYP2C19 gene single nucleotide polymorphisms (SNPs) should be considered in the clinical use of clopidogrel as they have important guiding value for predicting the risk of bleeding and thrombosis after clopidogrel treatment. The CRISPR/Cas system is increasingly used for SNP detection owing to its single-nucleotide mismatch specificity. Simultaneous detection of multiple SNPs for rapid identification of the CYP2C19 genotype is important, but there is no method to detect a wide variety of CYP2C19 SNPs. This study proposes a new integrated system that integrates the PCR reaction and CRISPR/Cas detection of three CYP2C19 genes on a device, achieving rapid, sensitive, and specific detection. In our design, magnetic beads with three different sizes capture target nucleic acid from the sample, which are dragged through different areas by magnetic force, for PCR amplification reaction and CRISPR/Cas13a detection of CYP2C19*2, CYP2C19*3 and CYP2C19*17 genes. Note that magnetic beads were sorted via microporous PC membranes of different apertures. This study exhibits a broad clinical application prospect and provides a favorable tool for clinical clopidogrel administration.
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Affiliation(s)
- Zhaokang Mai
- Department of Cardiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510630, China.
| | - Tao Zhou
- Department of Cardiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510630, China.
| | - Zhun Lin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
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11
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Grimm MS, Myhrvold C. Using CRISPR for viral nucleic acid detection. Methods Enzymol 2025; 712:245-275. [PMID: 40121076 DOI: 10.1016/bs.mie.2025.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
Abstract
Pathogenic microorganisms, such as viruses, have threatened human health and will continue to contribute to future epidemics and pandemics, highlighting the importance of developing effective diagnostics. To contain viral outbreaks within populations, fast and early diagnosis of infected individuals is essential. Although current standard methods are highly sensitive and specific, like RT-qPCR, some can have slow turnaround times, which can hinder the prevention of viral transmission. The discovery of CRISPR-Cas systems in bacteria and archaea initially revolutionized the world of genome editing. Intriguingly, CRISPR-Cas enzymes also have the ability to detect nucleic acids with high sensitivity and specificity, which sparked the interest of researchers to also explore their potential in diagnosis of viral pathogens. In particular, the CRISPR-Cas13 system has been used as a tool for detecting viral nucleic acids. Cas13's capability to detect both target RNA and non-specific RNAs has led to the development of detection methods that leverage these characteristics through designing specific detection read-outs. Optimization of viral sample collection, amplification steps and the detection process within the Cas13 detection workflow has resulted in assays with high sensitivity, rapid turnaround times and the capacity for large-scale implementation. This review focuses on the significant innovations of various CRISPR-Cas13-based viral nucleic acid detection methods, comparing their strengths and weaknesses while highlighting Cas13's great potential as a tool for viral diagnostics.
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Affiliation(s)
- Maaike S Grimm
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ, United States; Department of Chemistry, Princeton University, Princeton, NJ, United States.
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12
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Li Y, Xu R, Quan F, Wu Y, Wu Y, Zhang Y, Liang Y, Zhang Z, Gao H, Deng R, Zhang K, Li J. Topologically constrained DNA-mediated one-pot CRISPR assay for rapid detection of viral RNA with single nucleotide resolution. EBioMedicine 2025; 112:105564. [PMID: 39862805 PMCID: PMC11873568 DOI: 10.1016/j.ebiom.2025.105564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 01/02/2025] [Accepted: 01/09/2025] [Indexed: 01/27/2025] Open
Abstract
BACKGROUND The widespread and evolution of RNA viruses, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the importance of fast identification of virus subtypes, particularly in non-laboratory settings. Rapid and inexpensive at-home testing of viral nucleic acids with single-base resolution remains a challenge. METHODS Topologically constrained DNA ring is engineered as substrates for the trans-cleavage of Cas13a to yield an accelerated post isothermal amplification. The capacity of CRISPR/Cas13a for discriminating single nucleotide variant (SNV) in viral genome is leveraged by designing synthetic mismatches and hairpin structure in CRISPR RNA (crRNA), enabling robust discrimination of different SARS-CoV-2 variants. Via optimisation of CasTDR3pot to be one-pot assay, CasTDR1pot can detect Omicron and its subvariants, with only a few copies in clinical samples in less than 30 min without pre-amplification. FINDINGS The detection system boasts high sensitivity (0.1 aM), single-base specificity, and the advantage of a rapid "sample-to-answer" process, which takes only 30 min. In the detection of SARS-CoV-2 clinical samples and their variant strains, CasTDR1pot has achieved 100% accuracy. Furthermore, the design of a portable signal-reading device facilitates user-friendly result interpretation. For the detection needs of different RNA viruses, the system can be adapted simply by designing the corresponding crRNA. INTERPRETATION Our study provides a rapid and accurate molecular diagnostic tool for point-of-care testing, epidemiological screening, and the detection of diseases associated with other RNA biomarkers with excellent single nucleotide differentiation, high sensitivity, and simplicity. FUNDING National Key Research and Development Program of China (No. 2023YFB3208302), National Natural Science Foundation of China (No. 22377110, 22034004, 82402749, 82073787, 22122409), National Key Research and Development Program of China (No. 2021YFA1200104), Henan Province Fund for Cultivating Advantageous Disciplines (No. 222301420019).
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Affiliation(s)
- Yanan Li
- School of Pharmaceutical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Ru Xu
- School of Pharmaceutical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China; Nanyang First People's Hospital, Nanyang, Henan, 473000, China
| | - Fenglei Quan
- School of Pharmaceutical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yonghua Wu
- School of Pharmaceutical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yige Wu
- School of Pharmaceutical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yongyuan Zhang
- Department of Pathogen Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yan Liang
- School of Pharmaceutical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Hua Gao
- Department of Pathogen Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China.
| | - Ruijie Deng
- College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China.
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China; Beijing Life Science Academy, Beijing, 102209, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, New Cornerstone Science Foundation, Beijing, 100084, China.
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13
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Cheng ZH, Luo XY, Yu SS, Min D, Zhang SX, Li XF, Chen JJ, Liu DF, Yu HQ. Tunable control of Cas12 activity promotes universal and fast one-pot nucleic acid detection. Nat Commun 2025; 16:1166. [PMID: 39885211 PMCID: PMC11782535 DOI: 10.1038/s41467-025-56516-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 01/17/2025] [Indexed: 02/01/2025] Open
Abstract
The CRISPR-based detection methods have been widely applied, yet they remain limited by the non-universal nature of one-pot diagnostic approaches. Here, we report a universal one-pot fluorescent method for the detection of epidemic pathogens, delivering results within 15-20 min. This method uses heparin sodium to precisely tunes the cis-cleavage capability of Cas12 via interference with the Cas12a-crRNA binding process, thereby generating significant fluorescence due to the accumulation of isothermal amplification products. Additionally, this universal assay accommodates both classic and suboptimal PAMs, as well as various Cas12a subtypes such as LbCas12a, AsCas12a, and AapCas12b. Such a robust method demonstrates sensitivity and specificity exceeding 95% in the detection of monkeypox pseudovirus, influenza A virus, and SARS-CoV-2 from saliva or wastewater samples, when compared with qPCR or RT-qPCR. Moreover, the cost of heparin sodium per thousand uses is $0.01 to $0.04 only. Collectively, this universal and fast one-pot approach based on heparin sodium offers potential possibilities for point-of-care testing.
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Affiliation(s)
- Zhou-Hua Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China
| | - Xi-Yan Luo
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China
| | - Sheng-Song Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China
| | - Shu-Xia Zhang
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, 350001, Fujian, China
| | - Xiao-Fan Li
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, 350001, Fujian, China
| | - Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China.
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China.
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14
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Teymur A, Hussain I, Tang C, Saxena R, Erickson D, Wu T. Portable Fluorescence Microarray Reader-Enabled Biomarker Panel Detection System for Point-of-Care Diagnosis of Lupus Nephritis. MICROMACHINES 2025; 16:156. [PMID: 40047601 PMCID: PMC11857597 DOI: 10.3390/mi16020156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2024] [Revised: 01/20/2025] [Accepted: 01/27/2025] [Indexed: 03/09/2025]
Abstract
Point-of-care (POC) testing has revolutionized diagnostics by providing rapid, accessible solutions outside traditional laboratory settings. However, many POC systems lack the sensitivity or multiplexing capability required for complex diseases. This study introduces an LED-based fluorescence reader designed for POC applications, enabling multiplex detection of lupus nephritis (LN) biomarkers using a biomarker microarray (BMA) slide. The reader integrates an LED excitation source, neutral density (ND) filters for precise intensity control, and onboard image processing with Gaussian smoothing and centroid thresholding to enhance signal detection and localization. Five LN biomarkers (VSIG4, OPN, VCAM1, ALCAM, and TNFRSF1B) were assessed, and performance was validated against a Genepix laser-based scanner. The LED reader demonstrated strong correlation coefficients (r = 0.96-0.98) with the Genepix system for both standard curves and patient samples, achieving robust signal-to-noise ratios and reproducibility across all biomarkers. The multiplex format reduced sample volume and allowed simultaneous analysis of multiple biomarkers. These results highlight the reader's potential to bridge the gap between laboratory-grade precision and POC accessibility. By combining portability, cost-effectiveness, and high analytical performance, this fluorescence reader provides a practical solution for POC diagnostics, particularly in resource-limited settings, improving the feasibility of routine monitoring and early intervention for diseases requiring comprehensive biomarker analysis.
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Affiliation(s)
- Aygun Teymur
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA; (A.T.); (C.T.)
| | - Iftak Hussain
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA;
| | - Chenling Tang
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA; (A.T.); (C.T.)
| | - Ramesh Saxena
- Department of Nephrology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA;
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA; (A.T.); (C.T.)
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15
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Allan-Blitz LT, Adams G, Sanders G, Shah P, Ramesh K, Jarolimova J, Ard KL, Branda JA, Klausner JD, Sabeti PC, Lemieux JE. Preliminary clinical performance of a Cas13a-based lateral flow assay for detecting Neisseria gonorrhoeae in urine specimens. mSphere 2025; 10:e0067724. [PMID: 39688405 PMCID: PMC11774021 DOI: 10.1128/msphere.00677-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 11/07/2024] [Indexed: 12/18/2024] Open
Abstract
Nucleic acid amplification testing (NAAT) for N. gonorrhoeae is unavailable in resource-limited settings. We previously developed a CRISPR-based lateral flow assay for detecting N. gonorrhoeae. We aimed to pair that assay with point-of-care DNA extraction, assess performance in clinical urine specimens, and optimize assay kinetics. We collected urine specimens among men presenting with urethritis enrolling in a clinical trial at the Massachusetts General Hospital Sexual Health Clinic. We assessed the quantified DNA yield of detergent-based extractions with and without heat. We selected one detergent for extracting all specimens, paired with isothermal recombinase polymerase amplification for 90 minutes and lateral flow Cas13a detection, interpreted via pixel intensity analysis. We also trained a smartphone-based machine-learning model on 1,008 images to classify lateral flow results. We used the model to interpret lateral flow results from the clinical specimens. We also tested a modified amplification chemistry with a second forward primer lacking the T7-promoter to accelerate reaction kinetics. Extraction with 0.02% Triton X resulted in an average DNA yield of 2.6 × 106 copies/µL (SD ± 6.7 × 105). We treated 40 urine specimens (n = 12 positive) with 0.02% Triton X, and using quantified pixel intensity analysis, the Cas13a-based assay correctly classified all specimens (100% agreement; 95% CI 91.2%-100%). The machine-learning model correctly classified 45/45 strips in the validation data set and all 40 lateral flow strips from clinical specimens. Including the second forward primer reduced incubation time to 60 minutes. Using point-of-care DNA extraction, our Cas13a-based lateral flow N. gonorrhoeae assay demonstrated promising performance among clinical urine specimens.IMPORTANCEUsing a CRISPR-based assay we previously developed for Neisseria gonorrhoeae detection, we developed new techniques to facilitate point-of-care use. We then demonstrated the promising performance of that assay in clinical specimens. Furthermore, we developed a smartphone-based machine learning application for assisting interpretation of lateral flow strip results. Such an assay has the potential to transform the care of sexually transmitted infections in low-resource settings where diagnostic tests are unavailable. A point-of-care pathogen-specific assay, paired with the connectivity offered by a smartphone application, can also support public health surveillance efforts in such areas.
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Affiliation(s)
- Lao-Tzu Allan-Blitz
- Division of Global Health Equity, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gordon Adams
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gabriela Sanders
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Palak Shah
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Krithik Ramesh
- Massachusetts Institute of Technology, Boston, Massachusetts, USA
| | - Jana Jarolimova
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kevin L. Ard
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John A. Branda
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jeffrey D. Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Jacob E. Lemieux
- Broad Institute of Massachusetts Institute of Technology and Harvard, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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16
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Jung J, Dreyer KS, Dray KE, Muldoon JJ, George J, Shirman S, Cabezas MD, d’Aquino AE, Verosloff MS, Seki K, Rybnicky GA, Alam KK, Bagheri N, Jewett MC, Leonard JN, Mangan NM, Lucks JB. Developing, Characterizing, and Modeling CRISPR-Based Point-of-Use Pathogen Diagnostics. ACS Synth Biol 2025; 14:129-147. [PMID: 39670656 PMCID: PMC11744932 DOI: 10.1021/acssynbio.4c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 12/14/2024]
Abstract
Recent years have seen intense interest in the development of point-of-care nucleic acid diagnostic technologies to address the scaling limitations of laboratory-based approaches. Chief among these are combinations of isothermal amplification approaches with CRISPR-based detection and readouts of target products. Here, we contribute to the growing body of rapid, programmable point-of-care pathogen tests by developing and optimizing a one-pot NASBA-Cas13a nucleic acid detection assay. This test uses the isothermal amplification technique NASBA to amplify target viral nucleic acids, followed by the Cas13a-based detection of amplified sequences. We first demonstrate an in-house formulation of NASBA that enables the optimization of individual NASBA components. We then present design rules for NASBA primer sets and LbuCas13a guide RNAs for the fast and sensitive detection of SARS-CoV-2 viral RNA fragments, resulting in 20-200 aM sensitivity. Finally, we explore the combination of high-throughput assay condition screening with mechanistic ordinary differential equation modeling of the reaction scheme to gain a deeper understanding of the NASBA-Cas13a system. This work presents a framework for developing a mechanistic understanding of reaction performance and optimization that uses both experiments and modeling, which we anticipate will be useful in developing future nucleic acid detection technologies.
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Affiliation(s)
- Jaeyoung
K. Jung
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Kathleen S. Dreyer
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Kate E. Dray
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Joseph J. Muldoon
- Department
of Medicine, University of California, San
Francisco, San Francisco, California 94143, United States
- Gladstone-UCSF
Institute of Genomic Immunology, San Francisco, California 94158, United States
| | - Jithin George
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, United States
- NSF-Simons
Center for Quantitative Biology, Northwestern
University, Evanston, Illinois 60208, United States
| | - Sasha Shirman
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- NSF-Simons
Center for Quantitative Biology, Northwestern
University, Evanston, Illinois 60208, United States
| | - Maria D. Cabezas
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Biomedical Engineering, Northwestern
University, Evanston, Illinois 60208, United States
| | - Anne E. d’Aquino
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Stemloop,
Inc., Evanston, Illinois 60201, United States
- Interdisciplinary
Biological Sciences Program, Northwestern
University, Evanston, Illinois 60208, United States
| | - Matthew S. Verosloff
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary
Biological Sciences Program, Northwestern
University, Evanston, Illinois 60208, United States
| | - Kosuke Seki
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Grant A. Rybnicky
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary
Biological Sciences Program, Northwestern
University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United States
| | | | - Neda Bagheri
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary
Biological Sciences Program, Northwestern
University, Evanston, Illinois 60208, United States
- Departments
of Biology and Chemical Engineering, University
of Washington, Seattle, Washington 98195, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Joshua N. Leonard
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary
Biological Sciences Program, Northwestern
University, Evanston, Illinois 60208, United States
| | - Niall M. Mangan
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, United States
- NSF-Simons
Center for Quantitative Biology, Northwestern
University, Evanston, Illinois 60208, United States
| | - Julius B. Lucks
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Water Research, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United States
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17
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Dong T, Qin L, Wang Z, Fan C, Shen C, Feng P, Kong Q, Ke B, Ying B, Li F. Point-of-Care Diagnosis of Tuberculosis Using a Portable Nucleic Acid Test with Distance-Based Readout. Anal Chem 2024; 96:20204-20212. [PMID: 39665389 DOI: 10.1021/acs.analchem.4c04180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2024]
Abstract
Rapid and accurate diagnosis of tuberculosis (TB) infection in resource-limited settings is critically needed to stop the spread of the disease but remains difficult to achieve. Herein, we report a fast, inexpensive nucleic acid test with distance-based readout (FINDR) for TB. Based on the unique chromatographic behavior of DNA intercalating dye on unmodified cellulose paper, our FINDR platform converted the amplicons of loop-mediated isothermal amplification (LAMP) into the migration distance on a paper-based analytical device. A suite of innovations were further introduced to enhance the accessibility of FINDR, including (1) screening optimal LAMP primers for distance-based readout; (2) developing a chip-on-cover design capable of streamlining LAMP amplification and distance-based detection in a fully sealed FINDR chip with a simple hand-based swirling for liquid transfer; and (3) integrating FINDR with an upstream portable pipetting-free DNA extractor and a downstream smartphone app to simplify sample processing and data interpretation. With these innovations, FINDR demonstrated a high clinical sensitivity (96.6%) and specificity (100%) upon validation against clinical sputum samples. Successful clinical validation was also achieved when FINDR was deployed as a point-of-care test for detecting TB under resource-limited conditions.
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Affiliation(s)
- Tianyu Dong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Liwen Qin
- Laboratory of Anesthesiology & Critical Care Medicine, Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Zhiyin Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Chen Fan
- Department of Orthopedics Surgery, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu 610041, P. R. China
| | - Chenlan Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Pin Feng
- Department of Orthopedics Surgery, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu 610041, P. R. China
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Qingquan Kong
- Department of Orthopedics Surgery, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu 610041, P. R. China
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Bowen Ke
- Laboratory of Anesthesiology & Critical Care Medicine, Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Binwu Ying
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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18
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Osborne M, Chen H, Kadhiresan P, Mahbub N, Malekjahani A, Kozlowski HN, Udugama B, Nguyen LNM, Perusini S, Mubareka S, Chan WCW. QBox: An Automated Portable System for Multiplex Quantum Dot Barcode Diagnostics. ACS NANO 2024; 18:33629-33642. [PMID: 39585955 DOI: 10.1021/acsnano.4c12306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2024]
Abstract
The COVID-19 pandemic accelerated the development of automated systems for detecting molecular targets for the point-of-care. However, these systems have limited multiplexing capabilities because of the need to alter their hardware to accommodate additional targets and probes. Quantum dot barcodes address this multiplexing obstacle, but their assays have multiple steps that rely on extensive training and laboratory equipment. Here, we built a portable cartridge-and-instrument system that automates the extraction, reverse transcription, amplification, and detection steps of a quantum dot barcode assay. This entire workflow can be completed in 40 minutes. We clinically validated the system with SARS-CoV-2 patient samples (n = 50, 92% sensitivity, 100% specificity). We then demonstrated multiplexing with 4-barcode respiratory and 5-barcode bloodborne pathogen panels. Our portable system opens quantum dot barcodes for broad use in rapid multiplexed detection of infectious pathogens with the potential for detecting cancer and other genetic diseases.
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Affiliation(s)
- Matthew Osborne
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Hongmin Chen
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Pranav Kadhiresan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Nafisa Mahbub
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Ayden Malekjahani
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Hannah N Kozlowski
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- MD/PhD Program, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Buddhisha Udugama
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Luan N M Nguyen
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | | | - Samira Mubareka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
| | - Warren C W Chan
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E2, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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19
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Pian H, Wang H, Wang H, Tang F, Li Z. Capillarity-powered and CRISPR/Cas12a-responsive DNA hydrogel distance sensor for highly sensitive visual detection of HPV DNA. Biosens Bioelectron 2024; 264:116657. [PMID: 39137521 DOI: 10.1016/j.bios.2024.116657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/30/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
The rapid and specific identification and sensitive detection of human papillomavirus (HPV) infection is critical for preventing cervical cancer, particularly in resource-limited regions. In this work, we hope to propose a capillarity-powered and CRISPR/Cas12a-responsive DNA hydrogel distance sensor for point-of-care (POC) DNA testing. Using the thermal reversibility of DNA hydrogel and capillarity, the novel DNA hydrogel distance sensor can be rapidly and simply constructed by loading an ultra-thin CRISPR/Cas12a-responsive DNA-crosslinked hydrogel film at the end of the capillary tube. The target DNA-specific recombinase polymerase reaction (RPA) amplicons activate the trans-cleavage activity of the Cas12a enzyme, cleaving the crosslinked DNA in hydrogel film, and causing an increase of hydrogel's permeability. As a result, a sample solution containing target DNA travels into the capillary tube at a longer distance compared to the negative samples. Reading the solution traveling distance in capillary tubes, the novel sensor realizes target DNA detection without any special equipment. Benefiting from the exponential target amplification of RPA and multiple turnover response of trans-cleavage of CRISPR/Cas12a, the developed sensor can visually and specifically detect as low as 1 aM HPV 16 DNA within 30 min. These outstanding features, including exceptional sensitivity and specificity, simple and portable design, mild measurement conditions, quick turnaround time, and user-friendly read-out, make the novel distance sensor a promising option for POC diagnostic applications.
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Affiliation(s)
- Hongru Pian
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Fu Tang
- School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
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20
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Zhao Y, Dai J, Zhang Z, Chen J, Chen Y, Hu C, Chen X, Guo A. CRISPR-Cas13a-Based Lateral Flow Assay for Detection of Bovine Leukemia Virus. Animals (Basel) 2024; 14:3262. [PMID: 39595314 PMCID: PMC11590953 DOI: 10.3390/ani14223262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 11/11/2024] [Accepted: 11/12/2024] [Indexed: 11/28/2024] Open
Abstract
Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis (EBL), which presents worldwide prevalence. BLV caused substantial economic loss in China around the 1980s; then, it could not be detected for some time, until recently. Due to its latent and chronic characteristics, the efficient and accurate detection of BLV is of utmost significance to the timely implementation of control measures. Therefore, this study harnessed the recombinase-aided amplification (RAA), clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 13a (Cas13a) technology, and lateral flow (LF) strips to develop an efficient method for detection of BLV. In this method, isothermal amplification of the targeted pol gene is performed at 37 °C with a detection threshold of 1 copy/µL, and the procedure is completed in 100 min. This assay demonstrated high selectivity for BLV, as indicated by the absence of a cross-reaction with six common bovine pathogens. Remarkably, 100 blood samples from dairy cows were tested in parallel with a conventional quantitative polymerase chain reaction (qPCR) and this method and the results showed 100% agreement. Furthermore, this method exhibited good repeatability. In conclusion, in this study, we established a sensitive and specific method for BLV detection, which shows promise for application in BLV surveillance.
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Affiliation(s)
- Yuxi Zhao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (J.C.); (Y.C.); (C.H.); (X.C.)
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-Products, China Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwen Dai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China;
| | - Zhen Zhang
- Henan Seed Industry Development Center, Zhengzhou 450045, China
| | - Jianguo Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (J.C.); (Y.C.); (C.H.); (X.C.)
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-Products, China Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingyu Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (J.C.); (Y.C.); (C.H.); (X.C.)
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-Products, China Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (J.C.); (Y.C.); (C.H.); (X.C.)
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-Products, China Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (J.C.); (Y.C.); (C.H.); (X.C.)
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-Products, China Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (J.C.); (Y.C.); (C.H.); (X.C.)
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-Products, China Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
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21
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Zhang T, Wang Y, Teng X, Deng R, Li J. Preamplification-free viral RNA diagnostics with single-nucleotide resolution using MARVE, an origami paper-based colorimetric nucleic acid test. Nat Protoc 2024; 19:3426-3455. [PMID: 39026122 DOI: 10.1038/s41596-024-01022-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024]
Abstract
The evolution and mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgent concerns as they pose the risk of vaccine failure and increased viral transmission. However, affordable and scalable tools allowing rapid identification of SARS-CoV-2 variants are not readily available, which impedes diagnosis and epidemiological surveillance. Here we present a colorimetric nucleic acid assay named MARVE (multiplexed, preamplification-free, single-nucleotide-resolved viral evolution) that is convenient to perform and yields single-nucleotide resolution. The assay integrates nucleic acid strand displacement reactions with enzymatic amplification to colorimetrically sense viral RNA using a metal ion-incorporated DNA probe (TEprobe). We provide detailed guidelines to design TEprobes for discriminating single-nucleotide variations in viral RNAs, and to fabricate a test paper for the detection of SARS-CoV-2 variants of concern. Compared with other nucleic acid assays, our assay is preamplification-free, single-nucleotide-resolvable and results are visible via a color change. Besides, it is smartphone readable, multiplexed, quick and cheap ($0.30 per test). The protocol takes ~2 h to complete, from the design and preparation of the DNA probes and test papers (~1 h) to the detection of SARS-CoV-2 or its variants (30-45 min). The design of the TEprobes requires basic knowledge of molecular biology and familiarity with NUPACK or the Python programming language. The fabrication of the origami papers requires access to a wax printer using the CAD and PDF files provided or requires users to be familiar with AutoCAD to design new origami papers. The protocol is also applicable for designing assays to detect other pathogens and their variants.
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Affiliation(s)
- Ting Zhang
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, New Cornerstone Science Institute, Tsinghua University, Beijing, China
- College of Biomass Science and Engineering, Department of Respiration and Critical Care Medine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxi Wang
- College of Biomass Science and Engineering, Department of Respiration and Critical Care Medine, West China Hospital, Sichuan University, Chengdu, China
| | - Xucong Teng
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, New Cornerstone Science Institute, Tsinghua University, Beijing, China
- Beijing Institute of Life Science and Technology, Beijing, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Department of Respiration and Critical Care Medine, West China Hospital, Sichuan University, Chengdu, China.
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, New Cornerstone Science Institute, Tsinghua University, Beijing, China.
- Beijing Institute of Life Science and Technology, Beijing, China.
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22
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Arevalo-Rodriguez I, Mateos-Haro M, Dinnes J, Ciapponi A, Davenport C, Buitrago-Garcia D, Bennouna-Dalero T, Roqué-Figuls M, Van den Bruel A, von Eije KJ, Emperador D, Hooft L, Spijker R, Leeflang MM, Takwoingi Y, Deeks JJ. Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2024; 10:CD015618. [PMID: 39400904 PMCID: PMC11472845 DOI: 10.1002/14651858.cd015618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
BACKGROUND Diagnosing people with a SARS-CoV-2 infection played a critical role in managing the COVID-19 pandemic and remains a priority for the transition to long-term management of COVID-19. Initial shortages of extraction and reverse transcription polymerase chain reaction (RT-PCR) reagents impaired the desired upscaling of testing in many countries, which led to the search for alternatives to RNA extraction/purification and RT-PCR testing. Reference standard methods for diagnosing the presence of SARS-CoV-2 infection rely primarily on real-time reverse transcription-polymerase chain reaction (RT-PCR). Alternatives to RT-PCR could, if sufficiently accurate, have a positive impact by expanding the range of diagnostic tools available for the timely identification of people infected by SARS-CoV-2, access to testing and the use of resources. OBJECTIVES To assess the diagnostic accuracy of alternative (to RT-PCR assays) laboratory-based molecular tests for diagnosing SARS-CoV-2 infection. SEARCH METHODS We searched the COVID-19 Open Access Project living evidence database from the University of Bern until 30 September 2020 and the WHO COVID-19 Research Database until 31 October 2022. We did not apply language restrictions. SELECTION CRITERIA We included studies of people with suspected or known SARS-CoV-2 infection, or where tests were used to screen for infection, and studies evaluating commercially developed laboratory-based molecular tests for the diagnosis of SARS-CoV-2 infection considered as alternatives to RT-PCR testing. We also included all reference standards to define the presence or absence of SARS-CoV-2, including RT-PCR tests and established clinical diagnostic criteria. DATA COLLECTION AND ANALYSIS Two authors independently screened studies and resolved disagreements by discussing them with a third author. Two authors independently extracted data and assessed the risk of bias and applicability of the studies using the QUADAS-2 tool. We presented sensitivity and specificity, with 95% confidence intervals (CIs), for each test using paired forest plots and summarised results using average sensitivity and specificity using a bivariate random-effects meta-analysis. We illustrated the findings per index test category and assay brand compared to the WHO's acceptable sensitivity and specificity threshold for diagnosing SARS-CoV-2 infection using nucleic acid tests. MAIN RESULTS We included data from 64 studies reporting 94 cohorts of participants and 105 index test evaluations, with 74,753 samples and 7517 confirmed SARS-CoV-2 cases. We did not identify any published or preprint reports of accuracy for a considerable number of commercially produced NAAT assays. Most cohorts were judged at unclear or high risk of bias in more than three QUADAS-2 domains. Around half of the cohorts were considered at high risk of selection bias because of recruitment based on COVID status. Three quarters of 94 cohorts were at high risk of bias in the reference standard domain because of reliance on a single RT-PCR result to determine the absence of SARS-CoV-2 infection or were at unclear risk of bias due to a lack of clarity about the time interval between the index test assessment and the reference standard, the number of missing results, or the absence of a participant flow diagram. For index tests categories with four or more evaluations and when summary estimations were possible, we found that: a) For RT-PCR assays designed to omit/adapt RNA extraction/purification, the average sensitivity was 95.1% (95% CI 91.1% to 97.3%), and the average specificity was 99.7% (95% CI 98.5% to 99.9%; based on 27 evaluations, 2834 samples and 1178 SARS-CoV-2 cases); b) For RT-LAMP assays, the average sensitivity was 88.4% (95% CI 83.1% to 92.2%), and the average specificity was 99.7% (95% CI 98.7% to 99.9%; 24 evaluations, 29,496 samples and 2255 SARS-CoV-2 cases); c) for TMA assays, the average sensitivity was 97.6% (95% CI 95.2% to 98.8%), and the average specificity was 99.4% (95% CI 94.9% to 99.9%; 14 evaluations, 2196 samples and 942 SARS-CoV-2 cases); d) for digital PCR assays, the average sensitivity was 98.5% (95% CI 95.2% to 99.5%), and the average specificity was 91.4% (95% CI 60.4% to 98.7%; five evaluations, 703 samples and 354 SARS-CoV-2 cases); e) for RT-LAMP assays omitting/adapting RNA extraction, the average sensitivity was 73.1% (95% CI 58.4% to 84%), and the average specificity was 100% (95% CI 98% to 100%; 24 evaluations, 14,342 samples and 1502 SARS-CoV-2 cases). Only two index test categories fulfil the WHO-acceptable sensitivity and specificity requirements for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. In addition, WHO-acceptable performance criteria were met for two assays out of 35 when tests were used according to manufacturer instructions. At 5% prevalence using a cohort of 1000 people suspected of SARS-CoV-2 infection, the positive predictive value of RT-PCR assays omitting/adapting RNA extraction/purification will be 94%, with three in 51 positive results being false positives, and around two missed cases. For TMA assays, the positive predictive value of RT-PCR assays will be 89%, with 6 in 55 positive results being false positives, and around one missed case. AUTHORS' CONCLUSIONS Alternative laboratory-based molecular tests aim to enhance testing capacity in different ways, such as reducing the time, steps and resources needed to obtain valid results. Several index test technologies with these potential advantages have not been evaluated or have been assessed by only a few studies of limited methodological quality, so the performance of these kits was undetermined. Only two index test categories with enough evaluations for meta-analysis fulfil the WHO set of acceptable accuracy standards for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. These assays might prove to be suitable alternatives to RT-PCR for identifying people infected by SARS-CoV-2, especially when the alternative would be not having access to testing. However, these findings need to be interpreted and used with caution because of several limitations in the evidence, including reliance on retrospective samples without information about the symptom status of participants and the timing of assessment. No extrapolation of found accuracy data for these two alternatives to any test brands using the same techniques can be made as, for both groups, one test brand with high accuracy was overrepresented with 21/26 and 12/14 included studies, respectively. Although we used a comprehensive search and had broad eligibility criteria to include a wide range of tests that could be alternatives to RT-PCR methods, further research is needed to assess the performance of alternative COVID-19 tests and their role in pandemic management.
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Affiliation(s)
- Ingrid Arevalo-Rodriguez
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS). CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Evidence Production & Methods Directorate, Cochrane, London, UK
| | - Miriam Mateos-Haro
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- Doctoral programme in Clinical Medicine and Public Health, Universidad de Granada, Granada, Spain
| | - Jacqueline Dinnes
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Agustín Ciapponi
- Argentine Cochrane Centre, Institute for Clinical Effectiveness and Health Policy (IECS-CONICET), Buenos Aires, Argentina
| | - Clare Davenport
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Diana Buitrago-Garcia
- Institute for Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Hospital Universitario Mayor - Méderi. Universidad del Rosario, Bogotá, Colombia
| | - Tayeb Bennouna-Dalero
- Preventive Medicine and Public Health Department, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Marta Roqué-Figuls
- Iberoamerican Cochrane Centre, Institut de Recerca Sant Pau (IR SANT PAU), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | | | - Karin J von Eije
- Department of Viroscience, ErasmusMC, University Medical Center, Rotterdam, Netherlands
| | | | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - René Spijker
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Yemisi Takwoingi
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
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23
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Qian X, Xu Q, Lyon CJ, Hu TY. CRISPR for companion diagnostics in low-resource settings. LAB ON A CHIP 2024; 24:4717-4740. [PMID: 39268697 PMCID: PMC11393808 DOI: 10.1039/d4lc00340c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/15/2024] [Indexed: 09/17/2024]
Abstract
New point-of-care tests (POCTs), which are especially useful in low-resource settings, are needed to expand screening capacity for diseases that cause significant mortality: tuberculosis, multiple cancers, and emerging infectious diseases. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic (CRISPR-Dx) assays have emerged as powerful and versatile alternatives to traditional nucleic acid tests, revealing a strong potential to meet this need for new POCTs. In this review, we discuss CRISPR-Dx assay techniques that have been or could be applied to develop POCTs, including techniques for sample processing, target amplification, multiplex assay design, and signal readout. This review also describes current and potential applications for POCTs in disease diagnosis and includes future opportunities and challenges for such tests. These tests need to advance beyond initial assay development efforts to broadly meet criteria for use in low-resource settings.
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Affiliation(s)
- Xu Qian
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China.
| | - Qiang Xu
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China.
| | - Christopher J Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
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24
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Gu X, Tang Q, Zhu Y, Sun C, Wu L, Ji H, Wang Q, Wu L, Qin Y. Advancements of CRISPR technology in public health-related analysis. Biosens Bioelectron 2024; 261:116449. [PMID: 38850734 DOI: 10.1016/j.bios.2024.116449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Pathogens and contaminants in food and the environment present significant challenges to human health, necessitating highly sensitive and specific diagnostic methods. Traditional approaches often struggle to meet these requirements. However, the emergence of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has revolutionized nucleic acid diagnostics. The present review provides a comprehensive overview of the biological sensing technology based on the CRISPR/Cas system and its potential applications in public health-related analysis. Additionally, it explores the enzymatic cleavage capabilities mediated by Cas proteins, highlighting the promising prospects of CRISPR technology in addressing bioanalysis challenges. We discuss commonly used CRISPR-Cas proteins and elaborate on their application in detecting foodborne bacteria, viruses, toxins, other chemical pollution, and drug-resistant bacteria. Furthermore, we highlight the advantages of CRISPR-based sensors in the field of public health-related analysis and propose that integrating CRISPR-Cas biosensing technology with other technologies could facilitate the development of more diverse detection platforms, thereby indicating promising prospects in this field.
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Affiliation(s)
- Xijuan Gu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China; Xinglin College, Nantong University, Qidong, Jiangsu, 226236, PR China
| | - Qu Tang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Yidan Zhu
- Medical School, Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Chenling Sun
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Lingwei Wu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Haiwei Ji
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Qi Wang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, PR China; School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Yuling Qin
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
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25
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Greensmith R, Lape IT, Riella CV, Schubert AJ, Metzger JJ, Dighe AS, Tan X, Hemmer B, Rau J, Wendlinger S, Diederich N, Schütz A, Riella LV, Kaminski MM. CRISPR-enabled point-of-care genotyping for APOL1 genetic risk assessment. EMBO Mol Med 2024; 16:2619-2637. [PMID: 39271961 PMCID: PMC11473833 DOI: 10.1038/s44321-024-00126-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/19/2024] [Accepted: 08/12/2024] [Indexed: 09/15/2024] Open
Abstract
Detecting genetic variants enables risk factor identification, disease screening, and initiation of preventative therapeutics. However, current methods, relying on hybridization or sequencing, are unsuitable for point-of-care settings. In contrast, CRISPR-based-diagnostics offer high sensitivity and specificity for point-of-care applications. While these methods have predominantly been used for pathogen sensing, their utilization for genotyping is limited. Here, we report a multiplexed CRISPR-based genotyping assay using LwaCas13a, PsmCas13b, and LbaCas12a, enabling the simultaneous detection of six genotypes. We applied this assay to identify genetic variants in the APOL1 gene prevalent among African Americans, which are associated with an 8-30-fold increase in the risk of developing kidney disease. Machine learning facilitated robust analysis across a multicenter clinical cohort of more than 100 patients, accurately identifying their genotypes. In addition, we optimized the readout using a multi-analyte lateral-flow assay demonstrating the ability for simplified genotype determination of clinical samples. Our CRISPR-based genotyping assay enables cost-effective point-of-care genetic variant detection due to its simplicity, versatility, and fast readout.
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Affiliation(s)
- Robert Greensmith
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Isadora T Lape
- Center for Transplantation Sciences, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Cristian V Riella
- Nephrology Division, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander J Schubert
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Jakob J Metzger
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anand S Dighe
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Xiao Tan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bernhard Hemmer
- Department of Neurology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Josefine Rau
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sarah Wendlinger
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nora Diederich
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Anja Schütz
- Protein Production & Characterization, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Leonardo V Riella
- Center for Transplantation Sciences, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA.
- Department of Surgery, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA.
- Division of Nephrology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA.
| | - Michael M Kaminski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Department of Nephrology and Medical Intensive Care, Charité Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
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26
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Rahimi S, Balusamy SR, Perumalsamy H, Ståhlberg A, Mijakovic I. CRISPR-Cas target recognition for sensing viral and cancer biomarkers. Nucleic Acids Res 2024; 52:10040-10067. [PMID: 39189452 PMCID: PMC11417378 DOI: 10.1093/nar/gkae736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024] Open
Abstract
Nucleic acid-based diagnostics is a promising venue for detection of pathogens causing infectious diseases and mutations related to cancer. However, this type of diagnostics still faces certain challenges, and there is a need for more robust, simple and cost-effective methods. Clustered regularly interspaced short palindromic repeats (CRISPRs), the adaptive immune systems present in the prokaryotes, has recently been developed for specific detection of nucleic acids. In this review, structural and functional differences of CRISPR-Cas proteins Cas9, Cas12 and Cas13 are outlined. Thereafter, recent reports about applications of these Cas proteins for detection of viral genomes and cancer biomarkers are discussed. Further, we highlight the challenges associated with using these technologies to replace the current diagnostic approaches and outline the points that need to be considered for designing an ideal Cas-based detection system for nucleic acids.
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Affiliation(s)
- Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Sri Renukadevi Balusamy
- Department of Food Science and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Republic of Korea
| | - Haribalan Perumalsamy
- Center for Creative Convergence Education, Hanyang University, Seoul 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, South Korea
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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27
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Yao Z, Li W, He K, Wang H, Xu Y, Xu X, Wu Q, Wang L. Precise pathogen quantification by CRISPR-Cas: a sweet but tough nut to crack. Crit Rev Microbiol 2024:1-19. [PMID: 39287550 DOI: 10.1080/1040841x.2024.2404041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 09/04/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024]
Abstract
Pathogen detection is increasingly applied in medical diagnosis, food processing and safety, and environmental monitoring. Rapid, sensitive, and accurate pathogen quantification is the most critical prerequisite for assessing protocols and preventing risks. Among various methods evolved, those based on clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas) have been developed as important pathogen detection strategies due to their distinct advantages of rapid target recognition, programmability, ultra-specificity, and potential for scalability of point-of-care testing (POCT). However, arguments and concerns on the quantitative capability of CRISPR-based strategies are ongoing. Herein, we systematically overview CRISPR-based pathogen quantification strategies according to the principles, properties, and application scenarios. Notably, we review future challenges and perspectives to address the of precise pathogen quantification by CRISPR-Cas. We hope the insights presented in this review will benefit development of CRISPR-based pathogen detection methods.
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Affiliation(s)
- Zhihao Yao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanglu Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongmei Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Hangzhou, China
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28
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Zhang L, Wang H, Yang S, Liu J, Li J, Lu Y, Cheng J, Xu Y. High-Throughput and Integrated CRISPR/Cas12a-Based Molecular Diagnosis Using a Deep Learning Enabled Microfluidic System. ACS NANO 2024; 18:24236-24251. [PMID: 39173188 DOI: 10.1021/acsnano.4c05734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
CRISPR/Cas-based molecular diagnosis demonstrates potent potential for sensitive and rapid pathogen detection, notably in SARS-CoV-2 diagnosis and mutation tracking. Yet, a major hurdle hindering widespread practical use is its restricted throughput, limited integration, and complex reagent preparation. Here, a system, microfluidic multiplate-based ultrahigh throughput analysis of SARS-CoV-2 variants of concern using CRISPR/Cas12a and nonextraction RT-LAMP (mutaSCAN), is proposed for rapid detection of SARS-CoV-2 and its variants with limited resource requirements. With the aid of the self-developed reagents and deep-learning enabled prototype device, our mutaSCAN system can detect SARS-CoV-2 in mock swab samples below 30 min as low as 250 copies/mL with the throughput up to 96 per round. Clinical specimens were tested with this system, the accuracy for routine and mutation testing (22 wildtype samples, 26 mutational samples) was 98% and 100%, respectively. No false-positive results were found for negative (n = 24) samples.
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Affiliation(s)
- Li Zhang
- School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Huili Wang
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
| | - Sheng Yang
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
| | - Jiajia Liu
- CapitalBiotech Technology, Beijing 101111, China
| | - Jie Li
- CapitalBiotech Technology, Beijing 101111, China
| | - Ying Lu
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Jing Cheng
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Youchun Xu
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
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29
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Lim J, Koprowski K, Stavins R, Xuan N, Hoang TH, Baek J, Kindratenko V, Khaertdinova L, Kim AY, Do M, King WP, Valera E, Bashir R. Point-of-Care Multiplex Detection of Respiratory Viruses. ACS Sens 2024; 9:4058-4068. [PMID: 39101394 DOI: 10.1021/acssensors.4c00992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
The COVID-19 pandemic, in addition to the co-occurrence of influenza virus and respiratory syncytial virus (RSV), has emphasized the requirement for efficient and reliable multiplex diagnostic methods for respiratory infections. While existing multiplex detection techniques are based on reverse transcription quantitative polymerase chain reaction (RT-qPCR) and extraction and purification kits, the need for complex instrumentation and elevated cost limit their scalability and availability. In this study, we have developed a point-of-care (POC) device based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) that can simultaneously detect four respiratory viruses (SARS-CoV-2, Influenza A, Influenza B, and RSV) and perform two controls in less than 30 min, while avoiding the use of the RNA extraction kit. The system includes a disposable microfluidic cartridge with mechanical components that automate sample processing, with a low-cost and portable optical reader and a smartphone app to record and analyze fluorescent images. The application as a real point-of-care platform was validated using swabs spiked with virus particles in nasal fluid. Our portable diagnostic system accurately detects viral RNA specific to respiratory pathogens, enabling deconvolution of coinfection information. The detection limits for each virus were determined using virus particles spiked in chemical lysis buffer. Our POC device has the potential to be adapted for the detection of new pathogens and a wide range of viruses by modifying the primer sequences. This work highlights an alternative approach for multiple respiratory virus diagnostics that is well-suited for healthcare systems in resource-limited settings or at home.
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Affiliation(s)
- Jongwon Lim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Katherine Koprowski
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Robert Stavins
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nhat Xuan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Trung-Hieu Hoang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Janice Baek
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Victoria Kindratenko
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Liliana Khaertdinova
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Alicia Yeun Kim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Minh Do
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - William P King
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Chan Zuckerberg Biohub Chicago, Chicago, Illinois 60642, United States
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30
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Kaur R, Gupta S, Chauhan A, Mishra V, Sharma MK, Singh J. Harnessing the power of clustered regularly interspaced short palindromic repeats (CRISPR) based microfluidics for next-generation molecular diagnostics. Mol Biol Rep 2024; 51:896. [PMID: 39115550 DOI: 10.1007/s11033-024-09840-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/31/2024] [Indexed: 02/06/2025]
Abstract
CRISPR-based (Clustered regularly interspaced short palindromic repeats-based) technologies have revolutionized molecular biology and diagnostics, offering unprecedented precision and versatility. However, challenges remain, such as high costs, demanding technical expertise, and limited quantification capabilities. To overcome these limitations, innovative microfluidic platforms are emerging as powerful tools for enhancing CRISPR diagnostics. This review explores the exciting intersection of CRISPR and microfluidics, highlighting their potential to revolutionize healthcare diagnostics. By integrating CRISPR's specificity with microfluidics' miniaturization and automation, researchers are developing more sensitive and portable diagnostic tools for a range of diseases. These microfluidic devices streamline sample processing, improve diagnostic performance, and enable point-of-care applications, allowing for rapid and accurate detection of pathogens, genetic disorders, and other health conditions. The review discusses various CRISPR/Cas systems, including Cas9, Cas12, and Cas13, and their integration with microfluidic platforms. It also examines the advantages and limitations of these systems, highlighting their potential for detecting DNA and RNA biomarkers. The review also explores the key challenges in developing and implementing CRISPR-driven microfluidic diagnostics, such as ensuring robustness, minimizing cross-contamination, and achieving robust quantification. Finally, it highlights potential future directions for this rapidly evolving field, emphasizing the transformative potential of these technologies for personalized medicine and global health.
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Affiliation(s)
- Rasanpreet Kaur
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Chaumuhan, 281406, Mathura, Uttar Pradesh, India
| | - Saurabh Gupta
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Chaumuhan, 281406, Mathura, Uttar Pradesh, India.
| | - Arjun Chauhan
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Chaumuhan, 281406, Mathura, Uttar Pradesh, India
| | - Vidhi Mishra
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Chaumuhan, 281406, Mathura, Uttar Pradesh, India
| | - Manish Kumar Sharma
- Department of Biotechnology, Dr. Rammanohar Lohia Avadh University, Ayodhya, 224001, Uttar Pradesh, India
| | - Jitendra Singh
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Saket Nagar, Bhopal, 462020, Madhya Pradesh, India
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31
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Liu J, Li N, Zhang L, Lu Y, Shen M, Zhang Y, Feng L, Jing J, Cheng J, Xu Y. A Wax Interface-Enabled One-Pot Multiplexed Nucleic Acid Testing Platform for Rapid and Sensitive Detection of Viruses and Variants. SMALL METHODS 2024; 8:e2400030. [PMID: 38716631 DOI: 10.1002/smtd.202400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/16/2024] [Indexed: 08/18/2024]
Abstract
High-quality, low-cost, and rapid detection is essential for the society to reopen the economy during the critical period of transition from Coronavirus Disease 2019 (COVID-19) pandemic response to pandemic control. In addition to performing sustainable and target-driven tracking of SARS-CoV-2, conducting comprehensive surveillance of variants and multiple respiratory pathogens is also critical due to the frequency of reinfections, mutation immune escape, and the growing prevalence of the cocirculation of multiple viruses. By utilizing a 0.05 cents wax interface, a Stable Interface assisted Multiplex Pathogenesis Locating Estimation in Onepot (SIMPLEone) using nested RPA and CRISPR/Cas12a enzymatic reporting system is successfully developed. This smartphone-based SIMPLEone system achieves highly sensitive one-pot detection of SARS-CoV-2 and its variants, or multiple respiratory viruses, in 40 min. A total of 89 clinical samples, 14 environmental samples, and 20 cat swab samples are analyzed by SIMPLEone, demonstrating its excellent sensitivity (3-6 copies/reaction for non-extraction detection of swab and 100-150 copies/mL for RNA extraction-based assay), accuracy (>97.7%), and specificity (100%). Furthermore, a high percentage (44.2%) of co-infection cases are detected in SARS-CoV-2-infected patients using SIMPLEone's multiplex detection capability.
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Affiliation(s)
- Jiajia Liu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- CapitalBiotech Technology, Beijing, 101111, China
| | - Nan Li
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute of Chinese Academy of Sciences, Beijing, 100190, China
| | - Li Zhang
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Ying Lu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Minjie Shen
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuanyue Zhang
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Li Feng
- CapitalBiotech Technology, Beijing, 101111, China
| | - Juhui Jing
- CapitalBiotech Technology, Beijing, 101111, China
| | - Jing Cheng
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
| | - Youchun Xu
- School of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- CapitalBiotech Technology, Beijing, 101111, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
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32
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Ding X, Wang Y, Gui Y, Yang C. Two-Stage Mixed-Dye-Based Isothermal Amplification with Ribonuclease-Cleavable Enhanced Probes for Dual-Visualization Detection of SARS-CoV-2 Variants of Interest. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401988. [PMID: 38829265 PMCID: PMC11304323 DOI: 10.1002/advs.202401988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/17/2024] [Indexed: 06/05/2024]
Abstract
Rapid and visual detection of SARS-CoV-2 variants is vital for timely assessment of variant transmission in resource-limited settings. Here, a closed-tube, two-stage, mixed-dye-based isothermal amplification method with ribonuclease-cleavable enhanced probes (REP), termed REP-TMAP, for dual-visualization detection of SARS-CoV-2 variants including JN.1, BA.2, BA.4/5, and Delta is introduced. The first stage of REP-TMAP is reverse transcription recombinase polymerase amplification and the second stage is dual-visualization detection synergistically mediated by the REP and the mixed dyes of cresol red and hydroxy naphthol blue. In REP-TMAP reaction, the color change under ambient light indicates SARS-CoV-2 infection, while the fluorescence change under blue light excitation specifies variant type. On detecting transcribed RNA of SARS-CoV-2 spike gene, this assay is rapid (within 40 min), highly sensitive (10-200 copies per reaction), and highly specific (identification of single-base mutations). Furthermore, the assay has been clinically validated to accurately detect JN.1, BA.2, and BA.4/5 variants from 102 human oropharyngeal swabs. The proposed assay therefore holds great potentials to provide a rapid, dual-visualization, sensitive, specific, point-of-care detection of SARS-CoV-2 variants and beyond.
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Affiliation(s)
- Xiong Ding
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Yaru Wang
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Yuxin Gui
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Chuankun Yang
- Center of Clinical Laboratory MedicineZhongda Hospital, Southeast UniversityNanjing210009P. R. China
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33
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Lin TH, Su W, Cui Y, Bahr R, Tentzeris MM. Battery-less long-range wireless fluidic sensing system using flexible additive manufacturing ambient energy harvester and microfluidics. Sci Rep 2024; 14:17787. [PMID: 39090193 PMCID: PMC11294458 DOI: 10.1038/s41598-024-68616-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024] Open
Abstract
Fluid sensing has been an important but missing part of the massive Internet-of-Things sensor networks due to challenges including excessive manufacturing time/cost, finite wireless interrogation range, limited immunity to ambient clutter, and excessive required power for autonomous microfluidics operability. Here, we proposed an additive manufacturing flexible system as a solution to those challenges while enabling fluid analysis from controlled labs to virtually everywhere. Energy harvesting provides all required power for the actuation of the micro-pump enabling battery-less liquid sample acquisition. Energy sources including ultra-high-frequency radio frequency identification and hand-held devices like two-way talk radio are harvested simultaneously to support energy requirements for periodic monitoring every 6.6 min and on-demand monitoring within 4.63 s. Backscattering topologies are used to significantly extend the reading range while increasing the immunity to interferences and reducing the cost to the reader. A new additive manufacturing process is proposed to reduce fabrication time and cost while enabling massive scalability of flexible microfluidics. The good flexibility makes the system suitable for working toward future wearable applications. Prototypes of a sweat sensing system are demonstrated and successfully interrogated at 3 m with more than 15 dB signal-to-noise ratio using only a 14 dBm transmitter equivalent isotropic radiated power.
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Affiliation(s)
- Tong-Hong Lin
- Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, 30332-250, USA.
| | - Wenjing Su
- Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, 30332-250, USA
| | - Yepu Cui
- Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, 30332-250, USA
| | - Ryan Bahr
- Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, 30332-250, USA
| | - Manos M Tentzeris
- Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, 30332-250, USA
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Guo D, Ling Z, Tang Y, Li G, Zhang T, Zhao H, Ren H, Shen Y, Yang X. An Ultra-Compact and Low-Cost LAMP-Based Virus Detection Device. SENSORS (BASEL, SWITZERLAND) 2024; 24:4912. [PMID: 39123959 PMCID: PMC11314854 DOI: 10.3390/s24154912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Abstract
Timely and accurate detection of viruses is crucial for infection diagnosis and treatment. However, it remains a challenge to develop a portable device that meets the requirement of being portable, powerless, user-friendly, reusable, and low-cost. This work reports a compact ∅30 × 48 mm portable powerless isothermal amplification detection device (material cost ∼$1 USD) relying on LAMP (Loop-Mediated Isothermal Amplification). We have proposed chromatographic-strip-based microporous permeation technology which can precisely control the water flow rate to regulate the exothermic reaction. This powerless heating combined with phase-change materials can maintain a constant temperature between 50 and 70 °C for a duration of up to 49.8 min. Compared with the conventional methods, it avoids the use of an additional insulation layer for heat preservation, greatly reducing the size and cost. We have also deployed a color card and a corresponding algorithm to facilitate color recognition, data analysis, and storage using a mobile phone. The experimental results demonstrate that our device exhibits the same limit of detection (LOD) as the ProFlex PCR for SARS-CoV-2 pseudovirus samples, with that for both being 103 copies/μL, verifying its effectiveness and reliability. This work offers a timely, low-cost, and easy way for respiratory infectious disease detection, which could provide support in curbing virus transmission and protecting the health of humans and animals, especially in remote mountainous areas without access to electricity or trained professionals.
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Affiliation(s)
- Dong Guo
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Zhengrong Ling
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Yifeng Tang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Gen Li
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Tieshan Zhang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Haoxiang Zhao
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Hao Ren
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Yajing Shen
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Xiong Yang
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong 999077, China
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35
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Sharma S, Caputi M, Asghar W. Development of a Diagnostic Microfluidic Chip for SARS-CoV-2 Detection in Saliva and Nasopharyngeal Samples. Viruses 2024; 16:1190. [PMID: 39205164 PMCID: PMC11360425 DOI: 10.3390/v16081190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 09/04/2024] Open
Abstract
The novel coronavirus SARS-CoV-2 was first isolated in late 2019; it has spread to all continents, infected over 700 million people, and caused over 7 million deaths worldwide to date. The high transmissibility of the virus and the emergence of novel strains with altered pathogenicity and potential resistance to therapeutics and vaccines are major challenges in the study and treatment of the virus. Ongoing screening efforts aim to identify new cases to monitor the spread of the virus and help determine the danger connected to the emergence of new variants. Given its sensitivity and specificity, nucleic acid amplification tests (NAATs) such as RT-qPCR are the gold standard for SARS-CoV-2 detection. However, due to high costs, complexity, and unavailability in low-resource and point-of-care (POC) settings, the available RT-qPCR assays cannot match global testing demands. An alternative NAAT, RT-LAMP-based SARS-CoV-2 detection offers scalable, low-cost, and rapid testing capabilities. We have developed an automated RT-LAMP-based microfluidic chip that combines the RNA isolation, purification, and amplification steps on the same device and enables the visual detection of SARS-CoV-2 within 40 min from saliva and nasopharyngeal samples. The entire assay is executed inside a uniquely designed, inexpensive disposable microfluidic chip, where assay components and reagents have been optimized to provide precise and qualitative results and can be effectively deployed in POC settings. Furthermore, this technology could be easily adapted for other novel emerging viruses.
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Affiliation(s)
- Sandhya Sharma
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Waseem Asghar
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
- Department of Biological Sciences (Courtesy Appointment), Florida Atlantic University, Boca Raton, FL 33431, USA
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36
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Adedokun G, Alipanah M, Fan ZH. Sample preparation and detection methods in point-of-care devices towards future at-home testing. LAB ON A CHIP 2024; 24:3626-3650. [PMID: 38952234 PMCID: PMC11270053 DOI: 10.1039/d3lc00943b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Timely and accurate diagnosis is critical for effective healthcare, yet nearly half the global population lacks access to basic diagnostics. Point-of-care (POC) testing offers partial solutions by enabling low-cost, rapid diagnosis at the patient's location. At-home POC devices have the potential to advance preventive care and early disease detection. Nevertheless, effective sample preparation and detection methods are essential for accurate results. This review surveys recent advances in sample preparation and detection methods at POC. The goal is to provide an in-depth understanding of how these technologies can enhance at-home POC devices. Lateral flow assays, nucleic acid tests, and virus detection methods are at the forefront of POC diagnostic technology, offering rapid and sensitive tools for identifying and measuring pathogens, biomarkers, and viral infections. By illuminating cutting-edge research on assay development for POC diagnostics, this review aims to accelerate progress towards widely available, user-friendly, at-home health monitoring tools that empower individuals in personalized healthcare in the future.
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Affiliation(s)
- George Adedokun
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
| | - Morteza Alipanah
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
| | - Z Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL 32611, USA
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611, USA
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37
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Choi W, Cha S, Kim K. Navigating the CRISPR/Cas Landscape for Enhanced Diagnosis and Treatment of Wilson's Disease. Cells 2024; 13:1214. [PMID: 39056796 PMCID: PMC11274827 DOI: 10.3390/cells13141214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system continues to evolve, thereby enabling more precise detection and repair of mutagenesis. The development of CRISPR/Cas-based diagnosis holds promise for high-throughput, cost-effective, and portable nucleic acid screening and genetic disease diagnosis. In addition, advancements in transportation strategies such as adeno-associated virus (AAV), lentiviral vectors, nanoparticles, and virus-like vectors (VLPs) offer synergistic insights for gene therapeutics in vivo. Wilson's disease (WD), a copper metabolism disorder, is primarily caused by mutations in the ATPase copper transporting beta (ATP7B) gene. The condition is associated with the accumulation of copper in the body, leading to irreversible damage to various organs, including the liver, nervous system, kidneys, and eyes. However, the heterogeneous nature and individualized presentation of physical and neurological symptoms in WD patients pose significant challenges to accurate diagnosis. Furthermore, patients must consume copper-chelating medication throughout their lifetime. Herein, we provide a detailed description of WD and review the application of novel CRISPR-based strategies for its diagnosis and treatment, along with the challenges that need to be overcome.
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Affiliation(s)
- Woong Choi
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
| | - Seongkwang Cha
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
- Neuroscience Research Institute, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
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38
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Yan Z, Eshed A, Tang AA, Arevalos NR, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches. Chem 2024; 10:2220-2244. [PMID: 39036067 PMCID: PMC11259118 DOI: 10.1016/j.chempr.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. We describe a class of aptamer-based RNA switches or aptaswitches that recognize target nucleic acid molecules and initiate folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide an intense fluorescent readout without intervening enzymes, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. Aptaswitches can be used to regulate folding of seven fluorogenic aptamers, providing a general means of controlling aptamers and an array of multiplexable reporter colors. Coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed all-in-one reactions against RNA from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that are readily integrated into rapid diagnostic assays.
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Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Nery R. Arevalos
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Zachary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts
Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT,
Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA,
USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School,
Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
- Lead contact
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39
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Zhang Y, Guo Y, Liu G, Zhou S, Su R, Ma Q, Ge Y, Lu YQ, Cui L, Wang G. Portable all-in-one microfluidic system for CRISPR-Cas13a-based fully integrated multiplexed nucleic acid detection. LAB ON A CHIP 2024; 24:3367-3376. [PMID: 38845509 DOI: 10.1039/d4lc00326h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Point-of-care testing of "sample in, answer out" is urgently needed for communicable diseases. Recently, rapid nucleic acid tests for infectious diseases have been developed for use in resource-limited areas, but they require types of equipment in central laboratories and are poorly integrated. In this work, a portable centrifugal microfluidic testing system is developed, integrated with magnetic bead-based nucleic acid extraction, recombinase-assisted amplification and CRISPR-Cas13a detection. The system, with the advantage of its power-supplied active rotating chip and highly programable flow control through integrated addressable active thermally-triggered wax valves, has a rapid turnaround time within 45 min, requiring only one user step. All reagents are preloaded into the chip and can be automatically released. By exploiting a multichannel chip, it is capable of simultaneously detecting 10 infectious viruses with limits of detection of 1 copy per reaction and 5 copies per reaction in plasmid samples and mock plasma samples, respectively. The system was used to analyse clinical plasma samples with good consistency compared to laboratory-based molecular testing. Moreover, the generalizability of our device is reported by successfully testing nasopharyngeal swabs and whole blood samples. The portable device does not require the operation of professional technicians, making it an excellent assay for on-site testing.
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Affiliation(s)
- Ya Zhang
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu 210093, China.
- Key Laboratory of Intelligent Optical Sensing and Integration of the Ministry of Education, Nanjing University, Jiangsu 210093, China
| | - Yue Guo
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu 210009, China
- Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu 210009, China.
| | - Guozhen Liu
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu 210093, China.
- Key Laboratory of Intelligent Optical Sensing and Integration of the Ministry of Education, Nanjing University, Jiangsu 210093, China
| | - Shiqi Zhou
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu 210093, China.
- Key Laboratory of Intelligent Optical Sensing and Integration of the Ministry of Education, Nanjing University, Jiangsu 210093, China
| | - Rouyu Su
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu 210093, China.
- Key Laboratory of Intelligent Optical Sensing and Integration of the Ministry of Education, Nanjing University, Jiangsu 210093, China
| | - Qian Ma
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu 210093, China.
- Key Laboratory of Intelligent Optical Sensing and Integration of the Ministry of Education, Nanjing University, Jiangsu 210093, China
| | - Yiyue Ge
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu 210009, China
- Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu 210009, China.
| | - Yan-Qing Lu
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu 210093, China.
| | - Lunbiao Cui
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu 210009, China
- Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Jiangsu 210009, China.
| | - Guanghui Wang
- College of Engineering and Applied Sciences, Nanjing University, Jiangsu 210093, China.
- Key Laboratory of Intelligent Optical Sensing and Integration of the Ministry of Education, Nanjing University, Jiangsu 210093, China
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40
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Zhang YB, Arizti-Sanz J, Bradley A, Huang Y, Kosoko-Thoroddsen TSF, Sabeti PC, Myhrvold C. CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza. J Mol Diagn 2024; 26:599-612. [PMID: 38901927 DOI: 10.1016/j.jmoldx.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/26/2024] [Accepted: 04/02/2024] [Indexed: 06/22/2024] Open
Abstract
The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.
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Affiliation(s)
- Yibin B Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts
| | - A'Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts
| | - Yujia Huang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | | | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts; Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, New Jersey; Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey; Department of Chemistry, Princeton University, Princeton, New Jersey.
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41
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Rolando JC, Melkonian AV, Walt DR. The Present and Future Landscapes of Molecular Diagnostics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:459-474. [PMID: 38360553 DOI: 10.1146/annurev-anchem-061622-015112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Nucleic acid testing is the cornerstone of modern molecular diagnostics. This review describes the current status and future directions of molecular diagnostics, focusing on four major techniques: polymerase chain reaction (PCR), next-generation sequencing (NGS), isothermal amplification methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR)-based detection methods. We explore the advantages and limitations of each technique, describe how each overlaps with or complements other techniques, and examine current clinical offerings. This review provides a broad perspective into the landscape of molecular diagnostics and highlights potential future directions in this rapidly evolving field.
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Affiliation(s)
- Justin C Rolando
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Arek V Melkonian
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - David R Walt
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
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42
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Mohammad N, Talton L, Dalgan S, Hetzler Z, Steksova A, Wei Q. Ratiometric nonfluorescent CRISPR assay utilizing Cas12a-induced plasmid supercoil relaxation. Commun Chem 2024; 7:130. [PMID: 38851849 PMCID: PMC11162422 DOI: 10.1038/s42004-024-01214-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Most CRISPR-based biosensors rely on labeled reporter molecules and expensive equipment for signal readout. A recent approach quantifies analyte concentration by sizing λ DNA reporters via gel electrophoresis, providing a simple solution for label-free detection. Here, we report an alternative strategy for label-free CRISPR-Cas12a, which relies on Cas12a trans-nicking induced supercoil relaxation of dsDNA plasmid reporters to generate a robust and ratiometric readout. The ratiometric CRISPR (rCRISPR) measures the relative percentage of supercoiled plasmid DNA to the relaxed circular DNA by gel electrophoresis for more accurate target concentration quantification. This simple method is two orders of magnitude more sensitive than the typical fluorescent reporter. This self-referenced strategy solves the potential application limitations of previously demonstrated DNA sizing-based CRISPR-Dx without compromising the sensitivity. Finally, we demonstrated the applicability of rCRISPR for detecting various model DNA targets such as HPV 16 and real AAV samples, highlighting its feasibility for point-of-care CRISPR-Dx applications.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Logan Talton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Selen Dalgan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Zach Hetzler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Anastasiia Steksova
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA.
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43
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Chhipa AS, Radadiya E, Patel S. CRISPR-Cas based diagnostic tools: Bringing diagnosis out of labs. Diagn Microbiol Infect Dis 2024; 109:116252. [PMID: 38479094 DOI: 10.1016/j.diagmicrobio.2024.116252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/30/2024]
Abstract
Timely detection is important for the effective management of infectious diseases. Reverse Transcription Polymerase Chain Reaction (RT-PCR) stands as the prime nucleic acid based test that is employed for the detection of infectious diseases. The method ensures sensitivity and specificity. However, RT-PCR is a relatively expensive technique due to the requirement of costly equipment and reagents. Further, it requires skilled personnel and established laboratories that are usually inaccessible in underdeveloped areas. On the other hand, rapid antigen based techniques are cost effective and easily accessible, but are less effective in terms of sensitivity and specificity. CRISPR-Cas systems are advanced diagnostic tools that combine the advantages of both PCR and antigen based detection techniques, and allows the rapid detection with high sensitivity/specificity. The present review aims to discuss the applicability of CRISPR-Cas based diagnostic tools for the infectious disease detection. The review further attempts to highlight the current limitations and future research directions to improve the CRISPR based diagnostic tools for rapid and effective disease detection.
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Affiliation(s)
- Abu Sufiyan Chhipa
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India
| | - Ekta Radadiya
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India
| | - Snehal Patel
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India.
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44
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Almulla N, Soltane R, Alasiri A, Kamal Allayeh A, Alqadi T, Alshehri F, Hamad Alrokban A, Zaghlool SS, Zayan AZ, Abdalla KF, Sayed AM. Advancements in SARS-CoV-2 detection: Navigating the molecular landscape and diagnostic technologies. Heliyon 2024; 10:e29909. [PMID: 38707469 PMCID: PMC11068538 DOI: 10.1016/j.heliyon.2024.e29909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
According to information from the World Health Organization, the world has experienced about 430 million cases of COVID-19, a world-wide health crisis caused by the SARS-CoV-2 virus. This outbreak, originating from China in 2019, has led to nearly 6 million deaths worldwide. As the number of confirmed infections continues to rise, the need for cutting-edge techniques that can detect SARS-CoV-2 infections early and accurately has become more critical. To address this, the Federal Drug Administration (FDA) has issued emergency use authorizations (EUAs) for a wide range of diagnostic tools. These include tests based on detecting nucleic acids and antigen-antibody reactions. The quantitative real-time reverse transcription PCR (qRT-PCR) assay stands out as the gold standard for early virus detection. However, despite its accuracy, qRT-PCR has limitations, such as complex testing protocols and a risk of false negatives, which drive the continuous improvement in nucleic acid and serological testing approaches. The emergence of highly contagious variants of the coronavirus, such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529), has increased the need for tests that can specifically identify these mutations. This article explores both nucleic acid-based and antigen-antibody serological assays, assessing the performance of recently approved FDA tests and those documented in scientific research, especially in identifying new coronavirus strains.
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Affiliation(s)
- Nuha Almulla
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Ahlam Alasiri
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Abdou Kamal Allayeh
- Virology Lab 176, Environment and Climate Change Institute, National Research Centre, Giza, 12622, Egypt
| | - Taha Alqadi
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Fatma Alshehri
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Ahlam Hamad Alrokban
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Sameh S. Zaghlool
- Department of Pharmacology and Toxicology, College of Pharmacy, Almaaqal University, 61014, Al-Maaqal, Basra, Iraq
| | - Abdallah Z. Zayan
- Department of Pharmaceutics, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
| | - Karam F. Abdalla
- Department of Pharmaceutics, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Collage of Pharmacy, Almaaqal University, 61014, Basrah, Iraq
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Lee H, You J, Lee H, Kim W, Jang K, Park J, Na S. Enhanced selective discrimination of point-mutated viral RNA through false amplification regulatory direct insertion in rolling circle amplification. Biosens Bioelectron 2024; 252:116145. [PMID: 38412685 DOI: 10.1016/j.bios.2024.116145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024]
Abstract
Coronaviruses are single-stranded RNA viruses with high mutation rates. Although a diagnostic method for coronaviruses has been developed, variants appear rapidly. Low test accuracy owing to single-point mutations is one of the main factors in the failure to prevent the early spread of coronavirus infection. Although reverse transcription-quantitative polymerase chain reaction can detect coronavirus infection, it cannot exclude the possibility of false positives, and an additional multiplexing kit is needed to discriminate single nucleotide polymorphism (SNP) variants. Therefore, in this study, we introduced a new nucleic acid amplification method to determine whether an infected person has a SNP mutation using a lateral flow assay (LFA) as a point-of-care test. Unlike traditional DNA amplification methods, direct insertion into rolling circle amplification amplifies the target genes without false amplification. After SNP-selective nucleic acid amplification, nuclease enzymes are used to make double-stranded DNA fragments that the LFA can detect, where specific mismatched DNA is found and cleaved to show different signals when a SNP-type is present. Therefore, wild- and SNP-type variants can be selectively detected. In this study, the limit of detection was 400 aM for viral RNA, and we successfully identified a dominant SNP variant selectively. Clinical tests were also conducted.
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Affiliation(s)
- Hakbeom Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Juneseok You
- Department of Mechanical Engineering, Kumoh National Institute of Technology, Gumi, 31977, Republic of Korea
| | - Hansol Lee
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woojoo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kuewhan Jang
- School of Mechanical Engineering, Hoseo University, Asan, 31499, Republic of Korea.
| | - Jinsung Park
- Department of Biomechatronics Engineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Suwon, 16419, Republic of Korea.
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea.
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Koksaldi I, Park D, Atilla A, Kang H, Kim J, Seker UOS. RNA-Based Sensor Systems for Affordable Diagnostics in the Age of Pandemics. ACS Synth Biol 2024; 13:1026-1037. [PMID: 38588603 PMCID: PMC11036506 DOI: 10.1021/acssynbio.3c00698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
In the era of the COVID-19 pandemic, the significance of point-of-care (POC) diagnostic tools has become increasingly vital, driven by the need for quick and precise virus identification. RNA-based sensors, particularly toehold sensors, have emerged as promising candidates for POC detection systems due to their selectivity and sensitivity. Toehold sensors operate by employing an RNA switch that changes the conformation when it binds to a target RNA molecule, resulting in a detectable signal. This review focuses on the development and deployment of RNA-based sensors for POC viral RNA detection with a particular emphasis on toehold sensors. The benefits and limits of toehold sensors are explored, and obstacles and future directions for improving their performance within POC detection systems are presented. The use of RNA-based sensors as a technology for rapid and sensitive detection of viral RNA holds great potential for effectively managing (dealing/coping) with present and future pandemics in resource-constrained settings.
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Affiliation(s)
- Ilkay
Cisil Koksaldi
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
| | - Dongwon Park
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Abdurahman Atilla
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
| | - Hansol Kang
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Jongmin Kim
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Urartu Ozgur Safak Seker
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
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Wang Y, Chen H, Lin K, Han Y, Gu Z, Wei H, Mu K, Wang D, Liu L, Jin R, Song R, Rong Z, Wang S. Ultrasensitive single-step CRISPR detection of monkeypox virus in minutes with a vest-pocket diagnostic device. Nat Commun 2024; 15:3279. [PMID: 38627378 PMCID: PMC11021474 DOI: 10.1038/s41467-024-47518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
The emerging monkeypox virus (MPXV) has raised global health concern, thereby highlighting the need for rapid, sensitive, and easy-to-use diagnostics. Here, we develop a single-step CRISPR-based diagnostic platform, termed SCOPE (Streamlined CRISPR On Pod Evaluation platform), for field-deployable ultrasensitive detection of MPXV in resource-limited settings. The viral nucleic acids are rapidly released from the rash fluid swab, oral swab, saliva, and urine samples in 2 min via a streamlined viral lysis protocol, followed by a 10-min single-step recombinase polymerase amplification (RPA)-CRISPR/Cas13a reaction. A pod-shaped vest-pocket analysis device achieves the whole process for reaction execution, signal acquisition, and result interpretation. SCOPE can detect as low as 0.5 copies/µL (2.5 copies/reaction) of MPXV within 15 min from the sample input to the answer. We validate the developed assay on 102 clinical samples from male patients / volunteers, and the testing results are 100% concordant with the real-time PCR. SCOPE achieves a single-molecular level sensitivity in minutes with a simplified procedure performed on a miniaturized wireless device, which is expected to spur substantial progress to enable the practice application of CRISPR-based diagnostics techniques in a point-of-care setting.
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Affiliation(s)
- Yunxiang Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Hong Chen
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Kai Lin
- Department of Clinical Laboratory, Air Force Medical Center, Air Force Medical University, 100142, Beijing, China
| | - Yongjun Han
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Zhixia Gu
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China
| | - Hongjuan Wei
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Kai Mu
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Dongfeng Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Liyan Liu
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China.
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China.
| | - Zhen Rong
- Bioinformatics Center of AMMS, 100850, Beijing, China.
| | - Shengqi Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China.
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48
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Zhou C, Cai Z, Jin B, Lin H, Xu L, Jin Z. Saliva-based detection of SARS-CoV-2: a bibliometric analysis of global research. Mol Cell Biochem 2024; 479:761-777. [PMID: 37178376 PMCID: PMC10182745 DOI: 10.1007/s11010-023-04760-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
Saliva has emerged as a promising noninvasive biofluid for the diagnosis of oral and systemic diseases, including viral infections. During the coronavirus disease 2019 (COVID-19) pandemic, a growing number of studies focused on saliva-based detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Taking advantage of the WoS core collection (WoSCC) and CiteSpace, we retrieved 1021 articles related to saliva-based detection of SARS-CoV-2 and conducted a comprehensive bibliometric analysis. We analyzed countries, institutions, authors, cited authors, and cited journals to summarize their contribution and influence and analyzed keywords to explore research hotspots and trends. From 2020 to 2021, research focused on viral transmission via saliva and verification of saliva as a reliable specimen, whereas from 2021 to the present, the focus of research has switched to saliva-based biosensors for SARS-CoV-2 detection. By far, saliva has been verified as a reliable specimen for SARS-CoV-2 detection, although a standardized procedure for saliva sampling and processing is needed. Studies on saliva-based detection of SARS-CoV-2 will promote the development of saliva-based diagnostics and biosensors for viral detection. Collectively, our findings could provide valuable information to help scientists perceive the basic knowledge landscapes on saliva-based detection of SARS-CoV-2, the past and current research hotspots, and future opportunities.
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Affiliation(s)
- Chun Zhou
- Jinhua People's Hospital Joint Center for Biomedical Research, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
- Department of Science and Education, the Affiliated Jinhua Hospital of Wenzhou Medical University, Jinhua, 321000, Zhejiang, China
| | - Zhaopin Cai
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Boxing Jin
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Huisong Lin
- Zhejiang Institute of Medical Device Testing, Hangzhou, Zhejiang, China
| | - Lingling Xu
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Zhigang Jin
- Jinhua People's Hospital Joint Center for Biomedical Research, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China.
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China.
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Zhang L, Parvin R, Lin S, Chen M, Zheng R, Fan Q, Ye F. Peptide Nucleic Acid Clamp-Assisted Photothermal Multiplexed Digital PCR for Identifying SARS-CoV-2 Variants of Concern. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306088. [PMID: 38243642 PMCID: PMC10987151 DOI: 10.1002/advs.202306088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/16/2023] [Indexed: 01/21/2024]
Abstract
The unprecedented demand for variants diagnosis in response to the COVID-19 epidemic has brought the spotlight onto rapid and accurate detection assays for single nucleotide polymorphisms (SNPs) at multiple locations. However, it is still challenging to ensure simplicity, affordability, and compatibility with multiplexing. Here, a novel technique is presented that combines peptide nucleic acid (PNA) clamps and near-infrared (NIR)-driven digital polymerase chain reaction (dPCR) to identify the Omicron and Delta variants. This is achieved by simultaneously identifying highly conserved mutated signatures at codons 19, 614, and 655 of the spike protein gene. By microfluidically introducing graphene-oxide-nanocomposite into the assembled gelatin microcarriers, they achieved a rapid temperature ramping-up rate and switchable gel-to-sol phase transformation synchronized with PCR activation under NIR irradiation. Two sets of duplex PCR reactions, each classifying respective PNA probes, are emulsified in parallel and illuminated together using a homemade vacuum-based droplet generation device and a programmable NIR control module. This allowed for selective amplification of mutant sequences due to single-base-pair mismatch with PNA blockers. Sequence-recognized bioreactions and fluorescent-color scoring enabled quick identification of variants. This technique achieved a detection limit of 5,100 copies and a 5-fold quantitative resolution, which is promising to unfold minor differences and dynamic changes.
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Affiliation(s)
- Lexiang Zhang
- Joint Centre of Translational Medicinethe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325035China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325000China
- Key Laboratory of Structural Malformations in Children of Zhejiang Provincethe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiang325027China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325000China
| | - Siyue Lin
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325000China
| | - Ruixuan Zheng
- Joint Centre of Translational Medicinethe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325035China
| | - Qihui Fan
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijingChina100190
| | - Fangfu Ye
- Joint Centre of Translational Medicinethe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiang325035China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhou325000China
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of SciencesBeijingChina100190
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50
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Sun Q, Lin H, Li Y, Yuan L, Li B, Ma Y, Wang H, Deng X, Chen H, Tang S. A photocontrolled one-pot isothermal amplification and CRISPR-Cas12a assay for rapid detection of SARS-CoV-2 Omicron variants. Microbiol Spectr 2024; 12:e0364523. [PMID: 38319081 PMCID: PMC10913417 DOI: 10.1128/spectrum.03645-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
CRISPR-Cas technology has widely been applied to detect single-nucleotide mutation and is considered as the next generation of molecular diagnostics. We previously reported the combination of nucleic acid amplification (NAA) and CRISPR-Cas12a system to distinguish major severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. However, the mixture of NAA and CRISPR-Cas12a reagents in one tube could interfere with the efficiency of NAA and CRISPR-Cas12a cleavage, which in turn affects the detection sensitivity. In the current study, we employed a novel photoactivated CRISPR-Cas12a strategy integrated with recombinase polymerase amplification (RPA) to develop one-pot RPA/CRISPR-Cas12a genotyping assay for detecting SARS-CoV-2 Omicron sub-lineages. The new system overcomes the potential inhibition of RPA due to early CRISPR-Cas12a activation and cleavage of the target template in traditional one-pot assay using photocleavable p-RNA, a complementary single-stranded RNA to specifically bind crRNA and precisely block Cas12a activation. The detection can be finished in one tube at 39℃ within 1 h and exhibits a low limit of detection of 30 copies per reaction. Our results demonstrated that the photocontrolled one-pot RPA/CRISPR-Cas12a assay could effectively identify three signature mutations in the spike gene of SARS-CoV-2 Omicron variant, namely, R346T, F486V, and 49X, and distinguish Omicron BA.1, BA.5.2, and BF.7 sub-lineages. Furthermore, the assay achieved a sensitivity of 97.3% and a specificity of 100.0% and showed a concordance of 98.3% with Sanger sequencing results.IMPORTANCEWe successfully developed one-pot recombinase polymerase amplification/CRISPR-Cas12a genotyping assay by adapting photocontrolled CRISPR-Cas technology to optimize the conditions of nucleic acid amplification and CRISPR-Cas12a-mediated detection. This innovative approach was able to quickly distinguish severe acute respiratory syndrome coronavirus 2 Omicron variants and can be readily modified for detecting any nucleic acid mutations. The assay system demonstrates excellent clinical performance, including rapid detection, user-friendly operations, and minimized risk of contamination, which highlights its promising potential as a point-of-care testing for wide applications in resource-limiting settings.
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Affiliation(s)
- Qian Sun
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongqing Lin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuan Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Liping Yuan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Baisheng Li
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Yunan Ma
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Hongliang Chen
- Department of Clinical Microbiology Laboratory, Chenzhou No. 1 People’s Hospital, Chenzhou, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
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