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Bhardwaj P, Nanaware NS, Behera SP, Kulkarni S, Deval H, Kumar R, Dwivedi GR, Kant R, Singh R. CRISPR/Cas12a-Based Detection Platform for Early and Rapid Diagnosis of Scrub Typhus. BIOSENSORS 2023; 13:1021. [PMID: 38131781 PMCID: PMC10742217 DOI: 10.3390/bios13121021] [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: 08/21/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 12/23/2023]
Abstract
Orientia tsutsugamushi is responsible for causing scrub typhus (ST) and is the leading cause of acute encephalitis syndrome (AES) in AES patients. A rapid and sensitive method to detect scrub typhus on-site is essential for the timely deployment of control measures. In the current study, we developed a rapid, sensitive, and instrument-free lateral flow assay (LFA) detection method based on CRISPR/Cas12a technology for diagnosing ST (named LoCIST). The method is completed in three steps: first, harnessing the ability of recombinase polymerase for isothermal amplification of the target gene; second, CRISPR/Cas12a-based recognition of the target; and third, end-point detection by LFA. The detection limit of LoCIST was found to be one gene copy of ST genomic DNA per reaction, and the process was complete within an hour. In 81 clinical samples, the assay showed no cross-reactivity with other rickettsial DNA and was 100% consistent with PCR detection of ST. LoCIST demonstrated 97.6% sensitivity and 100% specificity. Overall, the LoCIST offers a novel alternative for the portable, simple, sensitive, and specific detection of ST, and it may help prevent and control AES outbreaks due to ST. In conclusion, LoCIST does not require specialized equipment and poses a potential for future applications as a point-of-care diagnostic.
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Affiliation(s)
- Pooja Bhardwaj
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | | | - Sthita Pragnya Behera
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | - Smita Kulkarni
- ICMR-National AIDS Research Institute, Bhosari, Pune 411026, India; (N.S.N.); (S.K.)
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | - Rajesh Kumar
- RGSC, Department of Genetics and Plant Breeding, Banaras Hindu University, Varanasi 221005, India;
| | - Gaurav Raj Dwivedi
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | - Rajni Kant
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre Gorakhpur, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (S.P.B.); (H.D.); (G.R.D.); (R.K.)
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Politza AJ, Liu T, Guan W. Programmable magnetic robot (ProMagBot) for automated nucleic acid extraction at the point of need. LAB ON A CHIP 2023; 23:3882-3892. [PMID: 37551930 PMCID: PMC11218199 DOI: 10.1039/d3lc00545c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Upstream sample preparation remains the bottleneck for point-of-need nucleic acid testing due to its complexity and time-consuming nature. Sample preparation involves extracting, purifying, and concentrating nucleic acids from various matrices. These processes are critical for ensuring the accuracy and sensitivity of downstream nucleic acid amplification and detection. However, current sample preparation methods are often laboratory-based, requiring specialized equipment, trained personnel, and several hours of processing time. As a result, sample preparation often limits the speed, portability, and cost-effectiveness of point-of-need nucleic acid testing. A universal, field-deployable sample preparation device is highly desirable for this critical need and unmet challenge. Here we reported a handheld, battery-powered, reconfigurable, and field-deployable nucleic acid sample preparation device. A programmable electromagnetic actuator was developed to drive a magnetic robot (ProMagBot) in X/Y 2D space, such that various magnetic bead-based sample preparations can be readily translated from the laboratory to point-of-need settings. The control of the electromagnetic actuator requires only a 3-phase unipolar voltage in X and Y directions, and therefore, the motion space is highly scalable. We validated the ProMagBot device with a model application by extracting HIV viral RNAs from plasma samples using two widely used magnetic bead kits: ChargeSwitch and MagMAX beads. In both cases, the ProMagBot could successfully extract viral RNAs from 50 μL plasma samples containing as low as 102 copies of viral RNAs in 20 minutes. Our results demonstrated the ability of ProMagBot to prepare samples from complex mediums at the point of need. We believe such a device would enable rapid and robust sample preparation in various settings, including resource-limited or remote environments, and accelerate the development of next-generation point-of-need nucleic acid testing.
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Affiliation(s)
- Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
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Ngo HT, Akarapipad P, Lee PW, Park JS, Chen FE, Trick AY, Hsieh K, Wang TH. Rapid and Portable Quantification of HIV RNA via a Smartphone-enabled Digital CRISPR Device and Deep Learning. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.12.23289911. [PMID: 37292781 PMCID: PMC10246075 DOI: 10.1101/2023.05.12.23289911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
For the 28.2 million people in the world living with HIV/AIDS and receiving antiretroviral therapy, it is crucial to monitor their HIV viral loads with ease. To this end, rapid and portable diagnostic tools that can quantify HIV RNA are critically needed. We report herein a rapid and quantitative digital CRISPR-assisted HIV RNA detection assay that has been implemented within a portable smartphone-based device as a potential solution. Specifically, we first developed a fluorescence-based reverse transcription recombinase polymerase amplification (RT-RPA)-CRISPR assay for isothermally and rapidly detecting HIV RNA at 42 °C in < 30 min. When realized within a commercial stamp-sized digital chip, this assay yields strongly fluorescent digital reaction wells corresponding to HIV RNA. The isothermal reaction condition and the strong fluorescence in the small digital chip unlock compact thermal and optical components in our device, allowing us to engineer a palm-size (70 × 115 × 80 mm) and lightweight (< 0.6 kg) device. Further leveraging the smartphone, we wrote a custom app to control the device, perform the digital assay, and acquire fluorescence images throughout the assay time. We additionally trained and verified a Deep Learning-based algorithm for analyzing fluorescence images and detecting strongly fluorescent digital reaction wells. Using our smartphone-enabled digital CRISPR device, we were able to detect 75 copies of HIV RNA in 15 min and demonstrate the potential of our device toward convenient monitoring of HIV viral loads and combating the HIV/AIDS epidemic.
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Sun R, Chen J, Wang Y, Zhang Z, Li Y, Li F, Ma C, Han Q, Shi Y. Rapid, specific and sensitive detection of Vibrio parahaemolyticus in seafood by accelerated strand exchange amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:655-662. [PMID: 36655424 DOI: 10.1039/d2ay01889f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Vibrio parahaemolyticus infectious diseases caused by seafood contamination may be life-threatening to people with weak immunity. The detection of the Vibrio parahaemolyticus pathogen in aquatic foods is critical for reducing the outbreak of human Vibrio parahaemolyticus-associated diseases. In this study, a highly sensitive, specific, and time-saving real-time narrow thermal-cycling amplification detection method was developed based on accelerated strand exchange amplification (ASEA). It can detect cultured Vibrio parahaemolyticus at concentrations as low as 25 CFU mL-1. In addition, for artificially spiked scallop meat, the detection limit was 1.8 × 103 CFU g-1 without pre-culture and 18 CFU g-1 of initial inoculum after 3 h enrichment. The whole assay, starting from DNA extraction, can be completed within 20 min. The ASEA detection method established in this study is an effective tool for the rapid detection of Vibrio parahaemolyticus strains in a large number of seafood samples.
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Affiliation(s)
- Ritong Sun
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Jiao Chen
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Yingeng Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, PR China
| | - Zheng Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, PR China
| | - Yong Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Fengmei Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Qingxia Han
- Bin Zhou Polytechnic, Qingdao, 256600, PR China
| | - Yanjing Shi
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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Jiang Q, Li Y, Huang L, Guo J, Wang A, Ma C, Shi C. Direct capture and amplification of nucleic acids using a universal, elution-free magnetic bead-based method for rapid pathogen detection in multiple types of biological samples. Anal Bioanal Chem 2023; 415:427-438. [PMID: 36385304 PMCID: PMC9668711 DOI: 10.1007/s00216-022-04422-8] [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: 09/13/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022]
Abstract
Nucleic acid amplification tests (NAATs) have become an attractive approach for pathogen detection, and obtaining high-quality nucleic acid extracts from biological samples plays a critical role in ensuring accurate NAATs. In this work, we established an elution-free magnetic bead (MB)-based method by introducing polyethylene-polypropylene glycol (PEPPG) F68 in lysis buffer and using NaOH solution instead of alcohols as the washing buffer for rapid nucleic acid extraction from multiple types of biological samples, including nasopharyngeal swabs, serum, milk, and pork, which bypassed the nucleic acid elution step and allowed the nucleic acid/MB composite to be directly used as the template for amplification reactions. The entire extraction process was able to be completed in approximately 7 min. Even though the nucleic acid/MB composite could not be used for quantitative real-time PCR (qPCR) assays, this elution-free MB-based method significantly improved the sensitivity of the loop-mediated isothermal amplification (LAMP) assay. The sensitivity of the quantitative real-time LAMP (qLAMP) assays combined with this elution-free MB-based method showed an improvement of one to three orders of magnitude compared with qLAMP or qPCR assays combined with the traditional MB-based method. In addition to manual operation, like the traditional MB-based method, this universal, rapid, and facile nucleic acid extraction method also has potential for integration into automated robotic processing, making it particularly suitable for the establishment of an analysis platform for ultrafast and sensitive pathogen detection in various biological samples both in centralized laboratories and at remote sites.
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Affiliation(s)
- Qianqian Jiang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Yang Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Lin Huang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Jinling Guo
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Ailin Wang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 People’s Republic of China
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences; Department of Pathogenic Biology, School of Basic Medicine; Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071 People’s Republic of China
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Huang X, Fu R, Qiao S, Zhang J, Xianyu Y. Nanotechnology-based diagnostic methods for coronavirus: From nucleic acid extraction to amplification. Biosens Bioelectron 2022; 13:100289. [PMID: 36530849 PMCID: PMC9733970 DOI: 10.1016/j.biosx.2022.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
The recent emergence of human coronaviruses (CoVs) causing severe acute respiratory syndrome (SARS) is posing a great threat to global public health. Therefore, the rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Applications of nucleic acid detection range from genotyping and genetic prognostics, to expression profiling and detection of infectious disease. The nucleic acid detection for infectious diseases is widely used, as evidenced by the widespread use of COVID-19 tests for the containment of the pandemic. Nanotechnology influences all medical disciplines and has been considered as an essential tool for novel diagnostics, nanotherapeutics, vaccines, medical imaging, and the utilization of biomaterials for regenerative medicine. In this review, the recent advances in the development of nanotechnology-based diagnostic methods for coronavirus, and their applications in nucleic acid detection are discussed in detail. The techniques for the amplification of nucleic acids are summarized, as well as the use of magnetic nanoparticles for nucleic acid extraction. Besides, current challenges and future prospects are proposed, along with the great potential of nanotechnology for the effective diagnosis of coronavirus.
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Affiliation(s)
- Xucheng Huang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ruijie Fu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China,State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Sai Qiao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Zhang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China,Corresponding author
| | - Yunlei Xianyu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China,State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China,Corresponding author. Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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He Z, Liu C, Li Z, Chu Z, Chen X, Chen X, Guo Y. Advances in the use of nanomaterials for nucleic acid detection in point-of-care testing devices: A review. Front Bioeng Biotechnol 2022; 10:1020444. [DOI: 10.3389/fbioe.2022.1020444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/23/2022] [Indexed: 01/03/2023] Open
Abstract
The outbreak of the coronavirus (COVID-19) has heightened awareness of the importance of quick and easy testing. The convenience, speed, and timely results from point-of-care testing (POCT) in all vitro diagnostic devices has drawn the strong interest of researchers. However, there are still many challenges in the development of POCT devices, such as the pretreatment of samples, detection sensitivity, specificity, and so on. It is anticipated that the unique properties of nanomaterials, e.g., their magnetic, optical, thermal, and electrically conductive features, will address the deficiencies that currently exist in POCT devices. In this review, we mainly analyze the work processes of POCT devices, especially in nucleic acid detection, and summarize how novel nanomaterials used in various aspects of POCT products can improve performance, with the ultimate aims of offering new ideas for the application of nanomaterials and the overall development of POCT devices.
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Daramola OB, Omole RK, Akinwale IV, Otuyelu FO, Akinsanola BA, Fadare TO, George RC, Torimiro N. Bio-Receptors Functionalized Nanoparticles: A Resourceful Sensing and Colorimetric Detection Tool for Pathogenic Bacteria and Microbial Biomolecules. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.885803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pathogenic bacteria and several biomolecules produced by cells and living organisms are common biological components posing a harmful threat to global health. Several studies have devised methods for the detection of varying pathogenic bacteria and biomolecules in different settings such as food, water, soil, among others. Some of the detection studies highlighting target pathogenic bacteria and biomolecules, mechanisms of detection, colorimetric outputs, and detection limits have been summarized in this review. In the last 2 decades, studies have harnessed various nanotechnology-based methods for the detection of pathogenic bacteria and biomolecules with much attention on functionalization techniques. This review considers the detection mechanisms, colorimetric prowess of bio-receptors and compares the reported detection efficiency for some bio-receptor functionalized nanoparticles. Some studies reported visual, rapid, and high-intensity colorimetric detection of pathogenic bacteria and biomolecules at a very low concentration of the analyte. Other studies reported slight colorimetric detection only with a large concentration of an analyte. The effectiveness of bio-receptor functionalized nanoparticles as detection component varies depending on their selectivity, specificity, and the binding interaction exhibited by nanoparticles, bio-receptor, and analytes to form a bio-sensing complex. It is however important to note that the colorimetric properties of some bio-receptor functionalized nanoparticles have shown strong and brilliant potential for real-time and visual-aided diagnostic results, not only to assess food and water quality but also for environmental monitoring of pathogenic bacteria and a wide array of biomolecules.
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