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Ding L, Wang X, Chen X, Xu X, Wei W, Yang L, Ji Y, Wu J, Xu J, Peng C. Development of a novel Cas13a/Cas12a-mediated 'one-pot' dual detection assay for genetically modified crops. J Adv Res 2024:S2090-1232(24)00311-4. [PMID: 39084403 DOI: 10.1016/j.jare.2024.07.027] [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: 04/12/2024] [Revised: 07/10/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024] Open
Abstract
INTRODUCTION Genetically modified (GM) crops have been widely cultivated across the world and the development of rapid, ultrasensitive, visual multiplex detection platforms that are suitable for field deployment is critical for GM organism regulation. OBJECTIVE In this study, we developed a novel one-pot system, termed MR-DCA (Multiplex RPA and Dual CRISPR assay), for the simultaneous detection of CaMV35S and NOS genetic targets in GM crops. This innovative approach combined Multiplex RPA (recombinase polymerase amplification) with the Dual CRISPR (clustered regularly interspaced short palindromic repeat) assay technique, to provide a streamlined and efficient method for GM crop detection. METHODS The RPA reaction used for amplification CaMV35S and NOS targets was contained in the tube base, while the dual CRISPR enzymes were placed in the tube cap. Following centrifugation, the dual CRISPR (Cas13a/Cas12a) detection system was initiated. Fluorescence visualization was used to measure CaMV35S through the FAM channel and NOS through the HEX channel. When using lateral flow strips, CaMV35S was detected using rabbit anti-digoxin (blue line), whilst NOS was identified using anti-mouse FITC (red line). Line intensity was quantified using Image J and depicted graphically. RESULTS Detection of the targets was completed in 35 min, with a limit of detection as low as 20 copies. In addition, two analysis systems were developed and they performed well in the MR-DCA assay. In an analysis of 24 blind samples from GM crops with a wide genomic range, MR-DCA gave consistent results with the quantitative PCR method, which indicated high accuracy, applicability and semi-quantitative ability. CONCLUSION The development of MR-DCA represents a significant advancement in the field of GM detection, offering a rapid, sensitive and portable method for multiple target detection that can be used in resource-limited environments.
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Affiliation(s)
- Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yi Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Dong Y, Zhou D, Zhang B, Xu X, Zhang J. Development of a real-time recombinase-aided amplification assay for rapid and sensitive detection of Edwardsiella piscicida. Front Cell Infect Microbiol 2024; 14:1355056. [PMID: 38606294 PMCID: PMC11007066 DOI: 10.3389/fcimb.2024.1355056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024] Open
Abstract
Edwardsiella piscicida, a significant intracellular pathogen, is widely distributed in aquatic environments and causes systemic infection in various species. Therefore, it's essential to develop a rapid, uncomplicated and sensitive method for detection of E. piscicida in order to control the transmission of this pathogen effectively. The recombinase-aided amplification (RAA) assay is a newly developed, rapid detection method that has been utilized for various pathogens. In the present study, a real-time RAA (RT-RAA) assay, targeting the conserved positions of the EvpP gene, was successfully established for the detection of E. piscicida. This assay can be performed in a one-step single tube reaction at a temperature of 39°C within 20 min. The RT-RAA assay exhibited a sensitivity of 42 copies per reaction at a 95% probability, which was comparable to the sensitivity of real-time quantitative PCR (qPCR) assay. The specificity assay confirmed that the RT-RAA assay specifically targeted E. piscicida without any cross-reactivity with other important marine bacterial pathogens. Moreover, when clinical specimens were utilized, a perfect agreement of 100% was achieved between the RT-RAA and qPCR assays, resulting a kappa value of 1. These findings indicated that the established RT-RAA assay provided a viable alternative for the rapid, sensitive, and specific detection of E. piscicida.
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Affiliation(s)
- Yuchen Dong
- School of Ocean, Yantai University, Yantai, China
| | - Dandan Zhou
- School of Ocean, Yantai University, Yantai, China
| | - Binzhe Zhang
- School of Ocean, Yantai University, Yantai, China
| | - Xiaoying Xu
- Yantai Marine Economic Research Institute, Yantai, China
| | - Jian Zhang
- School of Ocean, Yantai University, Yantai, China
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Cui H, Xu S, Xu X, Ji J, Kan Y, Yao L, Bi Y, Xie Q. Multienzyme isothermal rapid amplification and lateral flow dipstick combination assay for visible detection of chicken chaphamaparvovirus. Poult Sci 2023; 102:103144. [PMID: 37839164 PMCID: PMC10589884 DOI: 10.1016/j.psj.2023.103144] [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: 08/18/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
Chicken chaphamaparvovirus (CkChpV) is a newly emerging pathogen that is currently prevalent in chickens with diarrhea symptoms. To diagnose CkChpV more conveniently and rapidly, this study established a multienzyme isothermal rapid amplification (MIRA) assay, with a reaction time of only 15 min and optimal reaction temperature of 38°C. In combination with the lateral flow dipstick assay, the CkChpV-MIRA assay can be completed within 20 min. We revealed that the detection limit of the MIRA assay using standard plasmids as templates was as low as 21.3 copies, and its sensitivity was 100 times higher than that of nested PCR. Moreover, the designed primer set and probe could only detect CkChpV specifically, and there was no cross reaction with avian nephritis virus, rotavirus, chicken parvovirus virus, Newcastle disease virus, and infectious bronchitis virus, which may cause diarrhea. These findings demonstrated that the CkChpV-MIRA assay established in this study is convenient, sensitive, and specific and does not require sophisticated equipment. It is more suitable for the detection of CkChpV in clinical samples.
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Affiliation(s)
- Hao Cui
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China; Chifeng Municipal Hospital, Chifeng, Inner Mongolia 024000, PR China
| | - Shuqi Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China.
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, PR China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
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Li Y, Kang T, Park HG. One-pot, ultrasensitive, and multiplex detection of SARS-CoV-2 genes utilizing self-priming hairpin-mediated isothermal amplification. Biosens Bioelectron 2023; 237:115522. [PMID: 37437457 DOI: 10.1016/j.bios.2023.115522] [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: 05/09/2023] [Revised: 06/26/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023]
Abstract
The global pandemic resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its emerging variants highlights the need for convenient and accurate detection protocols to facilitate timely prevention and management of the disease. Herein, we propose a new self-priming hairpin-mediated isothermal amplification (SIAM) protocol enabling one-pot and ultrasensitive identification of SARS-CoV-2 in a multiplexed way. This approach works by targeting a specific RNA sequence with a self-priming hairpin (SP) probe and promoting continuously repeated extension and nicking reactions to produce numerous trigger molecules, which could specifically bind to molecular beacons (MBs) and produce fluorescent signals. Under an isothermal condition of 37 °C, this technique allowed for the simultaneous identification of the spike (S) and nucleocapsid (N) genes of SARS-CoV-2 down to single copy/μL levels. We further validated the practical diagnostic capabilities of the SIAM method by accurately testing 20 clinical samples with 100% sensitivity and specificity. The SIAM method has a lot of potential to be a reliable nucleic acid testing protocol to identify infections caused by a wide range of pathogens.
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Affiliation(s)
- Yan Li
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Mueller BL, Liberman MJ, Kolpashchikov DM. OWL2: a molecular beacon-based nanostructure for highly selective detection of single-nucleotide variations in folded nucleic acids. NANOSCALE 2023; 15:5735-5742. [PMID: 36880268 DOI: 10.1039/d2nr05590b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Hybridization probes have been used in the detection of specific nucleic acids for the last 50 years. Despite the extensive efforts and the great significance, the challenges of the commonly used probes include (1) low selectivity in detecting single nucleotide variations (SNV) at low (e.g. room or 37 °C) temperatures; (2) low affinity in binding folded nucleic acids, and (3) the cost of fluorescent probes. Here we introduce a multicomponent hybridization probe, called OWL2 sensor, which addresses all three issues. The OWL2 sensor uses two analyte binding arms to tightly bind and unwind folded analytes, and two sequence-specific strands that bind both the analyte and a universal molecular beacon (UMB) probe to form fluorescent 'OWL' structure. The OWL2 sensor was able to differentiate single base mismatches in folded analytes in the temperature range of 5-38 °C. The design is cost-efficient since the same UMB probe can be used for detecting any analyte sequence.
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Affiliation(s)
- Brittany L Mueller
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
| | - Mark J Liberman
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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Hardinge P. Molecular Beacons - Loop-Mediated Amplification (MB-LAMP). Methods Mol Biol 2023; 2638:289-299. [PMID: 36781650 DOI: 10.1007/978-1-0716-3024-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
High specificity has been demonstrated in polymerase chain reaction (PCR) with the use of molecular beacons (MBs) to detect amplified sequences containing mutations or single-nucleotide polymorphisms (SNPs). MBs have been adapted for use with the isothermal nucleic acid amplification technology loop-mediated amplification (LAMP) by targeting single-stranded loop sequences under optimized conditions to enable applications such as plant genotyping. LAMP has several benefits over PCR, such as rapid amplification, single-temperature reaction conditions enabling low-cost equipment, and robustness to certain PCR inhibitors. However, and despite the increased number of primers required, the specificity of LAMP is limited, and false positive results can be problematic. In this chapter, design considerations for molecular beacons in LAMP assays are described, as well as a method for MB-LAMP amplification and detection, with an example of gene sequences in genetically modified (GM) maize samples.
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7
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Politza AJ, Nouri R, Guan W. Digital CRISPR Systems for the Next Generation of Nucleic Acid Quantification. Trends Analyt Chem 2023; 159:116917. [PMID: 36744100 PMCID: PMC9894100 DOI: 10.1016/j.trac.2023.116917] [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: 01/09/2023]
Abstract
Digital CRISPR (dCRISPR) assays are an emerging platform of molecular diagnostics. Digital platforms introduce absolute quantification and increased sensitivity to bulk CRISPR assays. With ultra-specific targeting, isothermal operation, and rapid detection, dCRISPR systems are well-prepared to lead the field of molecular diagnostics. Here we summarized the common Cas proteins used in CRISPR detection assays. The methods of digital detection and critical performance factors are examined. We formed three strategies to frame the landscape of dCRISPR systems: (1) amplification free, (2) in-partition amplification, and (3) two-stage amplification. We also compared the performance of all systems through the limit of detection (LOD), testing time, and figure of merit (FOM). This work summarizes the details of digital CRISPR platforms to guide future development. We envision that improvements to LOD and dynamic range will position dCRISPR as the leading platform for the next generation of molecular biosensing.
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Affiliation(s)
- Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Reza Nouri
- 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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8
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Shirshikov FV, Bespyatykh JA. Loop-Mediated Isothermal Amplification: From Theory to Practice. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:1159-1174. [PMID: 36590469 PMCID: PMC9788664 DOI: 10.1134/s106816202206022x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022]
Abstract
Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.
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Affiliation(s)
- F. V. Shirshikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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Establishment of a rapid method for skipjack tuna (Katsuwonus pelamis) authentication using molecular beacons in loop-mediated isothermal amplification. Food Chem 2022; 382:132365. [DOI: 10.1016/j.foodchem.2022.132365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/20/2022]
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10
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Nouri R, Dong M, Politza AJ, Guan W. Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison. ACS Sens 2022; 7:900-911. [PMID: 35238530 PMCID: PMC9191621 DOI: 10.1021/acssensors.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Simplified Detection of Epstein-Barr Virus for Diagnosis of Endemic Burkitt Lymphoma. Blood Adv 2022; 6:3650-3654. [PMID: 35240680 DOI: 10.1182/bloodadvances.2022007297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/25/2022] [Indexed: 11/20/2022] Open
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Ye H, Nowak C, Liu Y, Li Y, Zhang T, Bleris L, Qin Z. Plasmonic LAMP: Improving the Detection Specificity and Sensitivity for SARS-CoV-2 by Plasmonic Sensing of Isothermally Amplified Nucleic Acids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107832. [PMID: 35129304 PMCID: PMC9052780 DOI: 10.1002/smll.202107832] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/19/2022] [Indexed: 05/16/2023]
Abstract
The ability to detect pathogens specifically and sensitively is critical to combat infectious diseases outbreaks and pandemics. Colorimetric assays involving loop-mediated isothermal amplification (LAMP) provide simple readouts yet suffer from the intrinsic non-template amplification. Herein, a highly specific and sensitive assay relying on plasmonic sensing of LAMP amplicons via DNA hybridization, termed as plasmonic LAMP, is developed for the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) RNA detection. This work has two important advances. First, gold and silver (Au-Ag) alloy nanoshells are developed as plasmonic sensors that have 4-times stronger extinction in the visible wavelengths and give a 20-times lower detection limit for oligonucleotides over Au counterparts. Second, the integrated method allows cutting the complex LAMP amplicons into short repeats that are amendable for hybridization with oligonucleotide-functionalized Au-Ag nanoshells. In the SARS-CoV-2 RNA detection, plasmonic LAMP takes ≈75 min assay time, achieves a detection limit of 10 copies per reaction, and eliminates the contamination from non-template amplification. It also shows better detection specificity and sensitivity over commercially available LAMP kits due to the additional sequence identification. This work opens a new route for LAMP amplicon detection and provides a method for virus testing at its early representation.
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Affiliation(s)
- Haihang Ye
- Department of Mechanical EngineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Chance Nowak
- Center of Systems BiologyThe University of Texas at DallasRichardsonTX75080USA
- Department of Biological SciencesThe University of Texas at DallasRichardsonTX75080USA
| | - Yaning Liu
- Department of Mechanical EngineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Yi Li
- Center of Systems BiologyThe University of Texas at DallasRichardsonTX75080USA
- Department of BioengineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Tingting Zhang
- Department of Mechanical EngineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Leonidas Bleris
- Center of Systems BiologyThe University of Texas at DallasRichardsonTX75080USA
- Department of Biological SciencesThe University of Texas at DallasRichardsonTX75080USA
- Department of BioengineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Zhenpeng Qin
- Department of Mechanical EngineeringThe University of Texas at DallasRichardsonTX75080USA
- Department of BioengineeringThe University of Texas at DallasRichardsonTX75080USA
- Center for Advanced Pain StudiesThe University of Texas at DallasRichardsonTX75080USA
- Department of SurgeryUniversity of Texas Southwestern Medical CenterDallasTX75390USA
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Zhu Y, Wu X, Gu A, Dobelle L, Cid C, Li J, Hoffmann MR. Membrane-Based In-Gel Loop-Mediated Isothermal Amplification (mgLAMP) System for SARS-CoV-2 Quantification in Environmental Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:862-873. [PMID: 34967203 PMCID: PMC8751019 DOI: 10.1021/acs.est.1c04623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 05/06/2023]
Abstract
Since the COVID-19 pandemic is expected to become endemic, quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambient waters is critical for environmental surveillance and for early detection of outbreaks. Herein, we report the development of a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system that is designed for the rapid point-of-use quantification of SARS-CoV-2 particles in environmental waters. The mgLAMP system integrates the viral concentration, in-assay viral lysis, and on-membrane hydrogel-based RT-LAMP quantification using enhanced fluorescence detection with a target-specific probe. With a sample-to-result time of less than 1 h, mgLAMP successfully detected SARS-CoV-2 below 0.96 copies/mL in Milli-Q water. In surface water, the lowest detected SARS-CoV-2 concentration was 93 copies/mL for mgLAMP, while the reverse transcription quantitative polymerase chain reaction (RT-qPCR) with optimal pretreatment was inhibited at 930 copies/mL. A 3D-printed portable device is designed to integrate heated incubation and fluorescence illumination for the simultaneous analysis of nine mgLAMP assays. Smartphone-based imaging and machine learning-based image processing are used for the interpretation of results. In this report, we demonstrate that mgLAMP is a promising method for large-scale environmental surveillance of SARS-CoV-2 without the need for specialized equipment, highly trained personnel, and labor-intensive procedures.
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Affiliation(s)
- Yanzhe Zhu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Xunyi Wu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Alan Gu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Leopold Dobelle
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Clément
A. Cid
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Jing Li
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Michael R. Hoffmann
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
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He Y, Chen W, Fan J, Fan S, Ding H, Chen J, Yi L. Recombinase-Aided Amplification Coupled with Lateral Flow Dipstick for Efficient and Accurate Detection of Porcine Parvovirus. Life (Basel) 2021; 11:life11080762. [PMID: 34440506 PMCID: PMC8401844 DOI: 10.3390/life11080762] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/12/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Porcine parvovirus (PPV) infection is the primary cause of SMEDI (stillbirth; mummification; embryonic death; infertility) syndrome, which is a global burden for the swine industry. Thus, it is crucial to establish a rapid and efficient detection method against PPV infection. In the present work, we developed a recombinase-aided amplification (RAA) assay, coupled with a lateral flow dipstick (LFD), to achieve an amplification of PPV DNA at 37 °C within 15 min. The detection limits of PPV RAA-LFD assay were 102 copies/μL recombinant plasmid pMD19-T-VP1, 6.38 × 10-7 ng/μL PPV DNA, and 10-1 TCID50/mL virus, respectively. This method was highly specific for PPV detection with no cross-reactivity for other swine pathogens. In contrast to polymerase chain reaction (PCR), the PPV RAA-LFD assay is more sensitive and cost-saving. Hence, the established PPV RAA-LFD assay provided an alternative for PPV detection, especially in resource-limited regions.
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Affiliation(s)
- Yihong He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
| | - Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Jindai Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (J.C.); (L.Y.)
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (J.C.); (L.Y.)
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Chen W, Fan J, Li Z, Zhang Y, Qin Y, Wu K, Li X, Li Y, Fan S, Zhao M. Development of Recombinase Aided Amplification Combined With Disposable Nucleic Acid Test Strip for Rapid Detection of Porcine Circovirus Type 2. Front Vet Sci 2021; 8:676294. [PMID: 34250063 PMCID: PMC8267240 DOI: 10.3389/fvets.2021.676294] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Porcine circovirus type 2 (PCV2) is the dominant causative agent of PCV2 systemic disease (PCV2-SD) in pigs. It can also associate with other diseases such as respiratory and enteric diseases, reproductive failure, porcine dermatitis and nephropathy syndrome in pigs. Currently, PCV2 infection is a considerable threat in the swine industry. Therefore, it is of great significance to prevent, control, and accurately detect PCV2 in pig farms. Recombinase aided amplification (RAA) technology is an isothermal nucleic acid amplification technology that could rapidly amplify the target gene fragment at a constant temperature. The amplification products labeled with specific molecules could be visually detected using the test strip with the corresponding antibody. In the present study, the RAA technology combined with a nucleic acid test strip (RAA-strip) was established for simple and specific detection of PCV2. Primers and probes targeting the PCV2 ORF2 gene were designed according to the RAA technology principles. The PCV2 RAA-strip established in this study could detect as low as 103 copies/μL of recombinant plasmids containing the PCV2 ORF2 gene fragment. The lowest detection limit about viral DNA and virus titers was 6.7 × 10-6 ng/μL and 10 TCID50/mL, respectively. Furthermore, no cross-reaction with other porcine viruses occurred at 37°C and within 15 min. We used 42 clinical samples to assess the performance of our established method. The positive rate of clinical samples detected by PCV2 RAA-strip was 50.00%. This was similar to that detected by PCV2 PCR (45.24%). In conclusion, due to the advantages of strong specificity, high sensitivity, excellent reproducibility, and simple operation method, our PCV2 RAA-strip is suitable for the rapid clinical detection of PCV2 on-site.
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Affiliation(s)
- Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Jindai Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuanyuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yuwei Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Jatayev S, Hu YG, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y. Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET. FRONTIERS IN PLANT SCIENCE 2021; 12:747886. [PMID: 35082803 PMCID: PMC8784781 DOI: 10.3389/fpls.2021.747886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 05/02/2023]
Abstract
The proposed method is a modified and improved version of the existing "Allele-specific q-PCR" (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.
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Affiliation(s)
- Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
- *Correspondence: Ruslan Kalendar
| | - Akmaral Baidyussen
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Marzhan Kuzbakova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Peter A. Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
- Yuri Shavrukov
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17
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Ding X, Yin K, Li Z, Pandian V, Smyth JA, Helal Z, Liu C. Cleavable hairpin beacon-enhanced fluorescence detection of nucleic acid isothermal amplification and smartphone-based readout. Sci Rep 2020; 10:18819. [PMID: 33139727 PMCID: PMC7608614 DOI: 10.1038/s41598-020-75795-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/20/2020] [Indexed: 01/11/2023] Open
Abstract
Fluorescence detection of nucleic acid isothermal amplification utilizing energy-transfer-tagged oligonucleotide probes provides a highly sensitive and specific method for pathogen detection. However, currently available probes suffer from relatively weak fluorescence signals and are not suitable for simple, affordable smartphone-based detection at the point of care. Here, we present a cleavable hairpin beacon (CHB)-enhanced fluorescence detection for isothermal amplification assay. The CHB probe is a single fluorophore-tagged hairpin oligonucleotide with five continuous ribonucleotides which can be cleaved by the ribonuclease to specifically initiate DNA amplification and generate strong fluorescence signals. By coupling with loop-mediated isothermal amplification (LAMP), the CHB probe could detect Borrelia burgdorferi (B. burgdorferi) recA gene with a sensitivity of 100 copies within 25 min and generated stronger specific fluorescence signals which were easily read and analysed by our programmed smartphone. Also, this CHB-enhanced LAMP (CHB-LAMP) assay was successfully demonstrated to detect B. burgdorferi DNA extracted from tick species, showing comparable results to real-time PCR assay. In addition, our CHB probe was compatible with other isothermal amplifications, such as isothermal multiple-self-matching-initiated amplification (IMSA). Therefore, CHB-enhanced fluorescence detection is anticipated to facilitate the development of simple, sensitive smartphone-based point-of-care pathogen diagnostics in resource-limited settings.
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Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Vikram Pandian
- Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Joan A Smyth
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Zeinab Helal
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA.
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Quantitative LAMP and PCR Detection of Salmonella in Chicken Samples Collected from Local Markets around Pathum Thani Province, Thailand. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2020; 2020:8833173. [PMID: 32695808 PMCID: PMC7368944 DOI: 10.1155/2020/8833173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Salmonella is a bacterium that infects people when they consume contaminated food or liquids. To prevent humans from becoming ill, it is useful to have an efficient method of detecting Salmonella before the disease is passed on through the food chain. In this research, the efficiency of Salmonella detection was compared using the following four methods: conventional loop-mediated isothermal amplification (LAMP), PCR, quantitative LAMP (qLAMP), and qPCR. The artificial infection of chicken samples started with incubating of 10 mL of 108 CFU of S. typhimurium for 6 hr. and enriching for 2 hr. to represent real contamination of the samples. The results show that the sensitivity of Salmonella DNA detection in PCR, qPCR, LAMP, and qLAMP were 50 ng, 5 ng, 50 pg, and and 500 fg, respectively. Thirty samples of 10 g chicken were collected from 10 markets in Pathum Thani, Thailand; then, the infection was detected. The conventional LAMP, qLAMP, and qPCR methods detected Salmonella in all the chicken samples. However, the conventional PCR method detected Salmonella infection in only eight of the samples. Overall, the qLAMP method had the highest sensitivity of Salmonella DNA detection.
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