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Santos JAP, Juanico E, Abello JJ, Bondoc JL, Rivera WL. Surveillance of human adenoviruses in water environments: Assessing the suitability of a locally developed quenching of unincorporated amplification signal reporters-loop-mediated isothermal amplification assay. J Virol Methods 2024; 330:115041. [PMID: 39384156 DOI: 10.1016/j.jviromet.2024.115041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 09/17/2024] [Accepted: 10/06/2024] [Indexed: 10/11/2024]
Abstract
The human adenovirus (HAdV) has shown greater environmental persistence, more water treatment resistance than bacteria, and cause infection even at low concentrations. HAdV causes gastrointestinal illnesses and is abundant in various environmental samples such as groundwater, surface water, recreational water, and drinking water. The detection of these pathogens calls for a more practical and affordable approach. A recent technology based on the quenching of unincorporated amplification signal reporters (QUASR) was adapted for the detection of human adenoviruses. This technology allows for non-inhibitory, single-step DNA detection in a closed tube. The QUASR-(loop-mediated isothermal amplification (LAMP) assay was previously optimized and was tested for its applicability to detect enteric HAdV in two areas where people can unintentionally be exposed to contaminated water. A total of 203 water samples were collected and tested using both real-time PCR and QUASR-LAMP assays. Results showed a higher positivity rate of 78.82 % (160/203) for QUASR-LAMP compared to qPCR with only 58.62 % (119/203). The sensitivity and specificity rates for QUASR-LAMP were calculated at 86.55 % and 32.14 %, respectively, when compared to qPCR. The QUASR-LAMP assay's ability to detect target analytes even at low concentrations can be attributed to its increased diagnostic sensitivity but lower specificity since there were samples that were positive in PCR but negative in the QUASR-LAMP assay. However, this characteristic does not diminish its utility as a valuable tool for the detection of HAdV. In fact, this attribute enhances its advantages in situations with constrained space and instrumentation requirements, making it suitable for rapid surveillance of important viruses. Finally, the capacity of the QUASR-LAMP assay to differentiate between positive and negative samples at a defined endpoint is highly beneficial for laboratory technicians who possess limited molecular biology expertise or experience. The QUASR-LAMP platform has demonstrated its usefulness as a diagnostic tool for surveillance of enteric adenoviruses in water sources.
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Affiliation(s)
- Joy Ann P Santos
- Biological Research and Services Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines.
| | - Elchin Juanico
- Biological Research and Services Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Joseth Jermaine Abello
- Biological Research and Services Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Jonah L Bondoc
- Research and Analytical Services Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
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Yang T, Li D, Luo Z, Wang J, Xiao F, Xu Y, Lin X. Space-Confined Amplification for In Situ Imaging of Single Nucleic Acid and Single Pathogen on Biological Samples. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2407055. [PMID: 39373849 DOI: 10.1002/advs.202407055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 09/20/2024] [Indexed: 10/08/2024]
Abstract
Direct in situ imaging of nucleic acids on biological samples is advantageous for rapid analysis without DNA extraction. However, traditional nucleic acid amplification in aqueous solutions tends to lose spatial information because of the high mobility of molecules. Similar to a cellular matrix, hydrogels with biomimetic 3D nanoconfined spaces can limit the free diffusion of nucleic acids, thereby allowing for ultrafast in situ enzymatic reactions. In this study, hydrogel-based in situ space-confined interfacial amplification (iSCIA) is developed for direct imaging of single nucleic acid and single pathogen on biological samples without formaldehyde fixation. With a polyethylene glycol hydrogel coating, nucleic acids on the sample are nanoconfined with restricted movement, while in situ amplification can be successfully performed. As a result, the nucleic acids are lighted-up on the large-scale surface in 20 min, with a detection limit as low as 1 copy/10 cm2. Multiplex imaging with a deep learning model is also established to automatically analyze multiple targets. Furthermore, the iSCIA imaging of pathogens on plant leaves and food is successfully used to monitor plant health and food safety. The proposed technique, a rapid and flexible system for in situ imaging, has great potential for food, environmental, and clinical applications.
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Affiliation(s)
- Tao Yang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Dong Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- The Rural Development Academy, Zhejiang University, Hangzhou, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jingjing Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Fangbin Xiao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yanqun Xu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Xingyu Lin
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, 310058, China
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Lee JE, Chang JY, Shim WB. Multiplex fluorescence loop-mediated isothermal amplification with lateral flow assay for rapid simultaneous detection of mecA and nuc genes in methicillin-resistant Staphylococcus aureus. Anal Chim Acta 2024; 1319:342984. [PMID: 39122282 DOI: 10.1016/j.aca.2024.342984] [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: 06/07/2024] [Accepted: 07/15/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), pose a significant threat to public health. Existing detection methods, like cultivation-based techniques, demand significant time and labor, while molecular diagnostic techniques, such as PCR, necessitate sophisticated instrumentation and skilled personnel. Although previous multiplex loop-mediated isothermal amplification assays based on fluorescent dyes (mfLAMP) offer simplicity and cost-effectiveness, they are prone to false-positive results. Therefore, developing a rapid and efficient multiplex assay for high-sensitivity MRSA is imperative to create a practical diagnostic tool for point-of-care testing. RESULTS Here, we developed a mfLAMP combined with a lateral flow assay (mfLAMP-LFA) for the visual and simultaneous detection of the mecA (PBP2a-specific marker) and nuc (S. aureus-specific marker) genes in MRSA. We optimized mfLAMP-LFA using graphene oxide (GO)-based purification and specific DNA probes and evaluated its sensitivity, specificity, and stability. Utilizing GO to mitigate false-positive results by acting as a trap for free DNA probes, the mfLAMP-LFA method successfully identified mecAf and nucf-probes, exhibiting distinct red, green, and yellow fluorescence signals. The detection sensitivity of the developed mfLAMP-LFA method (1 CFU mL-1 in phosphate-buffered saline (PBS)) was comparable to other highly sensitive MRSA detection methods (1 CFU mL-1 in PBS). Furthermore, the method demonstrated specificity for MRSA, detecting it in irrigation water samples within the desired range and achieving reliable recovery rates from spiked samples. SIGNIFICANCE This novel strategy is the first to incorporate GO into mfLAMP-LFA, enabling specific and sensitive MRSA detection and advancing rapid bacterial detection. This assay facilitates MRSA diagnostics, contributing to improved public health and food safety by delivering rapid, cost-effective point-of-care results. It enables the simultaneous detection of multiple bacteria, even in irrigation water samples artificially inoculated with MRSA, which contain aerobic bacteria at 2.7 × 102 CFU mL-1.
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Affiliation(s)
- Jeong-Eun Lee
- Institute for Smart Farm, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
| | - Ji Yoon Chang
- Division of Applied Life Science (BK21), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea; Division of Food Science and Technology, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
| | - Won-Bo Shim
- Institute for Smart Farm, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea; Division of Food Science and Technology, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea.
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Agel E, Altın KH. Field-applicable simultaneous multiplex LAMP assay for screening HBV and HCV co-infection in a single tube. BMC Infect Dis 2024; 24:805. [PMID: 39123117 PMCID: PMC11311944 DOI: 10.1186/s12879-024-09567-8] [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: 01/20/2024] [Accepted: 06/25/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Globally, around 7 to 20 million people are believed to be suffering from coinfection with both hepatitis B virus (HBV) and hepatitis C virus (HCV). The loop-mediated isothermal amplification (LAMP) approach, introduced by Notomi and colleagues, has undergone substantial advancements as an effective molecular tool that enables the simultaneous analysis of multiple samples in a single tube. METHODS The present study examined the simultaneous detection of HBV and HCV in a single tube using melt curve analysis multiplex LAMP (mLAMP), which is based on the identification of unique melting peak temperatures. Selected regions for primer design including the S gene of HBV and the UTR gene of HCV. Primer optimization is initially performed through individual HBV and HCV LAMP analysis. Following the optimization process, the mLAMP assay was evaluated by optimizing the multiplex reaction mixture, determining the reaction time, and analyzing the limit of detection (LOD). The results are also analyzed using lateral flow dipsticks (LFD), which enable the visual detection of HBV and HCV by adding 20 pmol FITC-labeled LF primers into the reaction mixture prior the mLAMP. RESULTS The LOD for the mLAMP assay was determined as 10 copies/µl, and no cross-reactivity with other microorganisms was detected. The detection results obtained from patient plasma were also visually demonstrated using LFD, and displayed significant concordance with those obtained from Real-Time Polymerase Chain Assay. The mLAMP assay revealed a diagnostic sensitivity of 95% for detecting the HBV, and LOD is 90% for HCV. The overall diagnostic sensitivity of the mLAMP assay for both viruses was 85%. The assay confirmed a specificity of 100%. CONCLUSION The mLAMP assay displays significant promise for analyzing coinfected samples by simultaneously detecting the dual targets HBV and HCV within a set temperature of 62 °C, all within a time frame of 1 h. Additionally, when paired with disposable LFD, the mLAMP assay enables rapid visual detection of assay results in a matter of minutes. The result contributes to the mLAMP assay being highly suitable for coinfection screening, particularly in field conditions.
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Affiliation(s)
- Esra Agel
- Scientific and Technological Research Council of Türkiye, Sensor Technologies Research Group TUBITAK Marmara Research Center, Gebze, Kocaeli, 41470, Türkiye.
| | - Kevser Hanne Altın
- Department of Medical Microbiology, Istanbul Medipol University, Beykoz, Istanbul, 34815, Türkiye
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El-Tholoth M, Bau HH. Molecular Detection of Respiratory Tract Viruses in Chickens at the Point of Need by Loop-Mediated Isothermal Amplification (LAMP). Viruses 2024; 16:1248. [PMID: 39205222 PMCID: PMC11359210 DOI: 10.3390/v16081248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Accurate and timely molecular diagnosis of respiratory diseases in chickens is essential for implementing effective control measures, preventing the spread of diseases within poultry flocks, minimizing economic loss, and guarding food security. Traditional molecular diagnostic methods like polymerase chain reaction (PCR) require expensive equipment and trained personnel, limiting their use to centralized labs with a significant delay between sample collection and results. Loop-mediated isothermal amplification (LAMP) of nucleic acids offers an attractive alternative for detecting respiratory viruses in broiler chickens with sensitivity comparable to that of PCR. LAMP's main advantages over PCR are its constant incubation temperature (∼65 °C), high amplification efficiency, and contaminant tolerance, which reduce equipment complexity, cost, and power consumption and enable instrument-free tests. This review highlights effective LAMP methods and variants that have been developed for detecting respiratory viruses in chickens at the point of need.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
- Veterinary Sciences Program, Health Sciences Division, Al Ain Men’s Campus, Higher Colleges of Technology, Al Ain 17155, United Arab Emirates
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA;
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Meiring C, Labuschagne M. Using QUASR-PCR as a field-based genotyping assay for a tick acaricide resistance marker. Sci Rep 2024; 14:13584. [PMID: 38866908 PMCID: PMC11169234 DOI: 10.1038/s41598-024-64401-0] [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: 03/22/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024] Open
Abstract
A novel, turnkey, field-based workflow was developed and validated using Rhipicephalus microplus DNA as a template to detect the presence of the voltage-gated sodium channel kdr mutation. The field-based compatible workflow comprises manual sample homogenization for DNA extraction, PCR amplification of the targets in a closed tube, and end-point detection of the PCR products. An R. microplus species-specific assay was also included to confirm species identity and ensure the validity of the kdr mutation assay. The assays were sensitive and specific to the targets, and the workflow resulted in a turnaround time of approximately 1 h at a low cost. The novel combination of PCR with closed-tube and end-point fluorescent detection allows for easy conversion of existing conventional lab-based PCR assays into field-based detection assays. The incorporation of custom-designed 3D-printed components in the workflow provides easy adaptability and modification of the components for diverse nucleic acid detection workflows.
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Affiliation(s)
- Christina Meiring
- , Clinglobal, B03/04, The Tamarin Commercial Hub, Jacaranda Avenue, Tamarin, 90903, Mauritius
- , Clinomics, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa
| | - Michel Labuschagne
- , Clinglobal, B03/04, The Tamarin Commercial Hub, Jacaranda Avenue, Tamarin, 90903, Mauritius.
- , Clinomics, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa.
- Department of Microbiology and Biochemistry, Faculty: Natural and Agricultural Sciences, PO Box 339, Bloemfontein, 9300, Republic of South Africa.
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7
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Crego-Vicente B, del Olmo MD, Muro A, Fernández-Soto P. Multiplexing LAMP Assays: A Methodological Review and Diagnostic Application. Int J Mol Sci 2024; 25:6374. [PMID: 38928080 PMCID: PMC11203869 DOI: 10.3390/ijms25126374] [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: 04/30/2024] [Revised: 05/27/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The loop-mediated isothermal amplification (LAMP) technique is a great alternative to PCR-based methods, as it is fast, easy to use and works with high sensitivity and specificity without the need for expensive instruments. However, one of the limitations of LAMP is difficulty in achieving the simultaneous detection of several targets in a single tube, as the methodologies that allow this rely on fluorogenic probes containing specific target sequences, complicating their adaptation and the optimization of assays. Here, we summarize different methods for the development of multiplex LAMP assays based on sequence-specific detection, illustrated with a schematic representation of the technique, and evaluate their practical application based on the real-time detection and quantification of results, the possibility to visualize the results at a glance, the prior stabilization of reaction components, promoting the point-of-care use, the maximum number of specific targets amplified, and the validation of the technique in clinical samples. The various LAMP multiplexing methodologies differ in their operating conditions and mechanism. Each methodology has its advantages and disadvantages, and the choice among them will depend on specific application interests.
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Affiliation(s)
| | | | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (M.D.d.O.)
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (B.C.-V.); (M.D.d.O.)
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8
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Jang WS, Park S, Bae JH, Yoon SY, Lim CS, Cho MC. Development of a multiplex Loop-Mediated Isothermal Amplification (LAMP) for the diagnosis of bacterial periprosthetic joint infection. PLoS One 2024; 19:e0302783. [PMID: 38753660 PMCID: PMC11098349 DOI: 10.1371/journal.pone.0302783] [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: 12/05/2023] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Periprosthetic joint infection (PJI) is one of the most serious and debilitating complications that can occur after total joint arthroplasty. Therefore, early diagnosis and appropriate treatment are important for a good prognosis. Recently, molecular diagnostic methods have been widely used to detect the causative microorganisms of PJI sensitively and rapidly. The Multiplex Loop-Mediated Isothermal Amplification (LAMP) method eliminates the complex temperature cycling and delays caused by temperature transitions seen in polymerase chain reaction (PCR) methods, making it faster and easier to perform compared to PCR-based assays. Therefore, this study developed a multiplex LAMP assay for diagnosing bacterial PJI using LAMP technology and evaluated its analytical and clinical performance. METHODS We developed a multiplex LAMP assay for the detection of five bacteria: Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus agalactiae, Pseudomonas aeruginosa, and Escherichia coli, frequently observed to be the causative agents of PJI. The method of analytical sensitivity and cross-reactivity were determined by spiking standard strains into the joint synovial fluid. The analytical sensitivity of the multiplex LAMP assay was compared with that of a quantitative real-time PCR (qPCR) assay. Clinical performance was evaluated using 20 joint synovial fluid samples collected from patients suspected of having bacterial PJI. RESULTS The analytical sensitivity of the gram-positive bacterial multiplex LAMP assay and qPCR were 105/104 CFU/mL, 103/103 CFU/mL, and 105/104 CFU/mL against S. agalactiae, S. epidermidis, and S. aureus, respectively. For P. aeruginosa and E. coli, the analytical sensitivity of the multiplex LAMP and qPCR assays were 105/104 and 106/104 CFU/mL, respectively. The multiplex LAMP assay detects target bacteria without cross-reacting with other bacteria, and exhibited 100% sensitivity and specificity in clinical performance evaluation. CONCLUSIONS This multiplex LAMP assay can rapidly detect five high-prevalence bacterial species causing bacterial PJI, with excellent sensitivity and specificity, in less than 1 h, and it may be useful for the early diagnosis of PJI.
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Affiliation(s)
- Woong Sik Jang
- Department of Emergency Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seoyeon Park
- Department of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Bae
- Department of Orthopaedic Surgery, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Young Yoon
- Department of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Min-Chul Cho
- Department of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
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Moehling TJ, Browne ER, Meagher RJ. Effects of single and multiple nucleotide mutations on loop-mediated isothermal amplification. Analyst 2024; 149:1701-1708. [PMID: 38426313 DOI: 10.1039/d3an01927f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Testing is pivotal for early identification of disease and subsequent infection control. Pathogens' nucleic acid sequence can change due to naturally-occurring genetic drift or intentional modification. Because of the reliance on molecular assays for human, animal, and plant disease diagnosis, we must understand how nucleotide mutations affect test accuracy. Primers designed against original lineages of a pathogen may be less efficient at detecting variants with genetic changes in priming regions. Here, we made single- and multi-point mutations in priming regions of a model SARS-CoV-2 template that was used as input for a loop-mediated isothermal amplification (LAMP) assay. We found that many of the modifications impacted assay sensitivity, amplification speed, or both. Further research exploring mutations at every position in each of the eight priming regions should be conducted to evaluate trends and determine generalizability.
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Affiliation(s)
- Taylor J Moehling
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, 7011 East Ave, Livermore, CA, USA 94550.
| | - Erica R Browne
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, 7011 East Ave, Livermore, CA, USA 94550.
| | - Robert J Meagher
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, 7011 East Ave, Livermore, CA, USA 94550.
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Dong M, Kshirsagar A, Politza AJ, Guan W. High Fidelity Machine-Learning-Assisted False Positive Discrimination in Loop-Mediated Isothermal Amplification Using Nanopore-Based Sizing and Counting. ACS NANO 2024; 18:7170-7179. [PMID: 38393338 PMCID: PMC11197460 DOI: 10.1021/acsnano.3c12053] [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] [Indexed: 02/25/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, sensitive, and cost-effective method for developing point-of-care nucleic acid testing due to its isothermal nature. Yet, LAMP can suffer from the issue of false positives, which can compromise the specificity of the results. LAMP false positives typically arise due to contamination, nonspecific amplification, and nonspecific signal reporting (intercalating dyes, colorimetric, turbidity, etc.). While dye-labeled primers or probes have been introduced for multiplexed detection and enhanced specificity in LAMP assays, they carry the risk of reaction inhibition. This inhibition can result from the labeled primers with fluorophores or quenchers and probes that do not fully dissociate during reaction. This work demonstrated a nanopore-based system for probe-free LAMP readouts by employing amplicon sizing and counting, analogous to an electronic version of gel electrophoresis. We first developed a model to explore LAMP kinetics and verified distinct patterns between true and false positives via gel electrophoresis. Subsequently, we implemented nanopore sized counting and calibrated the event charge deficit (ECD) values and frequencies to ensure a fair analysis of amplicon profiles. This sized counting method, integrated with machine learning, achieved 91.67% accuracy for false positive discrimination, enhancing LAMP's reliability for nucleic acid detection.
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Affiliation(s)
- Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Aneesh Kshirsagar
- 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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Xu T, Yang X, Feng X, Luo H, Luo C, Jia MA, Lei L. Sensitive and Visual Detection of Brassica Yellows Virus Using Reverse Transcription Loop-Mediated Isothermal Amplification-Coupled CRISPR-Cas12 Assay. PHYTOPATHOLOGY 2024; 114:474-483. [PMID: 37589413 DOI: 10.1094/phyto-06-23-0195-r] [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: 08/18/2023]
Abstract
Brassica yellows virus (BrYV) is an economically important virus on cruciferous species. In this study, a one-pot reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system was developed for the detection of BrYV. The limit of detection of this method reached 32.8 copies of the BrYV ORF5, which is 100-fold more sensitive than the RT-LAMP method. Moreover, there was no cross-reactivity with other rapeseed-infecting RNA viruses or poleroviruses. We dried the CRISPR/Cas12a reagent in a trehalose and pullulan mixture to retain its efficacy at the RT-LAMP temperature of 63°C in order to allow portable BrYV detection in a water bath. The entire process can be performed in about 1 h, and a positive result can be rapidly and conveniently detected using a handheld UV lamp. In the field, the RT-LAMP-CRISPR/Cas12a assay was accurate and had higher sensitivity than RT-LAMP and reverse transcription-polymerase chain reaction assays. The novel RT-LAMP-CRISPR/Cas12a assay allows convenient, portable, rapid, low-cost, highly sensitive, and specific detection of BrYV and has great potential for on-site monitoring of BrYV.
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Affiliation(s)
- Tengzhi Xu
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xiaolan Yang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xia Feng
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Hao Luo
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Chun Luo
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Meng-Ao Jia
- Guizhou Academy of Tobacco Sciences, Guiyang, Guizhou 550001, China
| | - Lei Lei
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
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12
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Sun Y, Zhang S, Qi L, Zhang X, Yang M, Guo Z, Wang Z, Du Y. Advancing Multiple Detection in RT-LAMP with a Specific Probe Assembled from Plural Three-Way-Junction Structures. Anal Chem 2023; 95:17808-17817. [PMID: 37972997 DOI: 10.1021/acs.analchem.3c03877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The timely detection of diseases and the accurate identification of pathogens require the development of efficient and reliable diagnostic methods. In this study, we have developed a novel specific multivariate probe termed MRTFP (multivariate real-time fluorescent probe) by assembling strand exchange three-way-junction (3WJ) structures. The 3WJ structures were incorporated into a four-angle probe (FP) and a hexagonal probe (HP), to target the multivariate genes of Salmonella. The FP and HP enable single-step and multiplexed detection in RT-LAMP (real-time loop-mediated isothermal amplification) with exceptional sensitivity and specificity. Encouragingly, real food samples contaminated with Salmonella (Salmonella enteritidis and Salmonella typhimurium) can be readily identified and distinguished with a minimum detectable concentration (MDC) of 103 CFU/mL without the need for further culture. The introduction of MRTFP allows for simultaneous detection of dual or three targets in a single tube for LAMP, thereby improving detection efficiency. The MRTFP simplifies the design of robust multivariate probes, exhibits excellent stability, and avoids interference from multiple probe units, offering significant potential for the development of specific probes for efficient and accurate disease detection and pathogen identification.
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Affiliation(s)
- Yi Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Sicai Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, Jilin 133002, China
| | - Lijuan Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaojun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Meiting Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Zhijun Guo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, Jilin 133002, China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
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13
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Li Y, Lin S, Xue Y, Jia Q, Wang Y, Xie Y, Shi C, Ma C. Boron nitride nanoplate-based improvement of the specificity and sensitivity in loop-mediated isothermal amplification for Vibrio parahaemolyticus detection. Anal Chim Acta 2023; 1280:341851. [PMID: 37858548 DOI: 10.1016/j.aca.2023.341851] [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: 07/26/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Nucleic acid testing based on DNA amplification is gradually entering people's modern life for clinical diagnosis, food safety monitoring and infectious disease prevention. Polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) are the most powerful techniques that have been the gold standard for quantitative nucleic acid analysis. However, the high nonspecific amplification rate caused by the formation of primer dimers, hairpin structures and mismatched hybridization severely restricts their real-world applications. It is highly desirable to explore a way for improving the specificity and sensitivity of PCR and LAMP assays. RESULTS In this work, we demonstrated that a nanomaterial boron nitride nanoplate (BNNP), due to its unique surface properties, can interact with the main components of the amplification reaction, such as single stranded primers and Bst DNA polymerase, and increase the thermal conductivity of the solution. As a result, the presence of BNNPs dramatically improved the specificity of PCR and LAMP. And BNNPs maintained the specificity even after five rounds of PCR. Moreover, the sensitivity of LAMP was also enhanced by BNNPs, and the detection limit of BNNP-based LAMP was two orders of magnitude lower than that of classical LAMP. Then the BNNP-based LAMP was applied to detect Vibrio parahaemolyticus in contaminated seafood samples with high specificity and a 10-fold increase in sensitivity. SIGNIFICANCE This is the first systematic demonstration of BNNPs as a promising additive to enhance the efficiency and fidelity of PCR and LAMP amplification reactions, thereby greatly expanding the application of nucleic acid detection in a wide range of laboratory and clinical settings.
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Affiliation(s)
- Yong Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Shuo Lin
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Yuxin Xue
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Qianyue Jia
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Ye Wang
- Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, 266042, Qingdao, China
| | - Yingqiu Xie
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - 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 the Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, 266071, Qingdao, China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China.
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14
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Jiang H, Li Y, Lv X, Deng Y, Li X. Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection. Talanta 2023; 260:124645. [PMID: 37148686 PMCID: PMC10156408 DOI: 10.1016/j.talanta.2023.124645] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.
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Affiliation(s)
- Hao Jiang
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuan Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xuefei Lv
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Xiaoqiong Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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15
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Yaren O, McCarter J, Morris AR, Bradley KM, Karalkar NB, McLendon DC, Kim D, Eastmond BH, Burkett-Cadena ND, Alto BW, Benner SA. Multiplex Surveillance Kit Using Sweetened Solid Support to Detect Arboviruses Isothermally in Mosquito Saliva from the Field. Anal Chem 2023; 95:10736-10743. [PMID: 37390024 DOI: 10.1021/acs.analchem.3c01735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Recently reported "displaceable probe" loop amplification (DP-LAMP) architecture has shown to amplify viral RNA from SARS-CoV-2 with little sample processing. The architecture allows signals indicating the presence of target nucleic acids to be spatially separated, and independent in sequence, from the complicated concatemer that LAMP processes create as part of their amplification process. This makes DP-LAMP an attractive molecular strategy to integrate with trap and sampling innovations to detect RNA from arboviruses carried by mosquitoes in the field. These innovations include (a) development of organically produced carbon dioxide with ethylene carbonate as a bait deployable in mosquito trap, avoiding the need for dry ice, propane tanks, or inorganic carbonates and (b) a process that induces mosquitoes to lay virus-infected saliva on a quaternary ammonium-functionalized paper (Q-paper) matrix, where (c) the matrix (i) inactivates the deposited viruses, (ii) releases their RNA, and (iii) captures viral RNA in a form that keeps it stable for days at ambient temperatures. We report this integration here, with a surprisingly simple workflow. DP-LAMP with a reverse transcriptase was found to amplify arboviral RNA directly from Q-paper, without requiring a separate elution step. This capture-amplification-detection architecture can be multiplexed, with the entire system integrated into a device that can support a campaign of surveillance, in the wild outdoors, that reports the prevalence of arboviruses from field-captured mosquitoes.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Jacquelyn McCarter
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Andrew R Morris
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- College of Medicine, University of Florida, Gainesville, Florida 32611,, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
| | - Nilesh B Karalkar
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
| | - Daniel C McLendon
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Dongmin Kim
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Bradley H Eastmond
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
- Thermo Fisher Scientific, Frederick, Maryland 02451, USA
| | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Barry W Alto
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida 32962-4699, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615-9495, United States
- Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
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16
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Burrow DT, Heggestad JT, Kinnamon DS, Chilkoti A. Engineering Innovative Interfaces for Point-of-Care Diagnostics. Curr Opin Colloid Interface Sci 2023; 66:101718. [PMID: 37359425 PMCID: PMC10247612 DOI: 10.1016/j.cocis.2023.101718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023]
Abstract
The ongoing Coronavirus disease 2019 (COVID-19) pandemic illustrates the need for sensitive and reliable tools to diagnose and monitor diseases. Traditional diagnostic approaches rely on centralized laboratory tests that result in long wait times to results and reduce the number of tests that can be given. Point-of-care tests (POCTs) are a group of technologies that miniaturize clinical assays into portable form factors that can be run both in clinical areas --in place of traditional tests-- and outside of traditional clinical settings --to enable new testing paradigms. Hallmark examples of POCTs are the pregnancy test lateral flow assay and the blood glucose meter. Other uses for POCTs include diagnostic assays for diseases like COVID-19, HIV, and malaria but despite some successes, there are still unsolved challenges for fully translating these lower cost and more versatile solutions. To overcome these challenges, researchers have exploited innovations in colloid and interface science to develop various designs of POCTs for clinical applications. Herein, we provide a review of recent advancements in lateral flow assays, other paper based POCTs, protein microarray assays, microbead flow assays, and nucleic acid amplification assays. Features that are desirable to integrate into future POCTs, including simplified sample collection, end-to-end connectivity, and machine learning, are also discussed in this review.
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Affiliation(s)
- Damon T Burrow
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
| | - Jacob T Heggestad
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
| | - David S Kinnamon
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708 USA
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17
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Crego-Vicente B, Fernández-Soto P, García-Bernalt Diego J, Febrer-Sendra B, Muro A. Development of a Duplex LAMP Assay with Probe-Based Readout for Simultaneous Real-Time Detection of Schistosoma mansoni and Strongyloides spp. -A Laboratory Approach to Point-Of-Care. Int J Mol Sci 2023; 24:ijms24010893. [PMID: 36614336 PMCID: PMC9821331 DOI: 10.3390/ijms24010893] [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: 11/17/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is the most popular technology for point-of-care testing applications due its rapid, sensitive and specific detection with simple instrumentation compared to PCR-based methods. Many systems for reading the results of LAMP amplifications exist, including real-time fluorescence detection using fluorophore-labelled probes attached to oligonucleotide sequences complementary to the target nucleic acid. This methodology allows the simultaneous detection of multiple targets (multiplexing) in one LAMP assay. A method for multiplexing LAMP is the amplification by release of quenching (DARQ) technique by using a 5'-quencher modified LAMP primer annealed to 3'-fluorophore-labelled acting as detection oligonucleotide. The main application of multiplex LAMP is the rapid and accurate diagnosis of infectious diseases, allowing differentiation of co-infecting pathogens in a single reaction. Schistosomiasis, caused among other species by Schistosoma mansoni and strongyloidiasis, caused by Strongyloides stercoralis, are the most common helminth-parasite infections worldwide with overlapping distribution areas and high possibility of coinfections in the human population. It would be of great interest to develop a duplex LAMP to detect both pathogens in the same reaction. In this study, we investigate the use of our two previously developed and well-stablished LAMP assays for S. mansoni and Strongyloides spp. DNA detection in a new duplex real-time eight-primer system based on a modified DARQ probe method that can be performed in a portable isothermal fluorimeter with minimal laboratory resources. We also applied a strategy to stabilize the duplexed DARQ-LAMP mixtures at room temperature for use as ready-to-use formats facilitating analysis in field settings as point-of-care diagnostics for schistosomiasis and strongyloidiasis.
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18
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Zhao Y, Zeng Y, Lu R, Wang Z, Zhang X, Wu N, Zhu T, Wang Y, Zhang C. Rapid point-of-care detection of BK virus in urine by an HFman probe-based loop-mediated isothermal amplification assay and a finger-driven microfluidic chip. PeerJ 2023; 11:e14943. [PMID: 36915661 PMCID: PMC10007963 DOI: 10.7717/peerj.14943] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Background BK virus (BKV)-associated nephropathy (BKVN) is one of the leading causes of renal dysfunction and graft loss in renal transplant recipients. Early monitoring of BKV in urine is crucial to minimize the deleterious effects caused by this virus on preservation of graft function. Methods We report a simple, rapid, sensitive loop-mediated isothermal amplification (LAMP) assay using an HFman probe for detecting BKV in urine. To evaluate the performance of the assay, a comparison of the HFman probe-based LAMP (HF-LAMP) assay with two qPCR assays was performed using urine samples from 132 HIV-1 infected individuals. We further evaluated the performance of HF-LAMP directly using the urine samples from these HIV-1 infected individuals and 30 kidney transplant recipients without DNA extraction. Furthermore, we combined the HF-LAMP assay with a portable finger-driven microfluidic chip for point-of-care testing (POCT). Results The assay has high specificity and sensitivity with a limit of detection (LOD) of 12 copies/reaction and can be completed within 30 min. When the DNA was extracted, the HF-LAMP assay showed an equivalent and potentially even higher sensitivity (93.5%) than the qPCR assays (74.2-87.1%) for 132 urine samples from HIV-1 infected individuals. The HF-LAMP assay can be applied in an extraction-free format and can be completed within 45 min using a simple heat block. Although some decreased performance was seen on urine samples from HIV-1 infected individuals, the sensitivity, specificity, and accuracy of the extraction-free BKV HF-LAMP assay were 95%, 100%, and 96.7% for 30 clinical urine samples from kidney transplant recipients, respectively. Conclusion The assay has high specificity and sensitivity. Combined with a portable finger-driven microfluidic chip for easy detection, this method shows great potential for POCT detection of BKV.
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Affiliation(s)
- Yongjuan Zhao
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Yi Zeng
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Renfei Lu
- Nantong Third Hospital Affiliated to Nantong University, Nantong, China
| | - Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Engineering Medicine, Beihang University, Beijing, China
| | | | - Nannan Wu
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Tongyu Zhu
- Shanghai Medical College, Shanghai, China.,Zhongshan Hospital, Shanghai, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Engineering Medicine, Beihang University, Beijing, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Shanghai, China
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19
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Detection of Salmonella enterica subsp. enterica via Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification. ScientificWorldJournal 2022; 2022:4567817. [PMID: 36619257 PMCID: PMC9822744 DOI: 10.1155/2022/4567817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/31/2022] Open
Abstract
Salmonella enterica is a major cause of diarrheal diseases in developing countries where timely surveillance and proper clinical management are inadequate. In this study, a rapid and cheap method of detecting S. enterica DNA was developed by employing the Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification (QUASR LAMP) platform. QUASR LAMP provides a closed-tube, target-specific endpoint detection of pathogens, wherein results can be analyzed visually through an LED transilluminator and verified through agarose gel electrophoresis. Based on the chromosomal SopD gene, primers and probes were first designed, then screened. The assay was subsequently optimized so that the presence of S. enterica is determined by incubating the extracted DNA at 65°C for only 60 minutes. The assay was repeatable and can be performed by simply using a thermal cycler or even a dry bath incubator. S. enterica positives appear bright yellow green when viewed through a yellow filter excited with blue LED. The developed assay had an in silico and in vitro specificity towards Salmonella enterica subsp. enterica serovars with a limit of detection of 104 copies per microliter. The Salmonella QUASR LAMP assay has the potential for food and environmental applications. Chiefly, as an alternative to traditional microbiology and PCR, this QUASR LAMP assay can be used for point-of-care salmonellosis testing of clinical specimens in low-resource settings.
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20
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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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21
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The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk. Int J Mol Sci 2022; 23:ijms232214110. [PMID: 36430586 PMCID: PMC9693045 DOI: 10.3390/ijms232214110] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.
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22
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Patchsung M, Homchan A, Aphicho K, Suraritdechachai S, Wanitchanon T, Pattama A, Sappakhaw K, Meesawat P, Wongsatit T, Athipanyasilp A, Jantarug K, Athipanyasilp N, Buahom J, Visanpattanasin S, Niljianskul N, Chaiyen P, Tinikul R, Wichukchinda N, Mahasirimongkol S, Sirijatuphat R, Angkasekwinai N, Crone MA, Freemont PS, Joung J, Ladha A, Abudayyeh O, Gootenberg J, Zhang F, Chewapreecha C, Chanarat S, Horthongkham N, Pakotiprapha D, Uttamapinant C. A Multiplexed Cas13-Based Assay with Point-of-Care Attributes for Simultaneous COVID-19 Diagnosis and Variant Surveillance. CRISPR J 2022; 6:99-115. [PMID: 36367987 PMCID: PMC7614457 DOI: 10.1089/crispr.2022.0048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Point-of-care (POC) nucleic acid detection technologies are poised to aid gold-standard technologies in controlling the COVID-19 pandemic, yet shortcomings in the capability to perform critically needed complex detection-such as multiplexed detection for viral variant surveillance-may limit their widespread adoption. Herein, we developed a robust multiplexed clustered regularly interspaced short palindromic repeats (CRISPR)-based detection using LwaCas13a and PsmCas13b to simultaneously diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and pinpoint the causative SARS-CoV-2 variant of concern (VOC)-including globally dominant VOCs Delta (B.1.617.2) and Omicron (B.1.1.529)-all the while maintaining high levels of accuracy upon the detection of multiple SARS-CoV-2 gene targets. The platform has several attributes suitable for POC use: premixed, freeze-dried reagents for easy use and storage; convenient direct-to-eye or smartphone-based readouts; and a one-pot variant of the multiplexed detection. To reduce reliance on proprietary reagents and enable sustainable use of such a technology in low- and middle-income countries, we locally produced and formulated our own recombinase polymerase amplification reaction and demonstrated its equivalent efficiency to commercial counterparts. Our tool-CRISPR-based detection for simultaneous COVID-19 diagnosis and variant surveillance that can be locally manufactured-may enable sustainable use of CRISPR diagnostics technologies for COVID-19 and other diseases in POC settings.
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Affiliation(s)
- Maturada Patchsung
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Aimorn Homchan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Thanyapat Wanitchanon
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom.,Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Hinxton, United Kingdom
| | - Archiraya Pattama
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Khomkrit Sappakhaw
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Artittaya Athipanyasilp
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Krittapas Jantarug
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Niracha Athipanyasilp
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Juthamas Buahom
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Supapat Visanpattanasin
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | | | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Nuanjun Wichukchinda
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Hinxton, United Kingdom
| | - Surakameth Mahasirimongkol
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Hinxton, United Kingdom
| | - Rujipas Sirijatuphat
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Nasikarn Angkasekwinai
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Michael A Crone
- London Biofoundry, Imperial College Translation and Innovation Hub, London, United Kingdom; Hinxton, United Kingdom.,Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom; Hinxton, United Kingdom.,UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom; Hinxton, United Kingdom
| | - Paul S Freemont
- London Biofoundry, Imperial College Translation and Innovation Hub, London, United Kingdom; Hinxton, United Kingdom.,Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom; Hinxton, United Kingdom.,UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom; Hinxton, United Kingdom
| | - Julia Joung
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Alim Ladha
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Omar Abudayyeh
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Jonathan Gootenberg
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA; Hinxton, United Kingdom
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; and Hinxton, United Kingdom.,Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sittinan Chanarat
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; Hinxton, United Kingdom
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Hinxton, United Kingdom
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23
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Chen CY, Yang HW, Hsieh PH, Hsieh CH, Wu MH. Development of a photothermal bead-based nucleic acid amplification test (pbbNAAT) technique for a high-performance loop-mediated isothermal amplification (LAMP)–based point-of-care test (POCT). Biosens Bioelectron 2022; 215:114574. [DOI: 10.1016/j.bios.2022.114574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
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24
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Efficient multiplexing and variant discrimination in reverse-transcription loop-mediated isothermal amplification with sequence-specific hybridization probes. Biotechniques 2022; 73:247-255. [DOI: 10.2144/btn-2022-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has proven a robust and reliable nucleic acid amplification method that is well suited for simplified and rapid molecular diagnostics. Various approaches have emerged for sequence-specific detection of LAMP products, but with limitations to their widespread utility or applicability for single-nucleotide polymorphism detection and multiplexing. Here we demonstrate the use of simple hybridization probes (as used for qPCR) that enable simple multiplexing and SARS-CoV-2 variant typing in reverse-transcription LAMP. This approach requires no modification to the LAMP primers and is amenable to the detection of single-nucleotide polymorphisms and small sequence changes, which is usually difficult in LAMP. By extending LAMP’s ability to be utilized for multitarget and single-base change detection, we hope to increase its potential to enable more and better molecular diagnostic testing.
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25
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Chia CT, Bender AT, Lillis L, Sullivan BP, Martin CD, Burke W, Landis C, Boyle DS, Posner JD. Rapid detection of hepatitis C virus using recombinase polymerase amplification. PLoS One 2022; 17:e0276582. [PMID: 36282844 PMCID: PMC9595512 DOI: 10.1371/journal.pone.0276582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Over 71 million people are infected with hepatitis C virus (HCV) worldwide, and approximately 400,000 global deaths result from complications of untreated chronic HCV. Pan-genomic direct-acting antivirals (DAAs) have recently become widely available and feature high cure rates in less than 12 weeks of treatment. The rollout of DAAs is reliant on diagnostic tests for HCV RNA to identify eligible patients with viremic HCV infections. Current PCR-based HCV RNA assays are restricted to well-resourced central laboratories, and there remains a prevailing clinical need for expanded access to decentralized HCV RNA testing to provide rapid chronic HCV diagnosis and linkage to DAAs in outpatient clinics. This paper reports a rapid, highly accurate, and minimally instrumented assay for HCV RNA detection using reverse transcription recombinase polymerase amplification (RT-RPA). The assay detects all HCV genotypes with a limit of detection of 25 copies per reaction for genotype 1, the most prevalent in the United States and worldwide. The clinical sensitivity and specificity of the RT-RPA assay were both 100% when evaluated using 78 diverse clinical serum specimens. The accuracy, short runtime, and low heating demands of RT-RPA may enable implementation in a point-of-care HCV test to expand global access to effective treatment via rapid chronic HCV diagnosis.
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Affiliation(s)
- Catherine T. Chia
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Andrew T. Bender
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | | | - Benjamin P. Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Coleman D. Martin
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Wynn Burke
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Charles Landis
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
| | | | - Jonathan D. Posner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
- Family Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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26
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Fang B, Shen Y, Peng B, Bai H, Wang L, Zhang J, Hu W, Fu L, Zhang W, Li L, Huang W. Small‐Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism, and Applications. Angew Chem Int Ed Engl 2022; 61:e202207188. [DOI: 10.1002/anie.202207188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Bin Fang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- State Key Laboratory of Solidification Processing School of Materials Science and Engineering Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 China
| | - Yu Shen
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Limin Wang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Jiaxin Zhang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Wenbo Hu
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Li Fu
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- State Key Laboratory of Solidification Processing School of Materials Science and Engineering Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 China
| | - Wei Zhang
- Teaching and Evaluation Center of Air Force Medical University Xi'an 710032 China
| | - Lin Li
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- The Institute of Flexible Electronics (IFE, Future Technologies) Xiamen University Xiamen 361005, Fujian China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- The Institute of Flexible Electronics (IFE, Future Technologies) Xiamen University Xiamen 361005, Fujian China
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27
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Improved visual detection of DNA amplification using pyridylazophenol metal sensing dyes. Commun Biol 2022; 5:999. [PMID: 36130997 PMCID: PMC9491268 DOI: 10.1038/s42003-022-03973-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Detection of nucleic acid amplification has typically required sophisticated laboratory instrumentation, but as the amplification techniques have moved away from the lab, complementary detection techniques have been implemented to facilitate point-of-care, field, and even at-home applications. Simple visual detection approaches have been widely used for isothermal amplification methods, but have generally displayed weak color changes or been highly sensitive to sample and atmospheric effects. Here we describe the use of pyridylazophenol dyes and binding to manganese ion to produce a strong visible color that changes in response to nucleic acid amplification. This detection approach is easily quantitated with absorbance, rapidly and clearly visible by eye, robust to sample effects, and notably compatible with both isothermal and PCR amplification. Nucleic acid amplification and molecular diagnostic methods are being used in an increasing number of novel applications and settings, and the ability to reliably and sensitively detect them without the need for additional instrumentation will enable even more access to these powerful techniques.
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28
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Ku J, Chauhan K, Hwang SH, Jeong YJ, Kim DE. Enhanced Specificity in Loop-Mediated Isothermal Amplification with Poly(ethylene glycol)-Engrafted Graphene Oxide for Detection of Viral Genes. BIOSENSORS 2022; 12:bios12080661. [PMID: 36005057 PMCID: PMC9405610 DOI: 10.3390/bios12080661] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that allows the simple, quick, and low-cost detection of various viral genes. LAMP assays are susceptible to generating non-specific amplicons, as high concentrations of DNA primers can give rise to primer dimerization and mismatched hybridizations, resulting in false-positive signals. Herein, we reported that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly enhance the specificity of LAMP, owing to its ability to adsorb single-stranded DNA (ssDNA). By adsorbing surplus ssDNA primers, PEG-nGO minimizes the non-specific annealing of ssDNAs, including erroneous priming and primer dimerization, leading to the enhanced specificity of LAMP. The detection of complementary DNAs transcribed from the hepatitis C virus (HCV) RNA was performed by the PEG-nGO-based LAMP. We observed that the inclusion of PEG-nGO significantly enhances the specificity and sensitivity of the LAMP assay through the augmented difference in fluorescence signals between the target and non-target samples. The PEG-nGO-based LAMP assay greatly facilitates the detection of HCV-positive clinical samples, with superior precision to the conventional quantitative real-time PCR (RT-qPCR). Among the 20 clinical samples tested, all 10 HCV-positive samples are detected as positive in the PEG-nGO-based LAMP, while only 7 samples are detected as HCV-positive in the RT-qPCR. In addition, the PEG-nGO-based LAMP method significantly improves the detection precision for the false-positive decision by 1.75-fold as compared to the LAMP without PEG-nGO. Thus, PEG-nGO can significantly improve the performance of LAMP assays by facilitating the specific amplification of target DNA with a decrease in background signal.
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Affiliation(s)
- Jamin Ku
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
| | - Khushbu Chauhan
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Yong-Joo Jeong
- School of Applied Chemistry, Kookmin University, Seoul 02707, Korea
- Correspondence: (Y.-J.J.); (D.-E.K.)
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
- Correspondence: (Y.-J.J.); (D.-E.K.)
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29
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Li Q, Xue H, Fei Y, Cao M, Xiong X, Xiong X, Yang Y, Wang L. Visual detection of rainbow trout ( Oncorhynchus mykiss) and Atlantic salmon ( Salmo salar) simultaneously by duplex loop-mediated isothermal amplification. FOOD CHEMISTRY. MOLECULAR SCIENCES 2022; 4:100107. [PMID: 35769395 PMCID: PMC9235052 DOI: 10.1016/j.fochms.2022.100107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is often confounded by the non-specific amplification arising from primer dimers, off-target priming, and other artifacts. Precipitation of the DNA produced during LAMP with the use of specific fluorescently labeled probe has proved the effectiveness in specific detection. Herein, two fluorophores (ROX and FAM) were attached to the primers S-LB-6 and R-FIP for Atlantic salmon and rainbow trout, respectively, which are self-quenched in unbound state and become de-quenched after binding to the dumbbell-shaped DNA specifically. The DNA precipitation and appearance of small sediment took 10 s of centrifugation at 1000 g, by adding polyethylenimine (PEI) 600. Each target species was specifically amplified with the predicted color of PEI-DNA sediment, namely red for Atlantic salmon, green for rainbow trout, and pale yellow for mixed species. The optimized duplex LAMP system has proved its specificity and can detect as little as 1 ng DNA in visual detection.
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Affiliation(s)
- Qiuping Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Yanjin Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Min Cao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Libin Wang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Jiangsu Province 210037, China
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30
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Fang B, Shen Y, Peng B, Bai H, Wang L, Zhang J, Hu W, Fu L, Zhang W, Li L, Huang W. Small Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism and Applications. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bin Fang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Yu Shen
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Bo Peng
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Hua Bai
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Limin Wang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Jiaxin Zhang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Wenbo Hu
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Li Fu
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Wei Zhang
- Air Force Medical University Teaching and Evaluation Center CHINA
| | - Lin Li
- Nanjing Tech University Institute of Advanced Materials 30 South Puzhu Road 210008 Nanjing CHINA
| | - Wei Huang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
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31
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Tan YL, Wang T, He J, Jiang JH. Droplet microfluidic-based loop-mediated isothermal amplification (dLAMP) for simultaneous quantification of multiple targets. STAR Protoc 2022; 3:101335. [PMID: 35496787 PMCID: PMC9043755 DOI: 10.1016/j.xpro.2022.101335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The quantification of trace nucleic acids in biological samples is a frequent requirement in experimental and clinical diagnostics. Here, we present a protocol for the digital quantification of multiple nucleic acid targets with droplet microfluidics-based loop-mediated isothermal amplification (dLAMP). Our protocol provides a fundamental platform for the absolute quantification of multiple nucleic acid targets with high specificity, allowing readily adaption in various in vitro diagnostic settings. For complete details on the use and execution of this protocol, please refer to Tan et al. (2021a, 2021b). Protocol for droplet microfluidic-based loop-mediated isothermal amplification (dLAMP) Fluorescence-activating scorpion-shaped probes-based dLAMP for fluorescence generation Fast and accurate fluorescence microscopy-based droplets counting Can be applied for the absolute quantification of multiple nucleic acid targets
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32
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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33
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Isothermal amplification using sequence-specific fluorescence detection of SARS coronavirus 2 and variants in nasal swabs. Biotechniques 2022; 72:263-272. [PMID: 35545967 PMCID: PMC9248022 DOI: 10.2144/btn-2022-0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease 2019 is a public health challenge requiring rapid testing for the detection of infections and transmission. Nucleic acid amplification tests targeting SARS coronavirus 2 (CoV2) are used to detect CoV2 in clinical samples. Real-time reverse transcription quantitative PCR is the standard nucleic acid amplification test for CoV2, although reverse transcription loop-mediated isothermal amplification is used in diagnostics. The authors demonstrate a sequence-specific reverse transcription loop-mediated isothermal amplification-based nucleic acid amplification assay that is finished within 30 min using minimally processed clinical nasal swab samples and describe a fluorescence-quenched reverse transcription loop-mediated isothermal amplification assay using labeled primers and a quencher oligonucleotide. This assay can achieve rapid (30 min) and sensitive (1000 plaque-forming units/ml) fluorescence detection of CoV2 (WA1/2020), B.1.1.7 (Alpha) and variants of concern Delta (B.1.617.2) and Omicron (B.1.1.529) in nasal samples. The authors describe a sequence-specific nucleic acid amplification assay (fluorescence-quenched reverse transcription loop-mediated isothermal amplification) based on a modified reverse transcription loop-mediated isothermal amplification assay that utilizes a fluorescence-labeled reporter primer and a short complementary oligonucleotide quencher to detect SARS coronavirus 2 in minimally processed clinical nasal swab samples. The fluorescence-quenched reverse transcription loop-mediated isothermal amplification assay is completed in 30 min without purifying RNA and achieves reproducible, sensitive and specific (1000 plaque-forming units/ml) detection of SARS coronavirus 2 WA1/2020 and three SARS coronavirus 2 variant viruses while not signaling on three closely related human coronaviruses or two other heterologous human respiratory viruses.
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34
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Dong Y, Zhao Y, Li S, Wan Z, Lu R, Yang X, Yu G, Reboud J, Cooper JM, Tian Z, Zhang C. Multiplex, Real-Time, Point-of-care RT-LAMP for SARS-CoV-2 Detection Using the HFman Probe. ACS Sens 2022; 7:730-739. [PMID: 35192340 PMCID: PMC8887655 DOI: 10.1021/acssensors.1c02079] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/08/2022] [Indexed: 12/11/2022]
Abstract
Viral evolution impacts diagnostic test performance through the emergence of variants with sequences affecting the efficiency of primer binding. Such variants that evade detection by nucleic acid-based tests are subject to selective pressure, enabling them to spread more efficiently. Here, we report a variant-tolerant diagnostic test for SARS-CoV-2 using a loop-mediated isothermal nucleic acid-based amplification (LAMP) assay containing high-fidelity DNA polymerase and a high-fidelity DNA polymerase-medicated probe (HFman probe). In addition to demonstrating a high tolerance to variable SARS-CoV-2 viral sequences, the mechanism also overcomes frequently observed limitations of LAMP assays arising from non-specific amplification within multiplexed reactions performed in a single "pot". Results showed excellent clinical performance (sensitivity 94.5%, specificity 100%, n = 190) when compared directly to a commercial gold standard reverse transcription quantitative polymerase chain reaction assay for the extracted RNA from nasopharyngeal samples and the capability of detecting a wide range of sequences containing at least alpha and delta variants. To further validate the test with no sample processing, directly from nasopharyngeal swabs, we also detected SARS-CoV-2 in positive clinical samples (n = 49), opening up the possibility for the assay's use in decentralized testing.
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Affiliation(s)
- Yajuan Dong
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjuan Zhao
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Shenwei Li
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Zhenzhou Wan
- Medical
Laboratory of Taizhou Fourth People’s Hospital, Taizhou 225300, China
| | - Renfei Lu
- Clinical
Laboratory, Nantong Third Hospital Affiliated
to Nantong University, Nantong 226006, China
| | - Xianguang Yang
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Guoying Yu
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Julien Reboud
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Jonathan M. Cooper
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Zhengan Tian
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Chiyu Zhang
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
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35
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Garrido-Maestu A, Prado M. Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens. Compr Rev Food Sci Food Saf 2022; 21:1913-1939. [PMID: 35122372 DOI: 10.1111/1541-4337.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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Ooi KH, Liu MM, Moo JR, Nimsamer P, Payungporn S, Kaewsapsak P, Tan MH. A Sensitive and Specific Fluorescent RT-LAMP Assay for SARS-CoV-2 Detection in Clinical Samples. ACS Synth Biol 2022; 11:448-463. [PMID: 34981924 DOI: 10.1021/acssynbio.1c00538] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The raging COVID-19 pandemic has created an unprecedented demand for frequent and widespread testing to limit viral transmission. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has emerged as a promising diagnostic platform for rapid detection of SARS-CoV-2, in part because it can be performed with simple instrumentation. However, isothermal amplification methods frequently yield spurious amplicons even in the absence of a template. Consequently, RT-LAMP assays can produce false positive results when they are based on generic intercalating dyes or pH-sensitive indicators. Here, we report the development of a sensitive RT-LAMP assay that leverages on a novel sequence-specific probe to guard against spurious amplicons. We show that our optimized fluorescent assay, termed LANTERN, takes only 30 min to complete and can be applied directly on swab or saliva samples. Furthermore, utilizing clinical RNA samples from 52 patients with COVID-19 infection and 21 healthy individuals, we demonstrate that our diagnostic test exhibits a specificity and positive predictive value of 95% with a sensitivity of 8 copies per reaction. Hence, our new probe-based RT-LAMP assay can serve as an inexpensive method for point-of-need diagnosis of COVID-19 and other infectious diseases.
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Affiliation(s)
- Kean Hean Ooi
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, 138672 Singapore
| | - Mengying Mandy Liu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, 138672 Singapore
| | - Jia Rong Moo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Pattaraporn Nimsamer
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchai Kaewsapsak
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, 138672 Singapore
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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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Malpartida-Cardenas K, Miglietta L, Peng T, Moniri A, Holmes A, Georgiou P, Rodriguez-Manzano J. Single-channel digital LAMP multiplexing using amplification curve analysis. SENSORS & DIAGNOSTICS 2022; 1:465-468. [PMID: 37034965 PMCID: PMC7614402 DOI: 10.1039/d2sd00038e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate LAMP multiplexing (5-plex) in a single reaction with a single fluorescent channel using the machine learning-based method amplification curve analysis, showing a classification accuracy of 91.33% for detection of respiratory pathogens.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
| | - Luca Miglietta
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
| | - Tianyi Peng
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Ahmad Moniri
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
| | - Alison Holmes
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
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Jang WS, Lim DH, Choe Y, Jee H, Moon KC, Kim C, Choi M, Park IS, Lim CS. Development of a Multiplex Loop-Mediated Isothermal Amplification Assay for Diagnosis of Plasmodium spp., Plasmodium falciparum and Plasmodium vivax. Diagnostics (Basel) 2021; 11:diagnostics11111950. [PMID: 34829295 PMCID: PMC8624697 DOI: 10.3390/diagnostics11111950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 11/16/2022] Open
Abstract
Malaria, caused by the parasite Plasmodium and transmitted by mosquitoes, is an epidemic that mainly occurs in tropical and subtropical regions. As treatments differ across species of malarial parasites, there is a need to develop rapid diagnostic methods to differentiate malarial species. Herein, we developed a multiplex malaria Pan/Pf/Pv/actin beta loop-mediated isothermal amplification (LAMP) to diagnose Plasmodium spp., P. falciparum, and P. vivax, as well as the internal control (IC), within 40 min. The detection limits of the multiplex malaria Pan/Pf/Pv/IC LAMP were 1 × 102, 1 × 102, 1 × 102, and 1 × 103 copies/µL for four vectors, including the 18S rRNA gene (Plasmodium spp.), lactate dehydrogenase gene (P. falciparum), 16S rRNA gene (P. vivax), and human actin beta gene (IC), respectively. The performance of the LAMP assay was compared and evaluated by evaluating 208 clinical samples (118 positive and 90 negative samples) with the commercial RealStar® Malaria S&T PCR Kit 1.0. The developed multiplex malaria Pan/Pf/Pv/IC LAMP assay showed comparable sensitivity (100%) and specificity (100%) with the commercial RealStar® Malaria S&T PCR Kit 1.0 (100%). These results suggest that the multiplex malaria Pan/Pf/Pv/IC LAMP could be used as a point-of-care molecular diagnostic test for malaria.
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Affiliation(s)
- Woong Sik Jang
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (W.S.J.); (K.C.M.)
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (D.H.L.); (Y.C.); (H.J.); (C.K.); (M.C.); (I.S.P.)
| | - Da Hye Lim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (D.H.L.); (Y.C.); (H.J.); (C.K.); (M.C.); (I.S.P.)
| | - YoungLan Choe
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (D.H.L.); (Y.C.); (H.J.); (C.K.); (M.C.); (I.S.P.)
| | - Hyunseul Jee
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (D.H.L.); (Y.C.); (H.J.); (C.K.); (M.C.); (I.S.P.)
| | - Kyung Chul Moon
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (W.S.J.); (K.C.M.)
| | - Chaewon Kim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (D.H.L.); (Y.C.); (H.J.); (C.K.); (M.C.); (I.S.P.)
| | - Minkyeong Choi
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (D.H.L.); (Y.C.); (H.J.); (C.K.); (M.C.); (I.S.P.)
| | - In Su Park
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (D.H.L.); (Y.C.); (H.J.); (C.K.); (M.C.); (I.S.P.)
| | - Chae Seung Lim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea; (D.H.L.); (Y.C.); (H.J.); (C.K.); (M.C.); (I.S.P.)
- Correspondence: ; Tel.: +82-2-2626-3245
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Hayden A, Kuentzel M, Chittur SV. Rapid, Affordable, and Scalable SARS-CoV-2 Detection From Saliva. J Biomol Tech 2021; 32:148-157. [PMID: 35027872 DOI: 10.7171/jbt.21-3203-010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here we present an inexpensive, rapid, and robust reverse-transcription loop-mediated isothermal amplification (RT-LAMP)-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection method that is easily scalable, enabling point-of-care facilities and clinical labs to determine results from patients' saliva directly in 30 minutes for less than $2 per reaction. The method uses a novel combination of widely available reagents that can be prepared in bulk, plated, and frozen and remain stable until samples are received. This innovation dramatically reduces preparation time, enabling high-throughput automation and testing with time to results (including setup) in less than 1 hour for 96 patient samples simultaneously when using a 384-well format. By using a dual reporter (phenol red pH indicator for end-point detection and SYTO-9 fluorescent dye for real time), the assay also provides internal validation of results and redundancy in the event of an instrument malfunction.
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Affiliation(s)
- Andrew Hayden
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA
| | - Marcy Kuentzel
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany, Rensselaer, New York, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, New York, USA
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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Soares RRG, Akhtar AS, Pinto IF, Lapins N, Barrett D, Sandh G, Yin X, Pelechano V, Russom A. Sample-to-answer COVID-19 nucleic acid testing using a low-cost centrifugal microfluidic platform with bead-based signal enhancement and smartphone read-out. LAB ON A CHIP 2021; 21:2932-2944. [PMID: 34114589 DOI: 10.1039/d1lc00266j] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With its origin estimated around December 2019 in Wuhan, China, the ongoing SARS-CoV-2 pandemic is a major global health challenge. The demand for scalable, rapid and sensitive viral diagnostics is thus particularly pressing at present to help contain the rapid spread of infection and prevent overwhelming the capacity of health systems. While high-income countries have managed to rapidly expand diagnostic capacities, such is not the case in resource-limited settings of low- to medium-income countries. Aiming at developing cost-effective viral load detection systems for point-of-care COVID-19 diagnostics in resource-limited and resource-rich settings alike, we report the development of an integrated modular centrifugal microfluidic platform to perform loop-mediated isothermal amplification (LAMP) of viral RNA directly from heat-inactivated nasopharyngeal swab samples. The discs were pre-packed with dried n-benzyl-n-methylethanolamine modified agarose beads used to selectively remove primer dimers, inactivate the reaction post-amplification and allowing enhanced fluorescence detection via a smartphone camera. Sample-to-answer analysis within 1 hour from sample collection and a detection limit of approximately 100 RNA copies in 10 μL reaction volume were achieved. The platform was validated with a panel of 162 nasopharyngeal swab samples collected from patients with COVID-19 symptoms, providing a sensitivity of 96.6% (82.2-99.9%, 95% CI) for samples with Ct values below 26 and a specificity of 100% (90-100%, 95% CI), thus being fit-for-purpose to diagnose patients with a high risk of viral transmission. These results show significant promise towards bringing routine point-of-care COVID-19 diagnostics to resource-limited settings.
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Affiliation(s)
- Ruben R G Soares
- KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden.
| | - Ahmad S Akhtar
- KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden.
| | - Inês F Pinto
- KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden.
| | - Noa Lapins
- KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden.
| | - Donal Barrett
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Gustaf Sandh
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Xiushan Yin
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden and Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, China and Biotech and Biomedicine Science Co. Ltd, Shenyang, China
| | - Vicent Pelechano
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Aman Russom
- KTH Royal Institute of Technology, Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, Solna, Sweden. and AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and, KTH Royal Institute of Technology, Stockholm, Sweden
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Sherrill-Mix S, Hwang Y, Roche AM, Glascock A, Weiss SR, Li Y, Haddad L, Deraska P, Monahan C, Kromer A, Graham-Wooten J, Taylor LJ, Abella BS, Ganguly A, Collman RG, Van Duyne GD, Bushman FD. Detection of SARS-CoV-2 RNA using RT-LAMP and molecular beacons. Genome Biol 2021; 22:169. [PMID: 34082799 PMCID: PMC8173101 DOI: 10.1186/s13059-021-02387-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rapid spread of SARS-CoV-2 has led to a global pandemic, resulting in the need for rapid assays to allow diagnosis and prevention of transmission. Reverse transcription-polymerase chain reaction (RT-PCR) provides a gold standard assay for SARS-CoV-2 RNA, but instrument costs are high and supply chains are potentially fragile, motivating interest in additional assay methods. Reverse transcription and loop-mediated isothermal amplification (RT-LAMP) provides an alternative that uses orthogonal and often less expensive reagents without the need for thermocyclers. The presence of SARS-CoV-2 RNA is typically detected using dyes to report bulk amplification of DNA; however, a common artifact is nonspecific DNA amplification, which complicates detection. RESULTS Here we describe the design and testing of molecular beacons, which allow sequence-specific detection of SARS-CoV-2 genomes with improved discrimination in simple reaction mixtures. To optimize beacons for RT-LAMP, multiple locked nucleic acid monomers were incorporated to elevate melting temperatures. We also show how beacons with different fluorescent labels can allow convenient multiplex detection of several amplicons in "single pot" reactions, including incorporation of a human RNA LAMP-BEAC assay to confirm sample integrity. Comparison of LAMP-BEAC and RT-qPCR on clinical saliva samples showed good concordance between assays. To facilitate implementation, we developed custom polymerases for LAMP-BEAC and inexpensive purification procedures, which also facilitates increasing sensitivity by increasing reaction volumes. CONCLUSIONS LAMP-BEAC thus provides an affordable and simple SARS-CoV-2 RNA assay suitable for population screening; implementation of the assay has allowed robust screening of thousands of saliva samples per week.
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Affiliation(s)
- Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Aoife M Roche
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Abigail Glascock
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Leila Haddad
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter Deraska
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Caitlin Monahan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew Kromer
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jevon Graham-Wooten
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Louis J Taylor
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin S Abella
- Department of Emergency Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ronald G Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gregory D Van Duyne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Wong Tzeling JM, Engku Nur Syafirah EAR, Irekeola AA, Yusof W, Aminuddin Baki NN, Zueter A, Harun A, Chan YY. One-step, multiplex, dual-function oligonucleotide of loop-mediated isothermal amplification assay for the detection of pathogenic Burkholderia pseudomallei. Anal Chim Acta 2021; 1171:338682. [PMID: 34112436 DOI: 10.1016/j.aca.2021.338682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/18/2022]
Abstract
This study highlights the development of a multiplex real-time loop-mediated isothermal amplification assay. The developed assay employed a dual-function oligonucleotide (DFO) which simultaneously monitors the emitted amplification signals and accelerates the amplification process. The DFO was a modification of loop primer (LP); the 5'-end and 3'-end of the LP was tagged with fluorophore and quencher, respectively. The DFO was quenched in its unbound state and fluoresces only when it anneals to the specific target during the amplification process. With the same working mechanism as LP, DFO allowed the detection of target genes in less than 1 h in a real time monitoring system. We demonstrated this detection platform with Burkholderia pseudomallei, the causative agent of melioidosis. An internal amplification control (IAC) was incorporated in the assay to rule out false negative result and to demonstrate that the assay was successfully developed in a multiplex system. The assay was 100% specific when it was evaluated against 96 B. pseudomallei clinical isolates and 48 other bacteria species. The detection limit (sensitivity) of the developed assay was 1 fg/μl of B. pseudomallei genomic DNA and 18.2 CFU/ml at the bacterial cell level. In spiked blood samples, the assay's detection limit was 14 CFU/ml. The assay's diagnostic evaluation showed 100% diagnostic sensitivity, diagnostic specificity, positive predictive value, and negative predictive value. An integrated multiplex LAMP and real-time monitoring system was successfully developed, simplifying the workflow for the rapid and specific nucleic acid diagnostic test.
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Affiliation(s)
- Jilien Michelle Wong Tzeling
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - E A R Engku Nur Syafirah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, PMB 4412, Offa Kwara State, Nigeria.
| | - Wardah Yusof
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Nurul Najian Aminuddin Baki
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - AbdelRahman Zueter
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Department of Medical Laboratory Sciences, Faculty of Applied Health Sciences, The Hashemite University, 13133, Zarqa, Jordan.
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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45
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Tan YL, Huang AQ, Tang LJ, Jiang JH. Multiplexed droplet loop-mediated isothermal amplification with scorpion-shaped probes and fluorescence microscopic counting for digital quantification of virus RNAs. Chem Sci 2021; 12:8445-8451. [PMID: 34221326 PMCID: PMC8221175 DOI: 10.1039/d1sc00616a] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Highly sensitive digital nucleic acid techniques are of great significance for the prevention and control of epidemic diseases. Here we report the development of multiplexed droplet loop-mediated isothermal amplification (multiplexed dLAMP) with scorpion-shaped probes (SPs) and fluorescence microscopic counting for simultaneous quantification of multiple targets. A set of target-specific fluorescence-activable SPs are designed, which allows establishment of a novel multiplexed LAMP strategy for simultaneous detection of multiple cDNA targets. The digital multiplexed LAMP assay is thus developed by implementing the LAMP reaction using a droplet microfluidic chip coupled to a droplet counting microwell chip. The droplet counting system allows rapid and accurate counting of the numbers of total droplets and the positive droplets by collecting multi-color fluorescence images of the droplets in a microwell. The multiplexed dLAMP assay was successfully demonstrated for the quantification of HCV and HIV cDNA with high precision and detection limits as low as 4 copies per reaction. We also verified its potential for simultaneous digital assay of HCV and HIV RNA in clinical plasma samples. This multiplexed dLAMP technique can afford a useful platform for highly sensitive and specific detection of nucleic acids of viruses and other pathogens, enabling rapid diagnosis and prevention of infectious diseases. The development of multiplexed dLAMP with scorpion-shaped probes and fluorescence microscopic counting affords simultaneous digital quantification of multiple virus RNAs.![]()
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Affiliation(s)
- Ya-Ling Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China +86-731-88822577 +86-731-88822872
| | - A-Qian Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China +86-731-88822577 +86-731-88822872
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China +86-731-88822577 +86-731-88822872
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China +86-731-88822577 +86-731-88822872
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Bektaş A, Covington MF, Aidelberg G, Arce A, Matute T, Núñez I, Walsh J, Boutboul D, Delaugerre C, Lindner AB, Federici F, Jayaprakash AD. Accessible LAMP-Enabled Rapid Test (ALERT) for Detecting SARS-CoV-2. Viruses 2021; 13:742. [PMID: 33922716 PMCID: PMC8146324 DOI: 10.3390/v13050742] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has highlighted bottlenecks in large-scale, frequent testing of populations for infections. Polymerase chain reaction (PCR)-based diagnostic tests are expensive, reliant on centralized labs, can take days to deliver results, and are prone to backlogs and supply shortages. Antigen tests that bind and detect the surface proteins of a virus are rapid and scalable but suffer from high false negative rates. To address this problem, an inexpensive, simple, and robust 60-minute do-it-yourself (DIY) workflow to detect viral RNA from nasal swabs or saliva with high sensitivity (0.1 to 2 viral particles/μL) and specificity (>97% true negative rate) utilizing reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed. ALERT (Accessible LAMP-Enabled Rapid Test) incorporates the following features: (1) increased shelf-life and ambient temperature storage, compared to liquid reaction mixes, by using wax layers to isolate enzymes from other reagents; (2) improved specificity compared to other LAMP end-point reporting methods, by using sequence-specific QUASR (quenching of unincorporated amplification signal reporters); (3) increased sensitivity, compared to methods without purification through use of a magnetic wand to enable pipette-free concentration of sample RNA and cell debris removal; (4) quality control with a nasopharyngeal-specific mRNA target; and (5) co-detection of other respiratory viruses, such as influenza B, by multiplexing QUASR-modified RT-LAMP primer sets. The flexible nature of the ALERT workflow allows easy, at-home and point-of-care testing for individuals and higher-throughput processing for labs and hospitals. With minimal effort, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific primer sets can be swapped out for other targets to repurpose ALERT to detect other viruses, microorganisms, or nucleic acid-based markers.
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Affiliation(s)
- Ali Bektaş
- Oakland Genomics Center, 355 30th Street, Oakland, CA 94609, USA; (M.F.C.)
| | - Michael F. Covington
- Oakland Genomics Center, 355 30th Street, Oakland, CA 94609, USA; (M.F.C.)
- Amaryllis Nucleics, 355 30th Street, Oakland, CA 94609, USA
| | - Guy Aidelberg
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, F-75006 Paris, France; (G.A.); (A.B.L.)
| | - Anibal Arce
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile; (A.A.); (T.M.); (I.N.); (F.F.)
- FONDAP Center for Genome Regulation, ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBIO), Santiago 8331150, Chile
| | - Tamara Matute
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile; (A.A.); (T.M.); (I.N.); (F.F.)
- FONDAP Center for Genome Regulation, ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBIO), Santiago 8331150, Chile
| | - Isaac Núñez
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile; (A.A.); (T.M.); (I.N.); (F.F.)
- FONDAP Center for Genome Regulation, ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBIO), Santiago 8331150, Chile
| | - Julia Walsh
- School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA;
| | - David Boutboul
- Clinical Immunology Department, U976 HIPI, Hôpital Saint Louis, Université de Paris, F-75006 Paris, France; (D.B.); (C.D.)
| | - Constance Delaugerre
- Clinical Immunology Department, U976 HIPI, Hôpital Saint Louis, Université de Paris, F-75006 Paris, France; (D.B.); (C.D.)
| | - Ariel B. Lindner
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, F-75006 Paris, France; (G.A.); (A.B.L.)
| | - Fernán Federici
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile; (A.A.); (T.M.); (I.N.); (F.F.)
- FONDAP Center for Genome Regulation, ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBIO), Santiago 8331150, Chile
| | - Anitha D. Jayaprakash
- Oakland Genomics Center, 355 30th Street, Oakland, CA 94609, USA; (M.F.C.)
- Girihlet Inc., 355 30th Street, Oakland, CA 94609, USA
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47
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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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48
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Joshi S, Dixit KK, Sharma V, Ramesh V, Singh R, Salotra P. Rapid Multiplex Loop-Mediated Isothermal Amplification (m-LAMP) Assay for Differential Diagnosis of Leprosy and Post-Kala-Azar Dermal Leishmaniasis. Am J Trop Med Hyg 2021; 104:2085-2090. [PMID: 33872215 PMCID: PMC8176499 DOI: 10.4269/ajtmh.19-0313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/09/2019] [Indexed: 11/07/2022] Open
Abstract
Leprosy and post-kala-azar dermal leishmaniasis (PKDL) are co-endemic neglected tropical diseases often misdiagnosed because of close resemblance in their clinical manifestations. The test that aids in differential diagnosis of leprosy and PKDL would be useful in endemic areas. Here, we report development of a multiplex loop-mediated isothermal amplification (m-LAMP) assay for differential detection of Mycobacterium leprae and Leishmania donovani using a real-time fluorometer. The m-LAMP assay was rapid with a mean amplification time of 15 minutes, and analytical sensitivity of 1 fg for L. donovani and 100 fg for M. leprae. The distinct mean Tm values for M. leprae and L. donovani allowed differentiation of the two organisms in the m-LAMP assay. Diagnostic sensitivity of the assay was evaluated by using confirmed cases of leprosy (n = 40) and PKDL (n = 40) (tissue and slit aspirate samples). All the leprosy and PKDL samples used in this study were positive by organism-specific QPCR and loop-mediated isothermal amplification assays. The diagnostic sensitivity of the m-LAMP assay was 100% (95% CI: 91.2-100.0%) for detecting PKDL and 95% for leprosy (95% CI: 83.1-99.4%). Our m-LAMP assay was successfully used to detect both M. leprae and L. donovani in a patient coinfected with leprosy and macular PKDL. The m-LAMP assay is rapid, accurate, and applicable for differential diagnosis of leprosy versus PKDL, especially in endemic areas.
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Affiliation(s)
- Shweta Joshi
- Molecular Parasitology Laboratory, ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Keerti K. Dixit
- Molecular Parasitology Laboratory, ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Vanila Sharma
- Molecular Parasitology Laboratory, ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - V. Ramesh
- Department of Dermatology, Safdarjung Hospital, New Delhi, India
| | - Ruchi Singh
- Molecular Parasitology Laboratory, ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Poonam Salotra
- Molecular Parasitology Laboratory, ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
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49
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Zhang Y, A Tanner N. Development of multiplexed reverse-transcription loop-mediated isothermal amplification for detection of SARS-CoV-2 and influenza viral RNA. Biotechniques 2021; 70:167-174. [PMID: 33535813 PMCID: PMC7860930 DOI: 10.2144/btn-2020-0157] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/15/2021] [Indexed: 11/23/2022] Open
Abstract
The ongoing pandemic has demonstrated the utility of widespread surveillance and diagnostic detection of the novel SARS-CoV-2. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) has enabled broader testing, but current LAMP tests only detect single targets and require separate reactions for controls. With flu season in the Northern Hemisphere, the ability to screen for multiple targets will be increasingly important, and the ability to include internal controls in RT-LAMP allows for improved efficiency. Here we describe multiplexed RT-LAMP with four targets (SARS-CoV-2, influenza A, influenza B, human RNA) in a single reaction using real-time and end point fluorescence detection. Such increased functionality of RT-LAMP will enable even broader adoption of this molecular testing approach and aid in the fight against this public health threat.
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Affiliation(s)
- Yinhua Zhang
- Nucleic Acid Replication Division, Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Nathan A Tanner
- Nucleic Acid Replication Division, Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
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50
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Moehling TJ, Choi G, Dugan LC, Salit M, Meagher RJ. LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community. Expert Rev Mol Diagn 2021; 21:43-61. [PMID: 33474990 DOI: 10.1080/14737159.2021.1873769] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Over the past decade, loop-mediated isothermal amplification (LAMP) technology has played an important role in molecular diagnostics. Amongst numerous nucleic acid amplification assays, LAMP stands out in terms of sample-to-answer time, sensitivity, specificity, cost, robustness, and accessibility, making it ideal for field-deployable diagnostics in resource-limited regions.Areas covered: In this review, we outline the front-end LAMP design practices for point-of-care (POC) applications, including sample handling and various signal readout methodologies. Next, we explore existing LAMP technologies that have been validated with clinical samples in the field. We summarize recent work that utilizes reverse transcription (RT) LAMP to rapidly detect SARS-CoV-2 as an alternative to standard PCR protocols. Finally, we describe challenges in translating LAMP from the benchtop to the field and opportunities for future LAMP assay development and performance reporting.Expert opinion: Despite the popularity of LAMP in the academic research community and a recent surge in interest in LAMP due to the COVID-19 pandemic, there are numerous areas for improvement in the fundamental understanding of LAMP, which are needed to elevate the field of LAMP assay development and characterization.
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Affiliation(s)
- Taylor J Moehling
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Gihoon Choi
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
| | - Lawrence C Dugan
- Lawrence Livermore National Laboratory, Biosciences & Biotechnology Div., Livermore, CA, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Lab and Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Robert J Meagher
- Sandia National Laboratories, Biotechnology & Bioengineering Dept., Livermore, CA, USA
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