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Jessing MP, Abuawad A, Bikulov T, Abresch JR, Offenhäusser A, Krause HJ. Isothermal Amplification Using Temperature-Controlled Frequency Mixing Magnetic Detection-Based Portable Field-Testing Platform. SENSORS (BASEL, SWITZERLAND) 2024; 24:4478. [PMID: 39065876 PMCID: PMC11281083 DOI: 10.3390/s24144478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
Abstract
Sensitive magnetic nucleic acid (NA) detection via frequency mixing magnetic detection (FMMD) requires amplified NA samples for which a reliable temperature control is necessary. The feasibility of recombinase polymerase amplification (RPA) was studied within a newly integrated temperature-controlled sensor unit of a mobile FMMD based setup. It has been demonstrated that the inherently generated heat of the low frequency (LF) excitation signal of FMMD can be utilized and controlled by means of pulse width modulation (PWM). To test control performance in a point of care (PoC) setting with changing ambient conditions, a steady state and dynamic response model for the thermal behavior at the sample position of the sensor were developed. We confirmed that in the sensor unit of the FMMD device, RPA performs similar as in a temperature-controlled water bath. For narrow steady state temperature regions, a linear extrapolation suffices for estimation of the sample position temperature, based on the temperature feedback sensor for PWM control. For any other ambient conditions, we identified and validated a lumped parameter model (LPM) performing with high estimation accuracy. We expect that the method can be used for NA amplification and magnetic detection using FMMD in resource-limited settings.
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Affiliation(s)
- Max P. Jessing
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.P.J.); (A.A.); (T.B.); (J.R.A.); (A.O.)
- Faculty of Mathematics, Computer Science and Natural Sciences, Rheinisch-Westfälische Technische Hochschule Aachen University, 52062 Aachen, Germany
| | - Abdalhalim Abuawad
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.P.J.); (A.A.); (T.B.); (J.R.A.); (A.O.)
- Faculty of Mathematics, Computer Science and Natural Sciences, Rheinisch-Westfälische Technische Hochschule Aachen University, 52062 Aachen, Germany
| | - Timur Bikulov
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.P.J.); (A.A.); (T.B.); (J.R.A.); (A.O.)
- Faculty of Mathematics, Computer Science and Natural Sciences, Rheinisch-Westfälische Technische Hochschule Aachen University, 52062 Aachen, Germany
| | - Jan R. Abresch
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.P.J.); (A.A.); (T.B.); (J.R.A.); (A.O.)
| | - Andreas Offenhäusser
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.P.J.); (A.A.); (T.B.); (J.R.A.); (A.O.)
- Faculty of Mathematics, Computer Science and Natural Sciences, Rheinisch-Westfälische Technische Hochschule Aachen University, 52062 Aachen, Germany
| | - Hans-Joachim Krause
- Institute of Biological Information Processing: Bioelectronics (IBI-3), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.P.J.); (A.A.); (T.B.); (J.R.A.); (A.O.)
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Zolotareva M, Cascalheira F, Caneiras C, Bárbara C, Caetano DM, Teixeira MC. In the flow of molecular miniaturized fungal diagnosis. Trends Biotechnol 2024:S0167-7799(24)00157-4. [PMID: 38987118 DOI: 10.1016/j.tibtech.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.
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Affiliation(s)
- Maria Zolotareva
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Francisco Cascalheira
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Cátia Caneiras
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, 2829-511 Almada, Portugal; Institute of Preventive Medicine and Public Health, Universidade de Lisboa, 1649-026 Lisboa, Portugal
| | - Cristina Bárbara
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Centro Hospitalar Universitário Lisboa Norte, 1600-190, Lisboa, Portugal
| | - Diogo Miguel Caetano
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; Department of Electrical and Computer Engineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
| | - Miguel Cacho Teixeira
- iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
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3
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Sakkhachornphop S, Thongkum W, Sornsuwan K, Juntit OA, Jirakunachayapisan K, Kongyai N, Tayapiwatana C. Development and evaluation of a high-sensitivity RT-PCR lateral flow assay for early detection of HIV-1 infection. Heliyon 2024; 10:e32784. [PMID: 38975074 PMCID: PMC11226822 DOI: 10.1016/j.heliyon.2024.e32784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024] Open
Abstract
Early diagnosis of HIV-1 is crucial to minimize transmission, morbidity, and mortality, particularly for neonates with developing immune systems. This study aimed to develop and evaluate a simplified, high-sensitivity assay for early HIV-1 detection before seroconversion. The assay utilizes reverse-transcription-polymerase chain reaction (RT-PCR) to amplify the HIV-1 RNA protease gene. Digoxigenin (dig)-labeled forward, and biotin-labeled universal reverse primers are used, generating digoxigenin-amplicon-biotin (DAB) products. These products are detected using a lateral flow assay (LFA) containing a conjugated pad with colloidal gold-labeled 6-histidine tag-fused maltose-binding protein-monomeric streptavidin (6HISMBP-mSA-CGC). Anti-dig monoclonal antibody (mAb) and biotinylated-BSA are immobilized in the test and control line zones, respectively. Five plasma samples with known viral load (VL) were used to simulate the efficacy of early HIV-1 detection. RNA extracted from these samples was amplified by RT-PCR using the labeled primers, and DAB products were examined on agarose gel electrophoresis and LFA. RT-PCR from diluted clinical samples yielded visible DNA bands in agarose gel electrophoresis, consistent with positive LFA results. Conversely, negative samples only displayed the control line on LFA. This assay exhibited a limit of detection (LOD) of 82.29 RNA copies/mL, comparable to other nucleic acid amplification tests (NAATs). This novel technique provides a highly sensitive assay for early HIV-1 diagnosis, even with low VL, making it suitable for resource-limited settings.
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Affiliation(s)
| | - Weeraya Thongkum
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kanokporn Sornsuwan
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - On-anong Juntit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Natedao Kongyai
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
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Nwe MK, Jangpromma N, Taemaitree L. Evaluation of molecular inhibitors of loop-mediated isothermal amplification (LAMP). Sci Rep 2024; 14:5916. [PMID: 38467647 PMCID: PMC10928092 DOI: 10.1038/s41598-024-55241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a cost-effective and easy-to-perform assay that enables the direct detection of DNA. Its use in point-of-care diagnostic tests is growing, while it has the potential to be used in presumptive on-the-field forensic tests. Samples are often collected from complex matrices that contain high levels of contaminants. Herein, we evaluate the effect of seven common DNA amplification inhibitors on LAMP - bile salts, calcium chloride, hematin, humic acid, immunoglobulin G, tannic acid and urea. We study the effect of each inhibitor individually in real-time detection systems coupled with end-point measurements to delineate their inhibitory effects from the matrix in which they may be found. Our studies show LAMP inhibitors generally delay the onset of amplicon formation and quench fluorescence at similar or higher concentrations compared to PCR, but that end-point measurements of LAMP amplicons are unaffected. This is important as LAMP amplicons can be detected in non-fluorometric ways thus contributing to the assertions that LAMP is more robust to inhibitors than PCR.
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Affiliation(s)
- May Khat Nwe
- Department of Integrated Science, Forensic Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nisachon Jangpromma
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Lapatrada Taemaitree
- Department of Integrated Science, Forensic Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
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Dixit R, Kodali NK, Biswal M, Prakash JAJ, Gopalan N, Das P, Behera SK. Polymerase Spiral Reaction (PSR) as a point-of-care diagnostic assay: A systematic review. Expert Rev Mol Diagn 2024; 24:79-88. [PMID: 38329468 DOI: 10.1080/14737159.2024.2315286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
INTRODUCTION The current systematic review aimed to collect and analyze the comprehensive evidence regarding Polymerase Spiral Reaction (PSR) and to estimate its diagnostic performance and usefulness as a point-of-care (PoC) assay. METHODS Literature was retrieved systematically from 2015 to 2023 from PubMed and Scopus. Studies were screened and selected against pre-determined inclusion and exclusion criteria. Quality assessment and risk of bias were critiqued using QUADAS-2. A systematic, qualitative narrative synthesis was employed to synthesize the data. RESULTS 11 studies were selected for the systematic review, testing diseases in humans utilizing PSR. Only 2 studies clinically validated the test with a sample size > 150. 5 studies were of poor quality; 3 studies were of moderate quality and 3 studies were deemed to be of high quality. 3 studies quantified the diagnostic throughput and reported clinical sensitivity and specificity of PSR approaching to be > 92% and ~ 100%, respectively. CONCLUSION Polymerase spiral reaction promises to be an optimistic isothermal assay; however, a huge research gap can be attributed to the lack of statistical and clinical evidence to validate the assay. Adequate research, focused on optimization, coupled with statistical and clinical validation, can help in estimating its true diagnostic potential and applicability. REGISTRATION AND PROTOCOL A detailed protocol of this review is registered and available in Prospero (registration number CRD42023406265).
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Affiliation(s)
- Rashi Dixit
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, India
| | - Naveen Kumar Kodali
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, India
| | - Manisha Biswal
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | | | - Natarajan Gopalan
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, India
| | - Padma Das
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Raipur, India
| | - Sujit Kumar Behera
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, India
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Liu T, Politza AJ, Kshirsagar A, Zhu Y, Guan W. Compact Point-of-Care Device for Self-Administered HIV Viral Load Tests from Whole Blood. ACS Sens 2023; 8:4716-4727. [PMID: 38011515 PMCID: PMC11222019 DOI: 10.1021/acssensors.3c01819] [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] [Indexed: 11/29/2023]
Abstract
Human immunodeficiency virus (HIV) is a significant problem to consider as it can lead to acquired immune deficiency syndrome (AIDS). Fortunately, AIDS is manageable through antiretroviral therapy (ART). However, frequent viral load monitoring is needed to monitor the effectiveness of the therapy. The current reverse transcription-polymerase chain reaction (RT-PCR) viral load monitoring is highly effective, but is challenged by being resource-intensive and inaccessible, and its turnaround time does not meet demand. An unmet need exists for an affordable, rapid, and user-friendly point-of-care device that could revolutionize and ensure therapeutic effectiveness, particularly in resource-limited settings. In this work, we explored a point-of-care HIV viral load device to address this need. This device can perform streamlined plasma separation, viral RNA extraction, and real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) semiquantitative testing in an ultracompact device. We developed an absorption-based membrane plasma separation method suitable for finger-prick blood samples, achieving an efficiency of 80%. We also designed a syringe-based RNA extraction method for on-site plasma processing with a viral recovery efficiency of 86%. We created a portable device with a smartphone interface for real-time semiquantitative RT-LAMP, which is useful for monitoring viral load. The device uses lyophilized reagents, processed with our lyophilization method, which remain stable for 16 weeks. The device can accurately categorize viral load into low, medium, and high categories with 95% accuracy. We believe this point-of-care HIV self-test device, offering convenience and long-term storage, could aid patients in home-based ART treatment monitoring.
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Affiliation(s)
- Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Yusheng Zhu
- Department of Pathology and Laboratory Medicine, Pennsylvania State University, Hershey 17033, USA
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
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Gavina K, Franco LC, Khan H, Lavik JP, Relich RF. Molecular point-of-care devices for the diagnosis of infectious diseases in resource-limited settings - A review of the current landscape, technical challenges, and clinical impact. J Clin Virol 2023; 169:105613. [PMID: 37866094 DOI: 10.1016/j.jcv.2023.105613] [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: 06/20/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Molecular point-of-care (POC) tests offer high sensitivity, rapid turnaround times, relative ease of use, and the convenience of laboratory-grade testing in the absence of formal laboratory spaces and equipment, making them appealing options for infectious disease diagnosis in resource-limited settings. In this review, we discuss the role and potential of molecular POC tests in resource-limited settings and their associated logistical challenges. We discuss U.S. Food and Drug Administration approval, Clinical Laboratory Improvement Amendments complexity levels, and the REASSURED criteria as a starting point for assessing options currently available inside and outside of the United States. We then present POC tests currently in research and development phases that have potential for commercialization and implementation in limited-resource settings. Finally, we review published studies that have assessed the clinical impact of molecular POC testing in limited- and moderate-resource settings.
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Affiliation(s)
- Kenneth Gavina
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Clinical Microbiology, Indiana University Health, Indianapolis, IN, USA
| | - Lauren C Franco
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Haseeba Khan
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John-Paul Lavik
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Clinical Microbiology, Indiana University Health, Indianapolis, IN, USA
| | - Ryan F Relich
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Clinical Microbiology, Indiana University Health, Indianapolis, IN, USA.
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Sial MU, Farooq T, Khalaf LK, Rahman S, Asad M, Ahamad Paray B. Two-step method for rapid isolation of genomic DNA and validation of R81T insecticide resistance mutation in Myzus persicae. Saudi J Biol Sci 2023; 30:103791. [PMID: 37711971 PMCID: PMC10497781 DOI: 10.1016/j.sjbs.2023.103791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023] Open
Abstract
Isolation and amplification of nucleic acid (DNA) is considered a vital and potent instrument in molecular biological research. However, its functioning outside of a laboratory setting is difficult because of complex procedures that demand expert personnel and expensive equipment in addition to the fulfillment of several additional requirements. DNA isolation from minute insects is sometimes difficult, making diagnostic and genotyping procedures problematic. Thus, the current work offers a high-throughput, cost-effective, straightforward, and faster approach for isolating DNA from the aphid Myzus persicae. Intriguingly, two-step DNA extraction process yielded a high yield of extremely pure genomic DNA and required only 10 s to complete. PCR investigation aiming at amplifying the non-synonymous R81T region on the loop D site of the nAChR gene of M. persicae was subsequently utilized to successfully validate the recovered DNA. Moreover, the proposed method was compared in terms of yield and purity with conventionally used DNA isolation methods including, phenol:chloroform, salt out, and commercially available kits. In conclusion, this newly developed method would enable researchers to quickly process many biological samples used to analyze genetic diversity, mutant screening, and large spectrum diagnosis both in laboratory and field conditions.
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Affiliation(s)
- Muhammad Umair Sial
- Department of Entomology, University of Agriculture, Faisalabad 38000, Pakistan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Tahir Farooq
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Luaay Kahtan Khalaf
- Department of Plant Protection, College of Agricultural Engineering Science, University of Baghdad, Baghdad, Iraq
| | - Saqib Rahman
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Bilal Ahamad Paray
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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Saengsawang N, Ruang-Areerate P, Kaeothaisong N, Leelayoova S, Mungthin M, Juntanawiwat P, Hanyanunt P, Potisuwan P, Kesakomol P, Butsararattanagomen P, Wichaiwong P, Dungchai W, Ruang-Areerate T. Validation of quantitative loop-mediated isothermal amplification assay using a fluorescent distance-based paper device for detection of Escherichia coli in urine. Sci Rep 2023; 13:18781. [PMID: 37907677 PMCID: PMC10618465 DOI: 10.1038/s41598-023-46001-6] [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: 09/20/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) causes up to 90% of urinary tract infections (UTI) which is more prevalent among females than males. In urine, patients with symptomatic UTI usually have a high concentration of bacterial infection, ≥ 105 colony-forming units (CFU) per mL, in which the culture method is regularly the gold standard diagnosis. In this study, a simple and inexpensive distance-based paper device (dPAD) combined with the fluorescent closed tube LAMP assay was validated for simultaneously screening and semi-quantifying the infection level of E. coli in 440 urine samples of patients with UTI. The dPAD could measure the LAMP amplicons and semi-quantify the levels of E. coli infection in heavy (≥ 104 CFU/mL), light (≤ 103 CFU/mL) and no infection. The sensitivity and specificity had reliable performances, achieving as high as 100 and 92.7%, respectively. The one step LAMP assay could be performed within 3 h, which was 7.5 times faster than the culture method. To empower early UTI diagnosis and fast treatment, this inexpensive dPAD tool combined with the fluorescent closed tube LAMP assay is simple, reliably fast and practically portable for point-of-care settings, particularly in resource-limited areas, which can be set up in all levels of healthcare facilities.
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Affiliation(s)
- Natkrittaya Saengsawang
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Panthita Ruang-Areerate
- BIOTEC, National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Nuanlaong Kaeothaisong
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Piraporn Juntanawiwat
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Patomroek Hanyanunt
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Patsanun Potisuwan
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Piyanate Kesakomol
- Department of Microbiology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Pornphan Butsararattanagomen
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Pattarawadee Wichaiwong
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Wijitar Dungchai
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand.
| | - Toon Ruang-Areerate
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand.
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10
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Chen X, Du C, Zhao Q, Zhao Q, Wan Y, He J, Yuan W. Rapid and visual identification of HIV-1 using reverse transcription loop-mediated isothermal amplification integrated with a gold nanoparticle-based lateral flow assay platform. Front Microbiol 2023; 14:1230533. [PMID: 37502395 PMCID: PMC10368893 DOI: 10.3389/fmicb.2023.1230533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Human immunodeficiency virus type one (HIV-1) infection remains a major public health problem worldwide. Early diagnosis of HIV-1 is crucial to treat and control this infection effectively. Here, for the first time, we reported a novel molecular diagnostic assay called reverse transcription loop-mediated isothermal amplification combined with a visual gold nanoparticle-based lateral flow assay (RT-LAMP-AuNPs-LFA), which we devised for rapid, specific, sensitive, and visual identification of HIV-1. The unique LAMP primers were successfully designed based on the pol gene from the major HIV-1 genotypes CRF01_AE, CRF07_BC, CRF08_BC, and subtype B, which are prevalent in China. The optimal HIV-1-RT-LAMP-AuNPs-LFA reaction conditions were determined to be 68°C for 35 min. The detection procedure, including crude genomic RNA isolation (approximately 5 min), RT-LAMP amplification (35 min), and visual result readout (<2 min), can be completed within 45 min. Our assay has a detection limit of 20 copies per test, and we did not observe any cross-reactivity with any other pathogen in our testing. Hence, our preliminary results indicated that the HIV-1-RT-LAMP-AuNPs-LFA assay can potentially serve as a useful point-of-care diagnostic tool for HIV-1 detection in a clinical setting.
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Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- Clinical Medical Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Cheng Du
- Department of Anesthesiology, The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Qiang Zhao
- Clinical Laboratory, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| | - Qi Zhao
- Gastroenterology of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Yonghu Wan
- Experiment Center, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Jun He
- Clinical Laboratory, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| | - Wei Yuan
- Department of Quality Control, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
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11
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Gulinaizhaer A, Zou M, Ma S, Yao Y, Fan X, Wu G. Isothermal nucleic acid amplification technology in HIV detection. Analyst 2023; 148:1189-1208. [PMID: 36825492 DOI: 10.1039/d2an01813f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleic acid testing for HIV plays an important role in the early diagnosis and monitoring of antiretroviral therapy outcomes in HIV patients and HIV-infected infants. Currently, the main molecular diagnostic methods employed are complex, time-consuming, and expensive to operate in resource-limited areas. Isothermal nucleic acid amplification technology overcomes some of the shortcomings of traditional assays and makes it possible to use point-of-care tests for molecular HIV detection. Here, we summarize and discuss the latest technological advances in isothermal nucleic acid amplification for HIV detection, with the intent of providing guidance for the development of subsequent HIV assays with high sensitivity and specificity.
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Affiliation(s)
- Abudushalamu Gulinaizhaer
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Mingyuan Zou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Shuo Ma
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Yuming Yao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Xiaobo Fan
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China. .,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, Jiangsu, China
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12
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Yang X, Guo C, Zhang Q, Chen Y, Liu Y, Zhang X. A portable thermostatic molecular diagnosis device based on high-efficiency photothermal conversion material for rapid field detection of SARS-CoV-2. Talanta 2023; 258:124422. [PMID: 36907162 PMCID: PMC9988313 DOI: 10.1016/j.talanta.2023.124422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
The outbreak of the novel coronavirus (SARS-CoV-2) has seriously harmed human health and economic development worldwide. Studies have shown that timely diagnosis and isolation are the most effective ways to prevent the spread of the epidemic. However, the current polymerase chain reaction (PCR) based molecular diagnostic platform has the problems of expensive equipment, high operation difficulty, and the need for stable power resources support, so it is difficult to popularize in low-resource areas. This study established a portable (<300 g), low-cost (<$10), and reusable molecular diagnostic device based on solar energy photothermal conversion strategy, which creatively introduces a sunflower-like light tracking system to improve light utilization, making the device suitable for both high and low-light areas. The experimental results show that the device can detect SARS-CoV-2 nucleic acid samples as low as 1 aM within 30 min.
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Affiliation(s)
- Xinyao Yang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China
| | - Chuanghao Guo
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China
| | - Qianling Zhang
- Graphene Composite Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China
| | - Yong Chen
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China; Graphene Composite Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, PR China.
| | - Yizhen Liu
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China.
| | - Xueji Zhang
- Research Center for Nanosensor Molecular Diagnostic & Treatment Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, PR China
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13
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Bacon A, Wang W, Lee H, Umrao S, Sinawang PD, Akin D, Khemtonglang K, Tan A, Hirshfield S, Demirci U, Wang X, Cunningham BT. Review of HIV Self Testing Technologies and Promising Approaches for the Next Generation. BIOSENSORS 2023; 13:298. [PMID: 36832064 PMCID: PMC9954708 DOI: 10.3390/bios13020298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 05/28/2023]
Abstract
The ability to self-test for HIV is vital to preventing transmission, particularly when used in concert with HIV biomedical prevention modalities, such as pre-exposure prophylaxis (PrEP). In this paper, we review recent developments in HIV self-testing and self-sampling methods, and the potential future impact of novel materials and methods that emerged through efforts to develop more effective point-of-care (POC) SARS-CoV-2 diagnostics. We address the gaps in existing HIV self-testing technologies, where improvements in test sensitivity, sample-to-answer time, simplicity, and cost are needed to enhance diagnostic accuracy and widespread accessibility. We discuss potential paths toward the next generation of HIV self-testing through sample collection materials, biosensing assay techniques, and miniaturized instrumentation. We discuss the implications for other applications, such as self-monitoring of HIV viral load and other infectious diseases.
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Affiliation(s)
- Amanda Bacon
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weijing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hankeun Lee
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saurabh Umrao
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
| | - Prima Dewi Sinawang
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Demir Akin
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kodchakorn Khemtonglang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anqi Tan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sabina Hirshfield
- Special Treatment and Research (STAR) Program, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, New York, NY 11203, USA
| | - Utkan Demirci
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Xing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brian T. Cunningham
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
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14
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Marangoni JM, Ng KKS, Emadi A. Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification. MICROMACHINES 2023; 14:472. [PMID: 36838172 PMCID: PMC9960872 DOI: 10.3390/mi14020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.
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Affiliation(s)
- Jesse M. Marangoni
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Arezoo Emadi
- Department of Electrical and Computer Engineering, University of Windsor, Windsor, ON N9B 3P4, Canada
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15
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Distance-based paper device using combined SYBR safe and gold nanoparticle probe LAMP assay to detect Leishmania among patients with HIV. Sci Rep 2022; 12:14558. [PMID: 36028548 PMCID: PMC9418321 DOI: 10.1038/s41598-022-18765-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
Abstract
Asymptomatic visceral leishmaniasis cases increase continuously, particularly among patients with HIV who are at risk to develop further symptoms of leishmaniasis. A simple, sensitive and reliable diagnosis is crucially needed due to risk populations mostly residing in rural communities with limited resources of laboratory equipment. In this study, a highly sensitive and selective determination of Leishmania among asymptomatic patients with Leishmania/HIV co-infection was achieved to simultaneously interpret and semi-quantify using colorimetric precipitates (gold-nanoparticle probe; AuNP-probe) and fluorescence (SYBR safe dye and distance-based paper device; dPAD) in one-step loop-mediated isothermal amplification (LAMP) assay. The sensitivities and specificities of 3 detection methods were equivalent and had reliable performances achieving as high as 95.5%. Detection limits were 102 parasites/mL (0.0147 ng/µL) which were 10 times more sensitive than other related studies. To empower leishmaniasis surveillance as well as prevention and control, this dPAD combined with SYBR safe and gold nanoparticle probe LAMP assay is reliably fast, simple, inexpensive and practical for field diagnostics to point-of-care settings in resource-limited areas which can be set up in all levels of healthcare facilities, especially in low to middle income countries.
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16
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Liu T, Choi G, Tang Z, Kshirsagar A, Politza AJ, Guan W. Fingerpick Blood-Based Nucleic Acid Testing on A USB Interfaced Device towards HIV self-testing. Biosens Bioelectron 2022; 209:114255. [PMID: 35429770 PMCID: PMC9110109 DOI: 10.1016/j.bios.2022.114255] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/25/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
HIV self-testing is an emerging innovative approach that allows individuals who want to know their HIV status to collect their own specimen, perform a test, and interpret the results privately. Existing HIV self-testing methods rely on rapid diagnostic tests (RDTs) to detect the presence of HIV-1/2 antibodies, which could miss a significant portion of asymptomatic carriers during the window period. In this work, we present a fully integrated nucleic acid testing (NAT) device towards streamlined HIV self-testing using 100 μL finger-prick whole blood. The device consists of a ready-to-use microfluidic reagent cartridge and an ultra-compact NAT-on-USB analyzer. The test requires simple steps from the user to drop the finger-prick blood sample into a collection tube with lysis buffer and load the lysate onto the microfluidic cartridge, and the testing result can be easily read out by a custom-built graphical user interface (GUI). The microfluidic cartridge and the analyzer automatically handle the complexity of sample preparation, purification, and real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP). With a turnaround time of ∼60 min, we achieved a limit of detection (LoD) of 214 viral RNA copies/mL of whole blood at a 95% confidence level. Due to its ease of use and high sensitivity, we anticipate the HIV NAT-on-USB device would be particularly useful for the high-risk populations seeking private self-testing at the early stages of exposure.
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17
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Zhang X, Li H, Liu Z, Zhao Y, Zeng Y, Dong Y, Li L, Zhang C. An HFman probe-based reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for HIV-1 detection. Mol Cell Probes 2022; 64:101834. [PMID: 35732248 DOI: 10.1016/j.mcp.2022.101834] [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: 03/19/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is suitable for the development of a rapid and cost-effective nucleic acid technique for point of care (POC) applications. However, LAMP methods often generate non-specific amplification, therefore inevitably resulting in false positive results especially when sequence-independent dyes are used to indirectly reflect the results. In this study, we established and optimized a reverse transcription LAMP (RT-LAMP) assay with a high-fidelity DNA polymerase-mediated fluorescent probe (HFman probe) for human immunodeficiency virus-1 (HIV-1) detection. The assay showed high sensitivity and specificity. Using 101 plasma samples with different HIV-1 viral load, we demonstrated that our assay can detect the major HIV-1 subtypes circulating in China, including CRF01_AE, CRF07_BC, CRF08_BC, CRF55_01B, and unique recombinant forms (URFs). We also compared our assay with an approved commercial real-time quantitative polymerase chain reaction (RT-qPCR) kit and found the sensitivity, specificity and consistency was 88.8%, 100% and 89.1%, respectively. The HFman probe-based RT-LAMP assay is a high specific detection method that is rapid, variant-tolerant and simple to operate, and thus is of great significance for timely disclosure of HIV status and rapid POC diagnosis.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ziwei Liu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yongjuan Zhao
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yi Zeng
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yajuan Dong
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center for Pathogen Research, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Lin Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Chiyu Zhang
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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18
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A sensitive visual DNAzyme-based strategy for Cronobacter sakazakii in PIF by aRPA. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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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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20
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Li RJ, Mauk MG, Seok Y, Bau HH. Electricity-free chemical heater for isothermal nucleic acid amplification with applications in COVID-19 home testing. Analyst 2021; 146:4212-4218. [PMID: 34075937 PMCID: PMC8238897 DOI: 10.1039/d1an00309g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Molecular detection of pathogenic nucleic acids from patient samples requires incubating biochemical reactions at specific temperatures to amplify DNA. This incubation is typically carried out with an electrical heater and a temperature controller. To reduce test cost, to eliminate the need for manufacturing incubators, which may require significant time, and to enable electricity-free operation, we use energetic compounds such as an Mg(Fe) alloy mixed with a phase-change material (PCM) that undergoes phase transformation at the desired incubation temperature. We dubbed this composite Energetic Phase Change Material (EPCM). When the EPCM is brought into contact with water, the magnesium alloy interacts with the water to produce heat. The EPCM heats up to its phase transition temperature. Any excess heat is absorbed as latent heat and the system is maintained at its desired incubation temperature, independent of ambient temperatures, long enough to facilitate enzymatic amplification. The EPCM together with colorimetric amplicon detection facilitates an inexpensive, disposable, point-of-need diagnostic test that does not require any electric power. We demonstrate the feasibility of our approach by detecting SARS-Cov-2 in saliva samples either without any instrumentation or with a palm-size CCD camera that enables us to follow the amplification process in real time.
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Affiliation(s)
- Rui Jie Li
- Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
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21
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Ruang-Areerate T, Sukphattanaudomchoke C, Thita T, Leelayoova S, Piyaraj P, Mungthin M, Suwannin P, Polpanich D, Tangchaikeeree T, Jangpatarapongsa K, Choowongkomon K, Siripattanapipong S. Development of loop-mediated isothermal amplification (LAMP) assay using SYBR safe and gold-nanoparticle probe for detection of Leishmania in HIV patients. Sci Rep 2021; 11:12152. [PMID: 34108543 PMCID: PMC8190085 DOI: 10.1038/s41598-021-91540-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/26/2021] [Indexed: 12/04/2022] Open
Abstract
Asymptomatic leishmaniasis cases have continuously increased, especially among patients with HIV who are at risk to develop further symptoms of cutaneous and visceral leishmaniasis. Thus, early diagnosis using a simple, sensitive and reliable diagnostic assay is important because populations at risk mostly reside in rural communities where laboratory equipment is limited. In this study, the highly sensitive and selective determination of Leishmania infection in asymptomatic HIV patients was achieved using dual indicators (SYBR safe and gold-nanoparticle probe; AuNP-probe) in one-step LAMP method based on basic instruments. The assay can be simply evaluated under the naked eye due to clear interpretation of fluorescent emission of LAMP-SYBR safe dye-complex and colorimetric precipitate of specific AuNP-probes. The sensitivities and specificities of fluorescent SYBR safe dye and AuNP-probe indicators were equal, which were as high as 94.1 and 97.1%, respectively. Additionally, detection limits were 102 parasites/mL (0.0147 ng/µL), ten times more sensitivity than other related studies. To empower leishmaniasis surveillance, this inexpensive one-step SYBR safe and AuNP-LAMP assay is reliably fast and simple for field diagnostics to point-of-care settings, which can be set up in all levels of health care facilities including resource limited areas, especially in low to middle income countries.
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Affiliation(s)
- Toon Ruang-Areerate
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand.
| | | | - Thanyapit Thita
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Phunlerd Piyaraj
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Patcharapan Suwannin
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Duangporn Polpanich
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Tienrat Tangchaikeeree
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Kulachart Jangpatarapongsa
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
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22
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Naseri M, Ziora ZM, Simon GP, Batchelor W. ASSURED‐compliant point‐of‐care diagnostics for the detection of human viral infections. Rev Med Virol 2021. [DOI: 10.1002/rmv.2263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mahdi Naseri
- Department of Chemical Engineering Bioresource Processing Research Institute of Australia (BioPRIA) Monash University Clayton VIC Australia
| | - Zyta M Ziora
- Institute for Molecular Bioscience The University of Queensland St Lucia QLD Australia
| | - George P Simon
- Department of Materials Science and Engineering Monash University Clayton VIC Australia
| | - Warren Batchelor
- Department of Chemical Engineering Bioresource Processing Research Institute of Australia (BioPRIA) Monash University Clayton VIC Australia
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23
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Yadav S, Sharma NN, Akhtar J. Nucleic acid analysis on paper substrates (NAAPs): an innovative tool for Point of Care (POC) infectious disease diagnosis. Analyst 2021; 146:3422-3439. [PMID: 33904559 DOI: 10.1039/d1an00214g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The cost-effective rapid diagnosis of infectious diseases is an essential and important factor for curing such diseases in the global public health care picture. Owing to poor infrastructure and lack of sanitation, these diseases have an extreme impact on remote and rural areas, especially in developing countries, and there are unresolved challenges. Molecular diagnosis, such as nucleic acid analysis, plays a key role in the significant treatment of numerous infectious diseases. Current molecular diagnostic assays require a sophisticated laboratory setup with expensive components. Molecular diagnosis on a microfluidic point-of-care (POC) platform is attractive to researchers for disease detection with proper prevention. Compared to various microfluidic substrate materials, paper-based POC technologies offer significant cost-effective solutions over high-cost clinical instruments to fill the gap between the needs of users and affordability. Low-cost paper-based microfluidic POC technologies provide portable and disposable diagnostic systems for multiple disease detection that may be extremely useful in remote areas. This article presents a critical review of paper-based microfluidic device technology which has become an imminent platform to adjust the current health scenario for the detection of diseases using different stages of nucleic acid analysis, such as extraction, amplification and detection of nucleic acid, with future perspectives for paper substrates.
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Affiliation(s)
- Supriya Yadav
- Department of Biosciences, Manipal University Jaipur, 303007, Rajasthan, India.
| | - Niti Nipun Sharma
- Department of Mechanical Engineering, Manipal University Jaipur, 303007, Rajasthan, India.
| | - Jamil Akhtar
- Department of Electronics & Communication Engineering, Manipal University Jaipur, 303007, Rajasthan, India.
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24
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Development of an in-situ signal amplified electrochemical assay for detection of Listeria monocytogenes with label-free strategy. Food Chem 2021; 358:129894. [PMID: 33933968 DOI: 10.1016/j.foodchem.2021.129894] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/23/2022]
Abstract
Listeria monocytogenes is an important foodborne pathogen, which imposes great burdens on public health. The current methods for detecting L. monocytogene are limited in several ways such as time consuming and lab equipment dependent. In this study, we developed a new electrochemical assay to improve the efficacy. This assay allows us to generate numerous G-quadruplex sequences while loop-mediated isothermal amplification happens. Then, these G-quadruplex sequences form DNAzyme to produce a color change and an electrochemical signal by oxidizing tetramethylbenzidine. This assay could be finished in 2 h, which significantly reduced the detection time. Also, we confirmed the limit of detection of this assay at 6.8 CFU/mL according to 3σ criterion. Our assay shows good sensitivity to detect bacteria range from 52.5 to 5.25 × 104 CFU/mL. This assay's reliability was also confirmed by detecting artificially contaminated pork samples. Thus, we propose this electrochemical assay for rapid and sensitive detection of L. monocytogenes in food.
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García-Bernalt Diego J, Fernández-Soto P, Muro A. LAMP in Neglected Tropical Diseases: A Focus on Parasites. Diagnostics (Basel) 2021; 11:diagnostics11030521. [PMID: 33804255 PMCID: PMC8000616 DOI: 10.3390/diagnostics11030521] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023] Open
Abstract
Neglected Tropical Diseases (NTDs), particularly those caused by parasites, remain a major Public Health problem in tropical and subtropical regions, with 10% of the world population being infected. Their management and control have been traditionally hampered, among other factors, by the difficulty to deploy rapid, specific, and affordable diagnostic tools in low resource settings. This is especially true for complex PCR-based methods. Isothermal nucleic acid amplification techniques, particularly loop-mediated isothermal amplification (LAMP), appeared in the early 21st century as an alternative to PCR, allowing for a much more affordable molecular diagnostic. Here, we present the status of LAMP assays development in parasite-caused NTDs. We address the progress made in different research applications of the technique: xenomonitoring, epidemiological studies, work in animal models and clinical application both for diagnosis and evaluation of treatment success. Finally, we try to shed a light on the improvements needed to achieve a true point-of-care test and the future perspectives in this field.
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26
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Hin S, Lopez-Jimena B, Bakheit M, Klein V, Stack S, Fall C, Sall A, Enan K, Mustafa M, Gillies L, Rusu V, Goethel S, Paust N, Zengerle R, Frischmann S, Weidmann M, Mitsakakis K. Fully automated point-of-care differential diagnosis of acute febrile illness. PLoS Negl Trop Dis 2021; 15:e0009177. [PMID: 33630852 PMCID: PMC7906357 DOI: 10.1371/journal.pntd.0009177] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Background In this work, a platform was developed and tested to allow to detect a variety of candidate viral, bacterial and parasitic pathogens, for acute fever of unknown origin. The platform is based on a centrifugal microfluidic cartridge, the LabDisk (“FeverDisk” for the specific application), which integrates all necessary reagents for sample-to-answer analysis and is processed by a compact, point-of-care compatible device. Methodology/Principal findings A sample volume of 200 μL per FeverDisk was used. In situ extraction with pre-stored reagents was achieved by bind-wash-elute chemistry and magnetic particles. Enzymes for the loop-mediated isothermal amplification (LAMP) were pre-stored in lyopellet form providing stability and independence from the cold chain. The total time to result from sample inlet to read out was 2 h. The proof-of-principle was demonstrated in three small-scale feasibility studies: in Dakar, Senegal and Khartoum, Sudan we tested biobanked samples using 29 and 9 disks, respectively; in Reinfeld, Germany we tested spiked samples and analyzed the limit of detection using three bacteria simultaneously spiked in whole blood using 15 disks. Overall during the three studies, the FeverDisk detected dengue virus (different serotypes), chikungunya virus, Plasmodium falciparum, Salmonella enterica Typhi, Salmonella enterica Paratyphi A and Streptococcus pneumoniae. Conclusions/Significance The FeverDisk proved to be universally applicable as it successfully detected all different types of pathogens as single or co-infections, while it also managed to define the serotype of un-serotyped dengue samples. Thirty-eight FeverDisks at the two African sites provided 59 assay results, out of which 51 (86.4%) were confirmed with reference assay results. The results provide a promising outlook for future implementation of the platform in larger prospective clinical studies for defining its clinical sensitivity and specificity. The technology aims to provide multi-target diagnosis of the origins of fever, which will help fight lethal diseases and the incessant rise of antimicrobial resistance. Infectious diseases in tropical regions may have a variety of viral, bacterial or parasitic origins and a patient may suffer from several diseases simultaneously, each presenting with acute fever as a clinical symptom. This makes it difficult to determine the origin of the pathogen causing the disease(s). In addition to the endemic infectious diseases, outbreaks of epidemics frequently complicate diagnostic demands. Accurate diagnosis for proper patient management requires the utilization of highly sensitive and specific, rapid, easy-to-use diagnostic tools compatible with point-of-care settings. We describe the use of a disk-shaped microfluidic platform, the “FeverDisk”, for differential diagnosis of acute fever. Our FeverDisk platform demonstrated its capability to detect bacteria, viruses and parasites that are typical of tropical single and co-infections from biobanked samples within only 2 hours and in very good agreement with reference method results. This, in combination with its easy-to-use and point-of-care compatible nature, render our platform a promising candidate for detection of tropical diseases and precise identification of the cause of acute fever, in endemic and epidemic settings. Future work will involve extensive clinical characterization of the platform in prospective studies.
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Affiliation(s)
- Sebastian Hin
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Benjamin Lopez-Jimena
- Institute of Aquaculture, University of Stirling, Scotland, United Kingdom
- Mast Group Ltd, Mast House, Bootle, Liverpool, United Kingdom
| | | | - Vanessa Klein
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Seamus Stack
- Mast Group Ltd, Mast House, Bootle, Liverpool, United Kingdom
| | - Cheikh Fall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Sall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Khalid Enan
- Department of Virology, Central Laboratory-The Ministry of Higher Education and Scientific Research, Khartoum, Sudan
| | - Mohamed Mustafa
- Department of Virology, Central Laboratory-The Ministry of Higher Education and Scientific Research, Khartoum, Sudan
| | - Liz Gillies
- Mast Group Ltd, Mast House, Bootle, Liverpool, United Kingdom
| | - Viorel Rusu
- MagnaMedics Diagnostics BV, Geleen, The Netherlands
| | - Sven Goethel
- MagnaMedics Diagnostics BV, Geleen, The Netherlands
| | - Nils Paust
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
| | | | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Scotland, United Kingdom
| | - Konstantinos Mitsakakis
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
- Hahn-Schickard, Freiburg, Germany
- * E-mail:
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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: 89] [Impact Index Per Article: 29.7] [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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Garneret P, Coz E, Martin E, Manuguerra JC, Brient-Litzler E, Enouf V, González Obando DF, Olivo-Marin JC, Monti F, van der Werf S, Vanhomwegen J, Tabeling P. Performing point-of-care molecular testing for SARS-CoV-2 with RNA extraction and isothermal amplification. PLoS One 2021; 16:e0243712. [PMID: 33428641 PMCID: PMC7799764 DOI: 10.1371/journal.pone.0243712] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/27/2020] [Indexed: 11/23/2022] Open
Abstract
To respond to the urgent need for COVID-19 testing, countries perform nucleic acid amplification tests (NAAT) for the detection of SARS-CoV-2 in centralized laboratories. Real-time RT-PCR (Reverse transcription-Polymerase Chain Reaction), used to amplify and detect the viral RNA., is considered, as the current gold standard for diagnostics. It is an efficient process, but the complex engineering required for automated RNA extraction and temperature cycling makes it incompatible for use in point of care settings [1]. In the present work, by harnessing progress made in the past two decades in isothermal amplification and paper microfluidics, we created a portable test, in which SARS-CoV-2 RNA is extracted, amplified isothermally by RT-LAMP (Loop-mediated Isothermal Amplification), and detected using intercalating dyes or fluorescent probes. Depending on the viral load in the tested samples, the detection takes between twenty minutes and one hour. Using a set of 16 pools of naso-pharyngal swab eluates, we estimated a limit of detection comparable to real-time RT-PCR (i.e. 1 genome copies per microliter of clinical sample) and no cross-reaction with eight major respiratory viruses currently circulating in Europe. We designed and fabricated an easy-to-use portable device called "COVIDISC" to carry out the test at the point of care. The low cost of the materials along with the absence of complex equipment will expedite the widespread dissemination of this device. What is proposed here is a new efficient tool to help managing the pandemics.
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29
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Everitt ML, Tillery A, David MG, Singh N, Borison A, White IM. A critical review of point-of-care diagnostic technologies to combat viral pandemics. Anal Chim Acta 2020; 1146:184-199. [PMID: 33461715 PMCID: PMC7548029 DOI: 10.1016/j.aca.2020.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
The COVID-19 global pandemic of 2019-2020 pointedly revealed the lack of diagnostic solutions that are able to keep pace with the rapid spread of the virus. Despite the promise of decades of lab-on-a-chip research, no commercial products were available to deliver rapid results or enable testing in the field at the onset of the pandemic. In this critical review, we assess the current state of progress on the development of point-of-care technologies for the diagnosis of viral diseases that cause pandemics. While many previous reviews have reported on progress in various lab-on-a-chip technologies, here we address the literature from the perspective of the testing needs of a rapidly expanding pandemic. First, we recommend a set of requirements to heed when designing point-of-care diagnostic technologies to address the testing needs of a pandemic. We then review the current state of assay technologies with a focus on isothermal amplification and lateral-flow immunoassays. Though there is much progress on assay development, we argue that the largest roadblock to deployment exists in sample preparation. We summarize current approaches to automate sample preparation and discuss both the progress and shortcomings of these developments. Finally, we provide our recommendations to the field of specific challenges to address in order to prepare for the next pandemic.
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Affiliation(s)
- Micaela L Everitt
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Alana Tillery
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Martha G David
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Nikita Singh
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Aviva Borison
- Fischell Department of Bioengineering, University of Maryland, United States
| | - Ian M White
- Fischell Department of Bioengineering, University of Maryland, United States.
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30
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Fu S, Jiang Y, Qin X, Yang T, Chen S, Yang X, Zhang W, Qu Y, Man C. Electricity-free amplification and visual detection of Cronobacter species in powdered infant formula. J Dairy Sci 2020; 103:6882-6893. [PMID: 32505404 DOI: 10.3168/jds.2019-17661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/09/2020] [Indexed: 01/24/2023]
Abstract
Due to the lack of electricity and thermostatic instruments in certain settings for convenient detection of Cronobacter species in powdered infant formula (PIF), a novel investigation was conducted to establish an electricity-free visual detection system for rapid detection of Cronobacter species in PIF. This system included a portable electricity-free heater that could use the exothermic reaction of calcium oxide and water and 3 kinds of phase change materials to supply 3 constant temperatures for immunomagnetic separation, DNA extraction, and loop-mediated isothermal amplification assay. Meanwhile, the amplified reaction combined with hydroxynaphthol blue could achieve rapid visual detection. Primers designed based on the 16S-23S ribosomal RNA internal transcribed spacer were used in loop-mediated isothermal amplification to specifically monitor Cronobacter species, and the detection limit can reach 4.2 × 102 cfu/g in PIF by an electricity-free heater in 2 h 30 min. Moreover, 2 h of pre-enrichment was necessary when the level of the PIF samples with Cronobacter spp. was 100 cfu/g. The stability of the system was evaluated in ambient temperature at 4°C, 25°C, and 37°C. The results suggested that the electricity-free heater can maintain 3 constant temperatures to support different processes. Therefore, this amplification and visual system is applicable for use in many fields for rapid and specific detection of Cronobacter species in PIF.
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Affiliation(s)
- Shiqian Fu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xue Qin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Tao Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Sihan Chen
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Wei Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanyan Qu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China.
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31
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Yao Y, Chen X, Zhang X, Liu Q, Zhu J, Zhao W, Liu S, Sui G. Rapid Detection of Influenza Virus Subtypes Based on an Integrated Centrifugal Disc. ACS Sens 2020; 5:1354-1362. [PMID: 32248677 DOI: 10.1021/acssensors.9b02595] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Influenza is a zoonotic disease, infecting a wide variety of warm-blooded animals. It is caused by an influenza virus, which has been found with hundreds of subtypes. These subtypes are often associated with different sources of infection and possess complex courses of infection. In the early stage of influenza infection, rapid subtype detection is very practicable to prevent the disease from getting worse. Herein, we presented a high-throughput microfluidic centrifugal disc for rapid detection of influenza virus subtypes. The disc realized detection reagent preloads, automated reagent control, and RT-LAMP detections. Six kinds of highly pathogenic influenza viruses could be simultaneously identified, including influenza A subtypes H1, H3, H5, H7, and H9 and influenza B virus. Two different fluorescent dyes could be used on the disc for real-time detection or read by the naked eye. The performance of the disc was demonstrated by testing the clinical samples. The integrated centrifugal disc was expected for rapid detection of influenza virus subtypes to facilitate accurate drug usage in resource-constrained settings and contribute to reduce the risk of the influenza pandemic.
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Affiliation(s)
- Yuhan Yao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
| | - Xi Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
| | - Xinlian Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
| | - Qi Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
| | - Jinhui Zhu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
| | - Wang Zhao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
| | - Sixiu Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CICAEET), Nanjing University of Information Science & Technology, Nanjing 210044, P. R. China
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32
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Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations. Mol Diagn Ther 2020; 23:723-733. [PMID: 31396882 DOI: 10.1007/s40291-019-00422-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation screening is elemental for clinical diagnosis and in determining therapeutic strategies. Nucleic acid-based techniques are considered to be the most accurate tools in genetic diagnosis. One such technique is loop-mediated isothermal amplification (LAMP) assay, which has seen tremendous applications in recent years. The advantages of the assay lie in its rapidity, efficiency, sensitivity, and cost. It works in isothermal conditions and amplifies the target gene using DNA polymerases that have strand displacement activity. To date, the assay has been widely used in different fields of research, including pathogen detection, crop development, and disease diagnosis. However, despite the potential, its application in mutation screening has been minimal. This review highlights the LAMP assay and its variants that have been developed for screening single-nucleotide polymorphisms and gene translocations in cancer.
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Kaminski MM, Alcantar MA, Lape IT, Greensmith R, Huske AC, Valeri JA, Marty FM, Klämbt V, Azzi J, Akalin E, Riella LV, Collins JJ. A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection. Nat Biomed Eng 2020; 4:601-609. [PMID: 32284553 DOI: 10.1038/s41551-020-0546-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/06/2020] [Indexed: 12/26/2022]
Abstract
In organ transplantation, infection and rejection are major causes of graft loss. They are linked by the net state of immunosuppression. To diagnose and treat these conditions earlier, and to improve long-term patient outcomes, refined strategies for the monitoring of patients after graft transplantation are needed. Here, we show that a fast and inexpensive assay based on CRISPR-Cas13 accurately detects BK polyomavirus DNA and cytomegalovirus DNA from patient-derived blood and urine samples, as well as CXCL9 messenger RNA (a marker of graft rejection) at elevated levels in urine samples from patients experiencing acute kidney transplant rejection. The assay, which we adapted for lateral-flow readout, enables-via simple visualization-the post-transplantation monitoring of common opportunistic viral infections and of graft rejection, and should facilitate point-of-care post-transplantation monitoring.
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Affiliation(s)
- Michael M Kaminski
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Miguel A Alcantar
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Isadora T Lape
- Schuster Transplantation Research Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert Greensmith
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Allison C Huske
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacqueline A Valeri
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Francisco M Marty
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Verena Klämbt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamil Azzi
- Schuster Transplantation Research Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Enver Akalin
- Montefiore Einstein Center for Transplantation, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Leonardo V Riella
- Schuster Transplantation Research Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - James J Collins
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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34
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Rosenbohm JM, Robson JM, Singh R, Lee R, Zhang JY, Klapperich CM, Pollock NR, Cabodi M. Rapid electrostatic DNA enrichment for sensitive detection of Trichomonas vaginalis in clinical urinary samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:1085-1093. [PMID: 35154421 PMCID: PMC8837197 DOI: 10.1039/c9ay02478f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Estimated to be the most common non-viral sexually transmitted infection globally, Trichomonas vaginalis (TV) can lead to pelvic inflammatory disease, pregnancy complications, and increased risk of acquiring and transmitting HIV. Once diagnosed, TV infection can be treated with oral antibiotics; however, infected individuals are often asymptomatic and do not seek treatment. The WHO and others have identified a need for point-of-care tests to expand access to TV testing and screening; ideal test characteristics include high sensitivity and specificity and the ability to use urine as a sample type, rather than invasively collected swab samples. Here, we report on a proof-of-concept prototype for rapid, electrostatic enrichment of DNA from urine samples and demonstrate the use of large volumes of urine to increase sensitivity of downstream nucleic acid amplification testing. We developed an internally controlled thermophilic helicase-dependent amplification (tHDA) assay with lateral flow immunoassay readout and demonstrate that this tHDA assay can be performed directly on our DNA capture filter. We validated our method using clinical urine samples with qPCR-quantified TV loads. Using 62 clinical urine samples and a simple sample processing device, our tHDA assay displayed 96.6% sensitivity and 100% specificity. Our analytical limit of detection was found to be approximately 7 genomic equivalents of TV DNA per mL of sample when 1 mL of sample was tested, comparable to existing isothermal tests for TV. Using large-volume simulated samples (40 mL of buffered urine with spiked-in TV DNA), we also demonstrated that sensitivity could be improved 28-fold to 0.25 genomic equivalents of TV DNA per mL, with a sample processing time of only 2 minutes.
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Affiliation(s)
| | - James M. Robson
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Rishabh Singh
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Rose Lee
- Department of Laboratory Medicine (NRP) and Division of Infectious Diseases (RL), Boston Children’s Hospital, Boston, MA, USA
| | - Jane Y. Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | | | - Nira R. Pollock
- Department of Laboratory Medicine (NRP) and Division of Infectious Diseases (RL), Boston Children’s Hospital, Boston, MA, USA
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
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Tunable and precise miniature lithium heater for point-of-care applications. Proc Natl Acad Sci U S A 2020; 117:4632-4641. [PMID: 32071225 DOI: 10.1073/pnas.1916562117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Point-of-care diagnostic assays often involve multistep reactions, requiring a wide range of precise temperatures. Although precise heating is critical to performing these assays, it is challenging to provide it in an electricity-free format away from established infrastructure. Chemical heaters are electricity-free and use exothermic reactions. However, they are unsuitable for point-of-care multistep reactions because they sacrifice portability, have a narrow range of achievable temperatures, and long ramp-up times. Here we developed a miniature heater by modulating the lithium-water reaction kinetics using bubbles in a channel. Our heaters are up to 8,000 times smaller than current devices and can provide precise (within 5 °C) and tunable heating from 37 °C to 65 °C (∆TRT = 12 °C to 40 °C) with ramp-up times of a minute. We demonstrate field portablity and stability and show their use in an electricity-free multistep workflow that needs a range of temperatures. Ultimately, we envision providing better access to cutting edge biochemical techniques, including diagnostics, by making portable and electricity-free heating available at any location.
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36
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Yao Y, Li Y, Liu Q, Zhou K, Zhao W, Liu S, Yang J, Jiang Y, Sui G. Rapid detection of hepatocellular carcinoma metastasis using reverse transcription loop-mediated isothermal amplification. Talanta 2020; 208:120402. [PMID: 31816739 DOI: 10.1016/j.talanta.2019.120402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
The main therapies of hepatocellular carcinoma (HCC) are hepatectomy and liver transplantation, but the recurrence rate of HCC after radical resection remains high. We established a novel method based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid identification of four cancer stem cell-specific biomarkers to estimate the potential risk of HCC metastasis. After optimizing the final concentrations of Mg2+ and betaine, the sensitivity limits for detection of CK19 and EpCAM could reach 10 to 20 copies, while the sensitivity limits for the detection of CD133 and CD90 could reach 10 copies. We detected clinical specimens from 10 HCC patients and performed analysis before and after receiving hepatectomy using RT-LAMP and quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results of both were consistent, but RT-LAMP was proved to be a more rapid, more sensitive, and more economic approach. This novel method is expected to estimate the recurrence and metastasis of HCC for clinical application by combining various low-cost circulating tumor cell sorting and detection tools.
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Affiliation(s)
- Yuhan Yao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China
| | - Yuancheng Li
- Institute of Biomedical Science, Fudan University, No. 138 Yixueyuan Road, Shanghai, 200032, PR China
| | - Qi Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China
| | - Kaiqian Zhou
- The Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Wang Zhao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China
| | - Sixiu Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China
| | - Jielin Yang
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, 200131, PR China
| | - Yuan Jiang
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, 200131, PR China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, 2205 Songhu Road, Shanghai, 200433, PR China; Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology (CICAEET), Nanjing University of Information Science & Technology, Nanjing, 210044, PR China.
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37
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Jia B, Li X, Liu W, Lu C, Lu X, Ma L, Li YY, Wei C. GLAPD: Whole Genome Based LAMP Primer Design for a Set of Target Genomes. Front Microbiol 2019; 10:2860. [PMID: 31921040 PMCID: PMC6923652 DOI: 10.3389/fmicb.2019.02860] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/26/2019] [Indexed: 11/23/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) technology has been applied in a wide range of fields such as detection of foodborne bacteria and clinical pathogens due to its simplicity and efficiency. However, existing LAMP primer designing systems require a conserved gene or a short genome region as input, and they can’t design group-specific primers. With the growing number of whole genomes available, it is possible to design better primers to target a set of genomes with high specificity based on whole genomes. We present here a whole Genome based LAMP primer designer (GLAPD), a new system to design LAMP primer for a set of target genomes using whole genomes. Candidate single primer regions are identified genome wide and then combined into LAMP primer sets. For a given set of target genomes, only primer sets amplifying them and only these genomes will be output. In order to accelerate the primer designing, a GPU version is provided as well. The effectiveness of primers designed by GLAPD has been assessed for a wide range of foodborne bacteria. GLAPD can be accessed at http://cgm.sjtu.edu.cn/GLAPD/ or https://github.com/jiqingxiaoxi/GLAPD.git. A simple online version is also supplied to help users to learn and test GLAPD: http://cgm.sjtu.edu.cn/GLAPD/online/.
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Affiliation(s)
- Ben Jia
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xueling Li
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Wei Liu
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Changde Lu
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Xiaoting Lu
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Liangxiao Ma
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Chaochun Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
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38
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Phillips EA, Moehling TJ, Ejendal KFK, Hoilett OS, Byers KM, Basing LA, Jankowski LA, Bennett JB, Lin LK, Stanciu LA, Linnes JC. Microfluidic rapid and autonomous analytical device (microRAAD) to detect HIV from whole blood samples. LAB ON A CHIP 2019; 19:3375-3386. [PMID: 31539001 PMCID: PMC7384476 DOI: 10.1039/c9lc00506d] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While identifying acute HIV infection is critical to providing prompt treatment to HIV-positive individuals and preventing transmission, existing laboratory-based testing methods are too complex to perform at the point of care. Specifically, molecular techniques can detect HIV RNA within 8-10 days of transmission but require laboratory infrastructure for cold-chain reagent storage and extensive sample preparation performed by trained personnel. Here, we demonstrate our point-of-care microfluidic rapid and autonomous analysis device (microRAAD) that automatically detects HIV RNA from whole blood. Inside microRAAD, we incorporate vitrified amplification reagents, thermally-actuated valves for fluidic control, and a temperature control circuit for low-power heating. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) products are visualized using a lateral flow immunoassay (LFIA), resulting in an assay limit of detection of 100 HIV-1 RNA copies when performed as a standard tube reaction. Even after three weeks of room-temperature reagent storage, microRAAD automatically isolates the virus from whole blood, amplifies HIV-1 RNA, and transports amplification products to the internal LFIA, detecting as few as 3 × 105 HIV-1 viral particles, or 2.3 × 107 virus copies per mL of whole blood, within 90 minutes. This integrated microRAAD is a low-cost and portable platform to enable automated detection of HIV and other pathogens at the point of care.
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Affiliation(s)
- Elizabeth A Phillips
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA.
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Point-of-Care HIV Viral Load Testing: an Essential Tool for a Sustainable Global HIV/AIDS Response. Clin Microbiol Rev 2019; 32:32/3/e00097-18. [PMID: 31092508 DOI: 10.1128/cmr.00097-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The global public health community has set ambitious treatment targets to end the HIV/AIDS pandemic. With the notable absence of a cure, the goal of HIV treatment is to achieve sustained suppression of an HIV viral load, which allows for immunological recovery and reduces the risk of onward HIV transmission. Monitoring HIV viral load in people living with HIV is therefore central to maintaining effective individual antiretroviral therapy as well as monitoring progress toward achieving population targets for viral suppression. The capacity for laboratory-based HIV viral load testing has increased rapidly in low- and middle-income countries, but implementation of universal viral load monitoring is still hindered by several barriers and delays. New devices for point-of-care HIV viral load testing may be used near patients to improve HIV management by reducing the turnaround time for clinical test results. The implementation of near-patient testing using these new and emerging technologies may be an essential tool for ensuring a sustainable response that will ultimately enable an end to the HIV/AIDS pandemic. In this report, we review the current and emerging technology, the evidence for decentralized viral load monitoring by non-laboratory health care workers, and the additional considerations for expanding point-of-care HIV viral load testing.
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40
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Banerjee I, Aralaguppe SG, Lapins N, Zhang W, Kazemzadeh A, Sönnerborg A, Neogi U, Russom A. Microfluidic centrifugation assisted precipitation based DNA quantification. LAB ON A CHIP 2019; 19:1657-1664. [PMID: 30931470 DOI: 10.1039/c9lc00196d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleic acid amplification methods are increasingly being used to detect trace quantities of DNA in samples for various diagnostic applications. However, quantifying the amount of DNA from such methods often requires time consuming purification, washing or labeling steps. Here, we report a novel microfluidic centrifugation assisted precipitation (μCAP) method for single-step DNA quantification. The method is based on formation of a visible precipitate, which can be quantified, when an intercalating dye (GelRed) is added to the DNA sample and centrifuged for a few seconds. We describe the mechanism leading to the precipitation phenomenon. We utilize centrifugal microfluidics to precisely control the formation of the visible and quantifiable mass. Using a standard CMOS sensor for imaging, we report a detection limit of 45 ng μl-1. Furthermore, using an integrated lab-on-DVD platform we recently developed, the detection limit is lowered to 10 ng μl-1, which is comparable to those of current commercially available instruments for DNA quantification. As a proof of principle, we demonstrate the quantification of LAMP products for a HIV-1B type genome containing plasmid on the lab-on-DVD platform. The simple DNA quantification system could facilitate advanced point of care molecular diagnostics.
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Affiliation(s)
- I Banerjee
- Division of Nanobiotechnology, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Sweden.
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41
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Shang Y, Sun J, Ye Y, Zhang J, Zhang Y, Sun X. Loop-mediated isothermal amplification-based microfluidic chip for pathogen detection. Crit Rev Food Sci Nutr 2018; 60:201-224. [DOI: 10.1080/10408398.2018.1518897] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yuting Shang
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiadi Sun
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Yongli Ye
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology School of Food Science National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety, Joint International Research Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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42
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Land KJ. The Many Roads to an Ideal Paper-based Device. PAPER-BASED DIAGNOSTICS 2018. [PMCID: PMC7119996 DOI: 10.1007/978-3-319-96870-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The recent Zika and Ebola virus outbreaks highlight the need for low-cost diagnostics that can be rapidly deployed and used outside of established clinical infrastructure. This demand for robust point-of-care (POC) diagnostics is further driven by the increasing burden of drug-resistant diseases, concern for food and water safety, and bioterrorism. As has been discussed in previous chapters, paper-based tests provide a simple and compelling solution to such needs.
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Affiliation(s)
- Kevin J. Land
- Council for Scientific and Industrial Research, Pretoria, South Africa
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43
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Zhang Z, Wang Y, Li Y, Yu D, Chen H, Cai Y, Fang W, Yang Z, Ji Y, Guan Y, Chu Y, Xu C. Portable fluorescence-based microRNA detection system based on isothermal signal amplification technology. Biotechnol Appl Biochem 2018; 66:82-90. [PMID: 30311952 DOI: 10.1002/bab.1699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/07/2018] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) diagnostics can be useful for diagnosing or confirming miRNA abundance and are used in screening tests and to assess changes in miRNAs in vivo. At present, the use of traditional nucleic acid amplification assays to detect miRNAs has been limited in laboratory environment because of the time, equipment, and technical expertise required to perform these assays. A specialized, rapid affordable miRNA detection system is necessary when there are limited resources or point-of-care testing needs. We designed a portable and affordable fluorescence-based miRNA detection system based on isothermal signal amplification technology, using SYBR Green II as a fluorescent dye. To reduce costs, we chose LED as a light source and designed the corresponding optical path for LED. The portable detection system shows results consistent with those by real-time PCR, and can be used to detect miR-183 with a limit of detection of approximately 2 fmol. We used the system to detect miR-183 in tissues and blood from patients with hepatocellular carcinoma (HCC). The results from the portable detection device were compared with those from clinical trials and indicated that the miR-183 fluorescence signal could successfully identify HCC and provide information related to cancer progression.
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Affiliation(s)
- Zhanying Zhang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Yanfei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Yanlei Li
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Dongsheng Yu
- Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Haiyan Chen
- Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Yi Cai
- Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Weikai Fang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Zhe Yang
- Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Yufeng Ji
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Yifu Guan
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Yannan Chu
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Chidong Xu
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
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44
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Goertz JP, Colvin KM, Lippe AB, Daristotle JL, Kofinas P, White IM. Multistage Chemical Heating for Instrument-Free Biosensing. ACS APPLIED MATERIALS & INTERFACES 2018; 10:33043-33048. [PMID: 30207445 DOI: 10.1021/acsami.8b11611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Improving the portability of diagnostic medicine is crucial for alleviating global access-to-care deficiencies. This requires not only designing devices that are small and lightweight, but also autonomous and independent of electricity. Here, we present a strategy for conducting automated multistep diagnostic assays using chemically generated, passively regulated heat. Ligation and polymerization reagents for rolling circle amplification of nucleic acids are separated by meltable phase-change partitions, thus replacing precise manual reagent additions with automated partition melting. To actuate these barriers and individually initiate the various steps of the reaction, field ration heaters exothermically generate heat in a thermos, whereas fatty acids embedded in a carbonaceous matrix passively buffer the temperature around their melting points. Achieving multistage temperature profiles extend the capability of instrument-free diagnostic devices and improve the portability of reaction automation systems built around phase-change partitions.
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45
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Gupta S, Kakkar V. Recent technological advancements in tuberculosis diagnostics - A review. Biosens Bioelectron 2018; 115:14-29. [PMID: 29783081 DOI: 10.1016/j.bios.2018.05.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/26/2018] [Accepted: 05/09/2018] [Indexed: 01/14/2023]
Abstract
Early diagnosis and on-time effective treatment are indispensable for Tuberculosis (TB) control - a life threatening infectious communicable disease. The conventional techniques for diagnosing TB normally take two to three weeks. This delay in diagnosis and further increase in detection complexity due to the emerging risks of XDR-TB (Extensively drug Resistant-TB) and MDR-TB (Multidrug Resistant-TB) are evoking interest of researchers in the field of developing rapid TB detection techniques such as biosensing and other point-of-care (POC) techniques. Biosensing technologies along with the collaboration with nanotechnology have enormous potential to boost the MTB detection and for overall management in clinical diagnosis. A diverse range of portable, sensitive and rapid biosensors based on different signal transducer principles and with different biomarkers detection capabilities have been developed for TB detection in the early stages. Further, a lot of progress has been achieved over the years in developing various point-of-care diagnostic tools including non-molecular methods and molecular techniques. The objective of this study is to present a succinct review of the available TB detection techniques that are either in use or under development. The focus of this review is on the current developments occurred in nano-biosensing technologies. A synopsis of ameliorations in different non-molecular diagnostic tools and progress in the field of molecular techniques along with the role of emerging Lab-on-Chip technology for diagnosing and mitigating the TB consequences have also been presented.
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Affiliation(s)
- Shagun Gupta
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra 182320, India.
| | - Vipan Kakkar
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra 182320, India.
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46
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Mauk MG, Song J, Liu C, Bau HH. Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests. BIOSENSORS 2018; 8:E17. [PMID: 29495424 PMCID: PMC5872065 DOI: 10.3390/bios8010017] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 01/10/2023]
Abstract
Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges ('chips') that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed.
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Affiliation(s)
- Michael G Mauk
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Jinzhao Song
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Changchun Liu
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Haim H Bau
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
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47
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Curtis KA, Morrison D, Rudolph DL, Shankar A, Bloomfield LSP, Switzer WM, Owen SM. A multiplexed RT-LAMP assay for detection of group M HIV-1 in plasma or whole blood. J Virol Methods 2018; 255:91-97. [PMID: 29474813 DOI: 10.1016/j.jviromet.2018.02.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Isothermal nucleic acid amplification techniques, such as reverse-transcription loop-mediated isothermal amplification (RT-LAMP), exhibit characteristics that are suitable for the development of a rapid, low-cost NAT that can be used at the POC. For demonstration of utility for global use, studies are needed to validate the performance of RT-LAMP for the detection of divergent subtypes. In this study, we designed and evaluated multiplexed HIV-1 integrase RT-LAMP primers to detect subtypes within group M, along with an RNase P positive internal processing and amplification control. Using a panel of 26 viral isolates representing the major circulating subtypes, we demonstrated detection of all isolates of subtypes A1, C, D, F1, F2, G, CRF01_AE, CRF02_AG, and two unique recombinant forms (URFs). A whole blood panel created with one representative isolate of each subtype was successfully amplified with the group M HIV-1 integrase and RNase P internal control primers. The group M HIV-1 RT-LAMP assay was further evaluated on 61 plasma specimens obtained from persons from Cameroon and Uganda. The sequence-conserved group M HIV-1 RT-LAMP primers, coupled to a low-cost amplification device, may improve diagnosis of acute infection at the POC and provide timely confirmation of HIV status.
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Affiliation(s)
- Kelly A Curtis
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Daphne Morrison
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Donna L Rudolph
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura S P Bloomfield
- Stanford University School of Medicine, Stanford, CA, USA; Emmett Interdisciplinary Program in Environment and Resources, Stanford, CA, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - S Michele Owen
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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48
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Carneiro J, Resende A, Pereira F. The HIV oligonucleotide database (HIVoligoDB). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074782. [PMID: 28365729 PMCID: PMC5502365 DOI: 10.1093/database/bax005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 01/16/2017] [Indexed: 02/04/2023]
Abstract
The human immunodeficiency virus (HIV) is associated with one of the most widespread infectious disease, the acquired immunodeficiency syndrome (AIDS). The development of antiretroviral drugs and methods for virus detection requires a comprehensive analysis of the HIV genomic diversity, particularly in the binding sites of oligonucleotides. Here, we describe a versatile online database (HIVoligoDB) with oligonucleotides selected for the diagnosis of HIV and treatment of AIDS. Currently, the database provides an interface for visualization, analysis and download of 380 HIV-1 and 65 HIV-2 oligonucleotides annotated according to curated reference genomes. The database also allows the selection of the most conserved HIV genomic regions for the development of molecular diagnostic assays and sequence-based candidate therapeutics. Database URL:http://portugene.com/HIVoligoDB
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Affiliation(s)
- João Carneiro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leix?Av. General Norton de Matos s/n 4450-208 Porto
| | - Adriana Resende
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leix?Av. General Norton de Matos s/n 4450-208 Porto
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49
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Zou Y, Mason MG, Wang Y, Wee E, Turni C, Blackall PJ, Trau M, Botella JR. Nucleic acid purification from plants, animals and microbes in under 30 seconds. PLoS Biol 2017; 15:e2003916. [PMID: 29161268 PMCID: PMC5697807 DOI: 10.1371/journal.pbio.2003916] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/17/2017] [Indexed: 12/27/2022] Open
Abstract
Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries.
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Affiliation(s)
- Yiping Zou
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
| | - Michael Glenn Mason
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
| | - Yuling Wang
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Eugene Wee
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, Australia
| | - Patrick J. Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St.Lucia, Australia
| | - Jose Ramon Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St.Lucia, Australia
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Affiliation(s)
- Haim H Bau
- a Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , PA , USA
| | - Changchun Liu
- a Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , PA , USA
| | - Michael Mauk
- a Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , PA , USA
| | - Jinzhao Song
- a Department of Mechanical Engineering and Applied Mechanics , University of Pennsylvania , Philadelphia , PA , USA
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