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Mughal TI, Radich JP, Deininger MW, Apperley JF, Hughes TP, Harrison CJ, Gambacorti-Passerini C, Saglio G, Cortes J, Daley GQ. Chronic myeloid leukemia: reminiscences and dreams. Haematologica 2016; 101:541-58. [PMID: 27132280 PMCID: PMC5004358 DOI: 10.3324/haematol.2015.139337] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/20/2016] [Indexed: 12/26/2022] Open
Abstract
With the deaths of Janet Rowley and John Goldman in December 2013, the world lost two pioneers in the field of chronic myeloid leukemia. In 1973, Janet Rowley, unraveled the cytogenetic anatomy of the Philadelphia chromosome, which subsequently led to the identification of the BCR-ABL1 fusion gene and its principal pathogenetic role in the development of chronic myeloid leukemia. This work was also of major importance to support the idea that cytogenetic changes were drivers of leukemogenesis. John Goldman originally made seminal contributions to the use of autologous and allogeneic stem cell transplantation from the late 1970s onwards. Then, in collaboration with Brian Druker, he led efforts to develop ABL1 tyrosine kinase inhibitors for the treatment of patients with chronic myeloid leukemia in the late 1990s. He also led the global efforts to develop and harmonize methodology for molecular monitoring, and was an indefatigable organizer of international conferences. These conferences brought together clinicians and scientists, and accelerated the adoption of new therapies. The abundance of praise, tributes and testimonies expressed by many serve to illustrate the indelible impressions these two passionate and affable scholars made on so many people's lives. This tribute provides an outline of the remarkable story of chronic myeloid leukemia, and in writing it, it is clear that the historical triumph of biomedical science over this leukemia cannot be considered without appreciating the work of both Janet Rowley and John Goldman.
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MESH Headings
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Cytogenetic Analysis/history
- Cytogenetic Analysis/methods
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/chemistry
- Fusion Proteins, bcr-abl/genetics
- History, 20th Century
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality
- Molecular Targeted Therapy/history
- Molecular Targeted Therapy/methods
- Mutation
- Philadelphia Chromosome
- Prognosis
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Research/history
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Affiliation(s)
| | - Jerald P Radich
- Fredrick Hutchinson Cancer Center, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | | | | | - George Q Daley
- Boston Children's Hospital, Harvard Medicine, School, Boston, MA, USA
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52
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Buser JR, Zhang X, Byrnes SA, Ladd PD, Heiniger EK, Wheeler MD, Bishop JD, Englund JA, Lutz B, Weigl BH, Yager P. A disposable chemical heater and dry enzyme preparation for lysis and extraction of DNA and RNA from microorganisms. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2016; 8:2880-2886. [PMID: 37457919 PMCID: PMC10348399 DOI: 10.1039/c6ay00107f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Sample preparation, including bacterial lysis, remains a hurdle in the realization of complete point-of-care tests for many pathogens. Here, we developed a sample preparation methodology for enzymatic lysis and sample heating for low-resource, point-of-care applications. We show an instrument-free chemical heater system for rapid lysis of a gram-positive bacterium (Staphylococcus aureus) and an RNA virus (human respiratory syncytial virus) using a dried lysis enzyme mixture (achromopeptidase) for S. aureus. After a lysis step (<1 minute), lysis enzymes are heat deactivated (<5 minutes) using a simple disposable chemical heater. We demonstrated that both DNA and RNA in the heat-treated sample could be directly amplified without purification, even in the presence of a clinically-obtained human nasal sample. This simple approach to dry enzyme storage and sample heating is adaptable to many applications where samples need to be lysed, including use in low-resource laboratories and in single-use or cartridge-based point-of-care diagnostic devices.
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Affiliation(s)
- J R Buser
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - X Zhang
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - S A Byrnes
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - P D Ladd
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - E K Heiniger
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - M D Wheeler
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - J D Bishop
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - J A Englund
- Program in Infectious Diseases, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington, Seattle, Washington, United States of America
| | - B Lutz
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - B H Weigl
- PATH, Seattle, WA, United States of America
| | - P Yager
- Box 355061, Department of Bioengineering, University of Washington, Seattle, WA, United States of America
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53
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Wang S, Lifson MA, Inci F, Liang LG, Sheng YF, Demirci U. Advances in addressing technical challenges of point-of-care diagnostics in resource-limited settings. Expert Rev Mol Diagn 2016; 16:449-59. [PMID: 26777725 DOI: 10.1586/14737159.2016.1142877] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The striking prevalence of HIV, TB and malaria, as well as outbreaks of emerging infectious diseases, such as influenza A (H7N9), Ebola and MERS, poses great challenges for patient care in resource-limited settings (RLS). However, advanced diagnostic technologies cannot be implemented in RLS largely due to economic constraints. Simple and inexpensive point-of-care (POC) diagnostics, which rely less on environmental context and operator training, have thus been extensively studied to achieve early diagnosis and treatment monitoring in non-laboratory settings. Despite great input from material science, biomedical engineering and nanotechnology for developing POC diagnostics, significant technical challenges are yet to be overcome. Summarized here are the technical challenges associated with POC diagnostics from a RLS perspective and the latest advances in addressing these challenges are reviewed.
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Affiliation(s)
- ShuQi Wang
- a State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine , Zhejiang University , Hangzhou , China.,b Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou , China.,c Institute for Translational Medicine , Zhejiang University , Hangzhou , China.,d The Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology , Stanford School of Medicine, Stanford University , Palo Alto , CA , USA
| | - Mark A Lifson
- d The Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology , Stanford School of Medicine, Stanford University , Palo Alto , CA , USA
| | - Fatih Inci
- d The Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology , Stanford School of Medicine, Stanford University , Palo Alto , CA , USA
| | - Li-Guo Liang
- a State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine , Zhejiang University , Hangzhou , China.,b Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou , China.,c Institute for Translational Medicine , Zhejiang University , Hangzhou , China
| | - Ye-Feng Sheng
- a State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine , Zhejiang University , Hangzhou , China.,b Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou , China.,c Institute for Translational Medicine , Zhejiang University , Hangzhou , China.,d The Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology , Stanford School of Medicine, Stanford University , Palo Alto , CA , USA
| | - Utkan Demirci
- d The Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology , Stanford School of Medicine, Stanford University , Palo Alto , CA , USA
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54
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Rapid Point-of-Care Diagnosis of Malaria and Dengue Infection. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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55
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Buser JR, Diesburg S, Singleton J, Guelig D, Bishop JD, Zentner C, Burton R, LaBarre P, Yager P, Weigl BH. Precision chemical heating for diagnostic devices. LAB ON A CHIP 2015; 15:4423-4432. [PMID: 26503640 DOI: 10.1039/c5lc01053e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Decoupling nucleic acid amplification assays from infrastructure requirements such as grid electricity is critical for providing effective diagnosis and treatment at the point of care in low-resource settings. Here, we outline a complete strategy for the design of electricity-free precision heaters compatible with medical diagnostic applications requiring isothermal conditions, including nucleic acid amplification and lysis. Low-cost, highly energy dense components with better end-of-life disposal options than conventional batteries are proposed as an alternative to conventional heating methods to satisfy the unique needs of point of care use.
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Affiliation(s)
- J R Buser
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA, USA.
| | - S Diesburg
- PATH: The Program for Appropriate Technology in Healthcare, Seattle, WA, USA
| | - J Singleton
- PATH: The Program for Appropriate Technology in Healthcare, Seattle, WA, USA
| | - D Guelig
- PATH: The Program for Appropriate Technology in Healthcare, Seattle, WA, USA
| | - J D Bishop
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA, USA.
| | - C Zentner
- PATH: The Program for Appropriate Technology in Healthcare, Seattle, WA, USA
| | - R Burton
- PATH: The Program for Appropriate Technology in Healthcare, Seattle, WA, USA
| | - P LaBarre
- PATH: The Program for Appropriate Technology in Healthcare, Seattle, WA, USA
| | - P Yager
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA, USA.
| | - B H Weigl
- PATH: The Program for Appropriate Technology in Healthcare, Seattle, WA, USA
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Sriworarat C, Phumee A, Mungthin M, Leelayoova S, Siriyasatien P. Development of loop-mediated isothermal amplification (LAMP) for simple detection of Leishmania infection. Parasit Vectors 2015; 8:591. [PMID: 26577333 PMCID: PMC4650110 DOI: 10.1186/s13071-015-1202-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/10/2015] [Indexed: 11/25/2022] Open
Abstract
Background Leishmaniasis is a neglected tropical disease that is caused by an obligate intracellular protozoan of the genus Leishmania. Recently, an increasing number of autochthonous leishmaniasis cases caused by L. martiniquensis and the novel species L. siamensis have been described in Thailand, rendering an accurate diagnosis of this disease critical. However, only a few laboratories are capable of diagnosing leishmaniasis in Thailand. To expand leishmaniasis diagnostic capabilities, we developed a simple colorimetric loop-mediated isothermal amplification (LAMP) technique for the direct detection of Leishmania DNA. Methods LAMP was performed for 75 min using four primers targeting the conserved region of the18S ribosomal RNA gene, and the DNA indicator used was malachite green (MG). To simulate crude samples, cultured promastigotes of L. siamensis were mixed with blood or saliva. Also, clinical samples (blood, saliva, and tissue biopsies) were obtained from patients with cutaneous leishmaniasis (CL) and visceral leishmaniasis (VL). All samples were boiled for 10 min and introduced directly into the LAMP reaction mixture without DNA purification. Results The use of MG resulted in an unambiguous differentiation of positive and negative controls. For L. siamensis, the detection limit was 103 parasites/mL or 2.5 parasites/tube. Saliva, tissue biopsies, and whole blood were indicative of active Leishmania infection, and their direct usages did not adversely affect the detection limit. In addition, this LAMP assay could detect DNA from multiple Leishmania species other than L. siamensis and L. martiniquensis, including L. aethiopica, L. braziliensis, L. donovani and L. tropica. Conclusions The simplicity and sensitivity of LAMP in detecting active Leishmania infection could enable the rapid diagnosis of leishmaniasis, thereby facilitating the survey and control of leishmaniasis in Thailand. However, our limited number of samples warranted a further validation with a larger cohort of patients before this assay could be deployed.
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Affiliation(s)
| | - Atchara Phumee
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand.
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand.
| | - Padet Siriyasatien
- Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand. .,Excellence Center for Emerging Infectious Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, 10330, Thailand.
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57
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Shah KG, Guelig D, Diesburg S, Buser J, Burton R, LaBarre P, Richards-Kortum R, Weigl B. Design of a New Type of Compact Chemical Heater for Isothermal Nucleic Acid Amplification. PLoS One 2015; 10:e0139449. [PMID: 26430883 PMCID: PMC4591995 DOI: 10.1371/journal.pone.0139449] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/13/2015] [Indexed: 11/18/2022] Open
Abstract
Previous chemical heater designs for isothermal nucleic acid amplification have been based on solid-liquid phase transition, but using this approach, developers have identified design challenges en route to developing a low-cost, disposable device. Here, we demonstrate the feasibility of a new heater configuration suitable for isothermal amplification in which one reactant of an exothermic reaction is a liquid-gas phase-change material, thereby eliminating the need for a separate phase-change compartment. This design offers potentially enhanced performance and energy density compared to other chemical and electric heaters.
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Affiliation(s)
- Kamal G. Shah
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
- PATH, Seattle, Washington, United States of America
- * E-mail:
| | - Dylan Guelig
- PATH, Seattle, Washington, United States of America
| | | | - Joshua Buser
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | | | - Paul LaBarre
- PATH, Seattle, Washington, United States of America
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58
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Oriero EC, Van Geertruyden JP, Nwakanma DC, D'Alessandro U, Jacobs J. Novel techniques and future directions in molecular diagnosis of malaria in resource-limited settings. Expert Rev Mol Diagn 2015; 15:1419-26. [PMID: 26413727 DOI: 10.1586/14737159.2015.1090878] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite being preventable and treatable, malaria remains a global health concern with approximately 1.2 billion people at high risk of being infected, 90% of whom are in the resource-limited settings of sub-Saharan Africa. The continued decline in malaria cases globally has rekindled the possibility of elimination in certain regions. As humans constitute the main reservoir of malaria, prompt and accurate diagnosis by microscopy or rapid diagnostic tests is part not only of effective disease management but also of control measures. However, for malaria elimination, more sensitive diagnostic tools are needed to detect asymptomatic and sub-microscopic infections that contribute to transmission. Molecular techniques, which involve amplification of nucleic acids, are being developed and modified to suit this purpose. This report provides a summary of the nucleic acid amplification tests that are currently available for diagnosis of malaria, with current improvements and adaptations for use in resource-limited settings.
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Affiliation(s)
- Eniyou Cheryll Oriero
- a 1 Medical Research Council Unit , Fajara, The Gambia.,b 2 International Health Unit, University of Antwerp , Antwerp, Belgium.,c 3 Institute of Tropical Medicine , Antwerp, Belgium
| | | | | | - Umberto D'Alessandro
- a 1 Medical Research Council Unit , Fajara, The Gambia.,c 3 Institute of Tropical Medicine , Antwerp, Belgium.,d 4 London School of Tropical Medicine and Hygiene , London, UK
| | - Jan Jacobs
- c 3 Institute of Tropical Medicine , Antwerp, Belgium.,e 5 Department of Microbiology and Immunology, University of Leuven , Leuven, Belgium
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59
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Schwenkbier L, Pollok S, Rudloff A, Sailer S, Cialla-May D, Weber K, Popp J. Non-instrumented DNA isolation, amplification and microarray-based hybridization for a rapid on-site detection of devastating Phytophthora kernoviae. Analyst 2015; 140:6610-8. [PMID: 26331157 DOI: 10.1039/c5an00855g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A rapid and simple instrument-free detection system was developed for the identification of the plant pathogen Phytophthora kernoviae (P. kernoviae). The on-site operable analysis steps include magnetic particle based DNA isolation, helicase-dependent amplification (HDA) and chip-based DNA hybridization. The isothermal approach enabled the convenient amplification of the yeast GTP-binding protein (Ypt1) target gene in a miniaturized HDA-zeolite-heater (HZH) by an exothermic reaction. The amplicon detection on the chip was performed under room temperature conditions – either by successive hybridization and enzyme binding or by a combined step. A positive signal is displayed by enzymatically generated silver nanoparticle deposits, which serve as robust endpoint signals allowing an immediate visual readout. The hybridization assay enabled the reliable detection of 10 pg μL(-1) target DNA. This is the first report of an entirely electricity-free, field applicable detection approach for devastating Phytophthora species, exemplarily shown for P. kernoviae.
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Affiliation(s)
- Lydia Schwenkbier
- Leibniz Institute of Photonic Technology (IPHT Jena), Jenaer BioChip Initiative, Albert-Einstein-Straße 9, 07745 Jena, Germany
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60
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Expanding the MDx toolbox for filarial diagnosis and surveillance. Trends Parasitol 2015; 31:391-400. [DOI: 10.1016/j.pt.2015.04.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 11/17/2022]
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61
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Abstract
Clinical tests based on primer-initiated amplification of specific nucleic acid sequences achieve high levels of sensitivity and specificity. Despite these desirable characteristics, these tests have not reached their full potential because their complexity and expense limit their usefulness to centralized laboratories. This paper describes a device that integrates sample preparation and loop-mediated isothermal amplification (LAMP) with end point detection using a hand-held UV source and camera phone. The prototype device integrates paper microfluidics (to enable fluid handling) and a multilayer structure, or a "paper machine", that allows a central patterned paper strip to slide in and out of fluidic path and thus allows introduction of sample, wash buffers, amplification master mix, and detection reagents with minimal pipetting, in a hand-held, disposable device intended for point-of-care use in resource-limited environments. This device creates a dynamic seal that prevents evaporation during incubation at 65 °C for 1 h. This interval is sufficient to allow a LAMP reaction for the Escherichia coli malB gene to proceed with an analytical sensitivity of 1 double-stranded DNA target copy. Starting with human plasma spiked with whole, live E. coli cells, this paper demonstrates full integration of sample preparation with LAMP amplification and end point detection with a limit of detection of 5 cells. Further, it shows that the method used to prepare sample enables concentration of DNA from sample volumes commonly available from fingerstick blood draw.
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Affiliation(s)
- John T Connelly
- †Diagnostics For All, 840 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Jason P Rolland
- †Diagnostics For All, 840 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - George M Whitesides
- ‡Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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62
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Choi JR, Tang R, Wang S, Wan Abas WAB, Pingguan-Murphy B, Xu F. Paper-based sample-to-answer molecular diagnostic platform for point-of-care diagnostics. Biosens Bioelectron 2015; 74:427-39. [PMID: 26164488 DOI: 10.1016/j.bios.2015.06.065] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/15/2015] [Accepted: 06/27/2015] [Indexed: 01/04/2023]
Abstract
Nucleic acid testing (NAT), as a molecular diagnostic technique, including nucleic acid extraction, amplification and detection, plays a fundamental role in medical diagnosis for timely medical treatment. However, current NAT technologies require relatively high-end instrumentation, skilled personnel, and are time-consuming. These drawbacks mean conventional NAT becomes impractical in many resource-limited disease-endemic settings, leading to an urgent need to develop a fast and portable NAT diagnostic tool. Paper-based devices are typically robust, cost-effective and user-friendly, holding a great potential for NAT at the point of care. In view of the escalating demand for the low cost diagnostic devices, we highlight the beneficial use of paper as a platform for NAT, the current state of its development, and the existing challenges preventing its widespread use. We suggest a strategy involving integrating all three steps of NAT into one single paper-based sample-to-answer diagnostic device for rapid medical diagnostics in the near future.
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Affiliation(s)
- Jane Ru Choi
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Ruihua Tang
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, PR China; Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, PR China
| | - ShuQi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China; Institute for Translational Medicine, Zhejiang University, Hangzhou, PR China
| | - Wan Abu Bakar Wan Abas
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
| | - Belinda Pingguan-Murphy
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China.
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63
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Dauner AL, Mitra I, Gilliland T, Seales S, Pal S, Yang SC, Guevara C, Chen JH, Liu YC, Kochel TJ, Wu SJL. Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus. Diagn Microbiol Infect Dis 2015; 83:30-6. [PMID: 26032430 PMCID: PMC7126901 DOI: 10.1016/j.diagmicrobio.2015.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/06/2015] [Accepted: 05/11/2015] [Indexed: 10/24/2022]
Abstract
During dengue outbreaks, acute diagnosis at the patient's point of need followed by appropriate supportive therapy reduces morbidity and mortality. To facilitate needed diagnosis, we developed and optimized a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay that detects all 4 serotypes of dengue virus (DENV). We used a quencher to reduce nonspecific amplification. The assay does not require expensive thermocyclers, utilizing a simple water bath to maintain the reaction at 63 °C. Results can be visualized using UV fluorescence, handheld readers, or lateral flow immunochromatographic tests. We report a sensitivity of 86.3% (95% confidence interval [CI], 72.7-94.8%) and specificity of 93.0% (95% CI, 83.0-98.1%) using a panel of clinical specimens characterized by DENV quantitative reverse transcription-polymerase chain reaction. This pan-serotype DENV RT-LAMP can be adapted to field-expedient formats where it can provide actionable diagnosis near the patient's point of need.
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Affiliation(s)
- Allison L Dauner
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Indrani Mitra
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Theron Gilliland
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Sajeewane Seales
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Subhamoy Pal
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA.
| | | | | | | | | | - Tadeusz J Kochel
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Shuenn-Jue L Wu
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
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64
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Buser JR, Wollen A, Heiniger EK, Byrnes SA, Kauffman PC, Ladd PD, Yager P. Electromechanical cell lysis using a portable audio device: enabling challenging sample preparation at the point-of-care. LAB ON A CHIP 2015; 15:1994-1997. [PMID: 25797443 DOI: 10.1039/c5lc00080g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Audio sources are ubiquitously available on portable electronic devices, including cell phones. Here we demonstrate lysis of Mycobacterium marinum and Staphylococcus epidermidis bacteria utilizing a portable audio device coupled with a simple and inexpensive electromagnetic coil. The resulting alternating magnetic field rotates a magnet in a tube with the sample and glass beads, lysing the cells and enabling sample preparation for these bacteria anywhere there is a cell phone, mp3 player, laptop, or other device with a headphone jack.
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Affiliation(s)
- J R Buser
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA, USA.
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65
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Carinelli S, Martí M, Alegret S, Pividori MI. Biomarker detection of global infectious diseases based on magnetic particles. N Biotechnol 2015; 32:521-32. [PMID: 25917978 DOI: 10.1016/j.nbt.2015.04.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
Abstract
Infectious diseases affect the daily lives of millions of people all around the world, and are responsible for hundreds of thousands of deaths, mostly in the developing world. Although most of these major infectious diseases are treatable, the early identification of individuals requiring treatment remains a major issue. The incidence of these diseases would be reduced if rapid diagnostic tests were widely available at the community and primary care level in low-resource settings. Strong research efforts are thus being focused on replacing standard clinical diagnostic methods, such as the invasive detection techniques (biopsy or endoscopy) or expensive diagnostic and monitoring methods, by affordable and sensitive tests based on novel biomarkers. The development of new methods that are needed includes solid-phase separation techniques. In this context, the integration of magnetic particles within bioassays and biosensing devices is very promising since they greatly improve the performance of a biological reaction. The diagnosis of clinical samples with magnetic particles can be easily achieved without pre-enrichment, purification or pretreatment steps often required for standard methods, simplifying the analytical procedures. The biomarkers can be specifically isolated and preconcentrated from complex biological matrixes by magnetic actuation, increasing specificity and the sensitivity of the assay. This review addresses these promising features of the magnetic particles for the detection of biomarkers in emerging technologies related with infectious diseases affecting global health, such as malaria, influenza, dengue, tuberculosis or HIV.
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Affiliation(s)
- Soledad Carinelli
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mercè Martí
- Laboratory of Cellular Immunology, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Alegret
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - María Isabel Pividori
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Development of loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Penicillium nordicum in dry-cured meat products. Int J Food Microbiol 2015; 202:42-7. [PMID: 25771218 DOI: 10.1016/j.ijfoodmicro.2015.02.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/05/2015] [Accepted: 02/18/2015] [Indexed: 11/21/2022]
Abstract
The need of powerful diagnostic tools for rapid, simple, and cost-effective detection of food-borne fungi has become very important in the area of food safety. Currently, several isothermal nucleic acid amplification methods have been developed as an alternative to PCR-based analyses. Loop-mediated isothermal amplification (LAMP) is one of these innovative methods; it requires neither gel electrophoresis to separate and visualize the products nor expensive laboratory equipment and it has been applied already for detection of pathogenic organisms. In the current study, we developed a LAMP assay for the specific detection of Penicillium nordicum, the major causative agent of ochratoxin A contamination in protein-rich food, especially dry-cured meat products. The assay was based on targeting otapksPN gene, a key gene in the biosynthesis of ochratoxin A (OTA) in P. nordicum. Amplification of DNA during the reaction was detected directly in-tube by color transition of hydroxynaphthol blue from violet to sky blue, visible to the naked eye, avoiding further post amplification analyses. Only DNAs isolated from several P. nordicum strains led to positive results and no amplification was observed from non-target OTA and non OTA-producing strains. The assay was able to detect down to 100 fg of purified targeted genomic DNA or 10(2) conidia/reaction within 60 min. The LAMP assay for detection and identification of P. nordicum was combined with a rapid DNA extraction method set up on serially diluted conidia, providing an alternative rapid, specific and sensitive DNA-based method suitable for application directly "on-site", notably in key steps of dry-cured meat production.
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67
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Li J, Macdonald J. Advances in isothermal amplification: novel strategies inspired by biological processes. Biosens Bioelectron 2015; 64:196-211. [DOI: 10.1016/j.bios.2014.08.069] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/20/2014] [Accepted: 08/22/2014] [Indexed: 01/02/2023]
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68
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Sema M, Alemu A, Bayih AG, Getie S, Getnet G, Guelig D, Burton R, LaBarre P, Pillai DR. Evaluation of non-instrumented nucleic acid amplification by loop-mediated isothermal amplification (NINA-LAMP) for the diagnosis of malaria in Northwest Ethiopia. Malar J 2015; 14:44. [PMID: 25626339 PMCID: PMC4323137 DOI: 10.1186/s12936-015-0559-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/13/2015] [Indexed: 11/15/2022] Open
Abstract
Background Malaria is a major public health problem in sub-Saharan African countries including Ethiopia. Early and accurate diagnosis followed by prompt and effective treatment is among the various tools available for prevention, control and elimination of malaria. This study aimed to evaluate the performance of non-instrumented nucleic acid amplification loop-mediated isothermal amplification (NINA-LAMP) compared to standard thick and thin film microscopy and nested PCR as gold standard for the sensitive diagnosis of malaria in Northwest Ethiopia. Methods A cross-sectional study was conducted in North Gondar, Ethiopia from March to July 2014. Eighty-two blood samples were collected from malaria suspected patients visiting Kola Diba Health Centre and analysed for Plasmodium parasites by microscopy, NINA-LAMP and nested PCR. The NINA-LAMP method was performed using the Loopamp™ Malaria Pan/Pf detection kits for detecting DNA of the genus Plasmodium and more specifically Plasmodium falciparum using an electricity-free heater. Diagnostic accuracy outcome measures (analytical sensitivity, specificity, predictive values, and Kappa scores) of NINA-LAMP and microscopy were compared to nested PCR. Results A total of 82 samples were tested in the primary analysis. Using nested PCR as reference, the sensitivity and specificity of the primary NINA-LAMP assay were 96.8% (95% confidence interval (CI), 83.2% - 99.5%) and 84.3% (95% CI, 71.4% - 92.9%), respectively for detection of Plasmodium genus, and 100% (95% CI, 75.1% - 100%) and 81.2% (95% CI, 69.9% - 89.6%), respectively for detection of P. falciparum parasite. Microscopy demonstrated sensitivity and specificity of 93.6% (95% CI, 78.5% - 99.0%) and 98.0% (95% CI, 89.5% - 99.7%), respectively for the detection of Plasmodium parasites. Post-hoc repeat NINA-LAMP analysis showed improvement in diagnostic accuracy, which was comparable to nested PCR performance and superior to microscopy for detection at both the Plasmodium genus level and P. falciparum parasites. Conclusion NINA-LAMP is highly sensitive for the diagnosis of malaria and detection of Plasmodium parasite infection at both the genus and species level when compared to nested PCR. NINA-LAMP is more sensitive than microscopy for the detection of P. falciparum and differentiation from non-falciparum species and may be a critical diagnostic modality in efforts to eradicate malaria from areas of low endemicity.
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Affiliation(s)
- Meslo Sema
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
| | - Abebe Alemu
- School of Medicine, College of Health Sciences and Medicine, Wolaita Sodo University, Wolaita, Ethiopia.
| | - Abebe Genetu Bayih
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada.
| | - Sisay Getie
- Department of Medical Parasitology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
| | - Gebeyaw Getnet
- Department of Medical Parasitology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
| | | | | | | | - Dylan R Pillai
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada. .,Department of Medical Parasitology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
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Niessen L. Current state and future perspectives of loop-mediated isothermal amplification (LAMP)-based diagnosis of filamentous fungi and yeasts. Appl Microbiol Biotechnol 2014; 99:553-74. [PMID: 25492418 DOI: 10.1007/s00253-014-6196-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 11/30/2022]
Abstract
Loop-mediated isothermal amplification is a rather novel method of enzymatic deoxyribonucleic acid amplification which can be applied for the diagnosis of viruses, bacteria, and fungi. Although firmly established in viral and bacterial diagnosis, the technology has only recently been applied to a noteworthy number of species in the filamentous fungi and yeasts. The current review gives an overview of the literature so far published on the topic by discussing the different groups of fungal organisms to which the method has been applied. Moreover, the method is described in detail as well as the different possibilities available for signal detection and quantification and sample preparation. Future perspective of loop-mediated isothermal amplification-based assays is discussed in the light of applicability for fungal diagnostics.
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Affiliation(s)
- Ludwig Niessen
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Gregor-Mendel-Straße 4, 85354, Freising, Germany,
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Electricity-free amplification and detection for molecular point-of-care diagnosis of HIV-1. PLoS One 2014; 9:e113693. [PMID: 25426953 PMCID: PMC4245218 DOI: 10.1371/journal.pone.0113693] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022] Open
Abstract
In resource-limited settings, the lack of decentralized molecular diagnostic testing and sparse access to centralized medical facilities can present a critical barrier to timely diagnosis, treatment, and subsequent control and elimination of infectious diseases. Isothermal nucleic acid amplification methods, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), are well-suited for decentralized point-of-care molecular testing in minimal infrastructure laboratories since they significantly reduce the complexity of equipment and power requirements. Despite reduced complexity, however, there is still a need for a constant heat source to enable isothermal nucleic acid amplification. This requirement poses significant challenges for laboratories in developing countries where electricity is often unreliable or unavailable. To address this need, we previously developed a low-cost, electricity-free heater using an exothermic reaction thermally coupled with a phase change material. This heater achieved acceptable performance, but exhibited considerable variability. Furthermore, as an enabling technology, the heater was an incomplete diagnostic solution. Here we describe a more precise, affordable, and robust heater design with thermal standard deviation <0.5°C at operating temperature, a cost of approximately US$.06 per test for heater reaction materials, and an ambient temperature operating range from 16°C to 30°C. We also pair the heater with nucleic acid lateral flow (NALF)-detection for a visual readout. To further illustrate the utility of the electricity-free heater and NALF-detection platform, we demonstrate sensitive and repeatable detection of HIV-1 with a ß-actin positive internal amplification control from processed sample to result in less than 80 minutes. Together, these elements are building blocks for an electricity-free platform capable of isothermal amplification and detection of a variety of pathogens.
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Crannell ZA, Rohrman B, Richards-Kortum R. Equipment-free incubation of recombinase polymerase amplification reactions using body heat. PLoS One 2014; 9:e112146. [PMID: 25372030 PMCID: PMC4221156 DOI: 10.1371/journal.pone.0112146] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/13/2014] [Indexed: 11/28/2022] Open
Abstract
The development of isothermal amplification platforms for nucleic acid detection has the potential to increase access to molecular diagnostics in low resource settings; however, simple, low-cost methods for heating samples are required to perform reactions. In this study, we demonstrated that human body heat may be harnessed to incubate recombinase polymerase amplification (RPA) reactions for isothermal amplification of HIV-1 DNA. After measuring the temperature of mock reactions at 4 body locations, the axilla was chosen as the ideal site for comfortable, convenient incubation. Using commonly available materials, 3 methods for securing RPA reactions to the body were characterized. Finally, RPA reactions were incubated using body heat while control RPA reactions were incubated in a heat block. At room temperature, all reactions with 10 copies of HIV-1 DNA and 90% of reactions with 100 copies of HIV-1 DNA tested positive when incubated with body heat. In a cold room with an ambient temperature of 10 degrees Celsius, all reactions containing 10 copies or 100 copies of HIV-1 DNA tested positive when incubated with body heat. These results suggest that human body heat may provide an extremely low-cost solution for incubating RPA reactions in low resource settings.
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Affiliation(s)
| | - Brittany Rohrman
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
- * E-mail:
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Lillis L, Lehman D, Singhal MC, Cantera J, Singleton J, Labarre P, Toyama A, Piepenburg O, Parker M, Wood R, Overbaugh J, Boyle DS. Non-instrumented incubation of a recombinase polymerase amplification assay for the rapid and sensitive detection of proviral HIV-1 DNA. PLoS One 2014; 9:e108189. [PMID: 25264766 PMCID: PMC4180440 DOI: 10.1371/journal.pone.0108189] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/20/2014] [Indexed: 02/05/2023] Open
Abstract
Sensitive diagnostic tests for infectious diseases often employ nucleic acid amplification technologies (NAATs). However, most NAAT assays, including many isothermal amplification methods, require power-dependent instrumentation for incubation. For use in low resource settings (LRS), diagnostics that do not require consistent electricity supply would be ideal. Recombinase polymerase amplification (RPA) is an isothermal amplification technology that has been shown to typically work at temperatures ranging from 25–43°C, and does not require a stringent incubation temperature for optimal performance. Here we evaluate the ability to incubate an HIV-1 RPA assay, intended for use as an infant HIV diagnostic in LRS, at ambient temperatures or with a simple non-instrumented heat source. To determine the range of expected ambient temperatures in settings where an HIV-1 infant diagnostic would be of most use, a dataset of the seasonal range of daily temperatures in sub Saharan Africa was analyzed and revealed ambient temperatures as low as 10°C and rarely above 43°C. All 24 of 24 (100%) HIV-1 RPA reactions amplified when incubated for 20 minutes between 31°C and 43°C. The amplification from the HIV-1 RPA assay under investigation at temperatures was less consistent below 30°C. Thus, we developed a chemical heater to incubate HIV-1 RPA assays when ambient temperatures are between 10°C and 30°C. All 12/12 (100%) reactions amplified with chemical heat incubation from ambient temperatures of 15°C, 20°C, 25°C and 30°C. We also observed that incubation at 30 minutes improved assay performance at lower temperatures where detection was sporadic using 20 minutes incubation. We have demonstrated that incubation of the RPA HIV-1 assay via ambient temperatures or using chemical heaters yields similar results to using electrically powered devices. We propose that this RPA HIV-1 assay may not need dedicated equipment to be a highly sensitive tool to diagnose infant HIV-1 in LRS.
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Affiliation(s)
| | - Dara Lehman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | | | | | | | - Paul Labarre
- PATH, Seattle, Washington, United States of America
| | | | - Olaf Piepenburg
- TwistDx Limited, Minerva Building, Babraham Research Campus, Babraham, Cambridge, United Kingdom
| | - Mathew Parker
- TwistDx Limited, Minerva Building, Babraham Research Campus, Babraham, Cambridge, United Kingdom
| | - Robert Wood
- Department of Atmospheric Sciences, University of Washington, Seattle, Washington, United States of America
| | - Julie Overbaugh
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David S. Boyle
- PATH, Seattle, Washington, United States of America
- * E-mail:
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Oriero EC, Jacobs J, Van Geertruyden JP, Nwakanma D, D'Alessandro U. Molecular-based isothermal tests for field diagnosis of malaria and their potential contribution to malaria elimination. J Antimicrob Chemother 2014; 70:2-13. [PMID: 25223973 PMCID: PMC7109677 DOI: 10.1093/jac/dku343] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In countries where malaria transmission has decreased substantially, thanks to the scale-up of control interventions, malaria elimination may be feasible. Nevertheless, this goal requires new strategies such as the active detection and treatment of infected individuals. As the detection threshold for the currently used diagnostic methods is 100 parasites/μL, most low-density, asymptomatic infections able to maintain transmission cannot be detected. Identifying them by molecular methods such as PCR is a possible option but the field deployment of these tests is problematic. Isothermal amplification of nucleic acids (at a constant temperature) offers the opportunity of addressing some of the challenges related to the field deployment of molecular diagnostic methods. One of the novel isothermal amplification methods for which a substantial amount of work has been done is the loop-mediated isothermal amplification (LAMP) assay. The present review describes LAMP and several other isothermal nucleic acid amplification methods, such as thermophilic helicase-dependent amplification, strand displacement amplification, recombinase polymerase amplification and nucleic acid sequence-based amplification, and explores their potential use as high-throughput, field-based molecular tests for malaria diagnosis.
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Affiliation(s)
- Eniyou C Oriero
- Medical Research Council, Banjul, The Gambia Institute of Tropical Medicine, Antwerp, Belgium International Health Unit, University of Antwerp, Antwerp, Belgium
| | - Jan Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Umberto D'Alessandro
- Medical Research Council, Banjul, The Gambia Institute of Tropical Medicine, Antwerp, Belgium
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Fernández-Soto P, Gandasegui Arahuetes J, Sánchez Hernández A, López Abán J, Vicente Santiago B, Muro A. A loop-mediated isothermal amplification (LAMP) assay for early detection of Schistosoma mansoni in stool samples: a diagnostic approach in a murine model. PLoS Negl Trop Dis 2014; 8:e3126. [PMID: 25187956 PMCID: PMC4154662 DOI: 10.1371/journal.pntd.0003126] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/18/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Human schistosomiasis, mainly due to Schistosoma mansoni species, is one of the most prevalent parasitic diseases worldwide. To overcome the drawbacks of classical parasitological and serological methods in detecting S. mansoni infections, especially in acute stage of the disease, development of cost-effective, simple and rapid molecular methods is still needed for the diagnosis of schistosomiasis. A promising approach is the loop-mediated isothermal amplification (LAMP) technology. Compared to PCR-based assays, LAMP has the advantages of reaction simplicity, rapidity, specificity, cost-effectiveness and higher amplification efficiency. Additionally, as results can be inspected by the naked eye, the technique has great potential for use in low-income countries. METHODOLOGY/PRINCIPAL FINDINGS A sequence corresponding to a mitochondrial S. mansoni minisatellite DNA region was selected as a target for designing a LAMP-based method to detect S. mansoni DNA in stool samples. We used a S. mansoni murine model to obtain well defined stool and sera samples from infected mice with S. mansoni cercariae. Samples were taken weekly from week 0 to 8 post-infection and the Kato-Katz and ELISA techniques were used for monitoring the infection. Primer set designed were tested using a commercial reaction mixture for LAMP assay and an in house mixture to compare results. Specificity of LAMP was tested using 16 DNA samples from different parasites, including several Schistosoma species, and no cross-reactions were found. The detection limit of our LAMP assay (SmMIT-LAMP) was 1 fg of S. mansoni DNA. When testing stool samples from infected mice the SmMIT-LAMP detected S. mansoni DNA as soon as 1 week post-infection. CONCLUSIONS/SIGNIFICANCE We have developed, for the first time, a cost-effective, easy to perform, specific and sensitive LAMP assay for early detection of S. mansoni in stool samples. The method is potentially and readily adaptable for field diagnosis and disease surveillance in schistosomiasis-endemic areas.
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Affiliation(s)
- Pedro Fernández-Soto
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
- * E-mail:
| | - Javier Gandasegui Arahuetes
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
| | - Alicia Sánchez Hernández
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
| | - Julio López Abán
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
| | - Belén Vicente Santiago
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
| | - Antonio Muro
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
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Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification. PLoS One 2014; 9:e103091. [PMID: 25118698 PMCID: PMC4138011 DOI: 10.1371/journal.pone.0103091] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/25/2014] [Indexed: 11/21/2022] Open
Abstract
Improved access to effective tests for diagnosing tuberculosis (TB) has been designated a public health priority by the World Health Organisation. In high burden TB countries nucleic acid based TB tests have been restricted to centralised laboratories and specialised research settings. Requirements such as a constant electrical supply, air conditioning and skilled, computer literate operators prevent implementation of such tests in many settings. Isothermal DNA amplification technologies permit the use of simpler, less energy intensive detection platforms more suited to low resource settings that allow the accurate diagnosis of a disease within a short timeframe. Recombinase Polymerase Amplification (RPA) is a rapid, low temperature isothermal DNA amplification reaction. We report here RPA-based detection of Mycobacterium tuberculosis complex (MTC) DNA in <20 minutes at 39°C. Assays for two MTC specific targets were investigated, IS6110 and IS1081. When testing purified MTC genomic DNA, limits of detection of 6.25 fg (IS6110) and 20 fg (IS1081)were consistently achieved. When testing a convenience sample of pulmonary specimens from suspected TB patients, RPA demonstrated superior accuracy to indirect fluorescence microscopy. Compared to culture, sensitivities for the IS1081 RPA and microscopy were 91.4% (95%CI: 85, 97.9) and 86.1% (95%CI: 78.1, 94.1) respectively (n = 71). Specificities were 100% and 88.6% (95% CI: 80.8, 96.1) respectively. For the IS6110 RPA and microscopy sensitivities of 87.5% (95%CI: 81.7, 93.2) and 70.8% (95%CI: 62.9, 78.7) were obtained (n = 90). Specificities were 95.4 (95% CI: 92.3,98.1) and 88% (95% CI: 83.6, 92.4) respectively. The superior specificity of RPA for detecting tuberculosis was due to the reduced ability of fluorescence microscopy to distinguish Mtb complex from other acid fast bacteria. The rapid nature of the RPA assay and its low energy requirement compared to other amplification technologies suggest RPA-based TB assays could be of use for integration into a point-of-care test for use in resource constrained settings.
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Albertoni G, Castelo Girão MJB, Schor N. Mini review: current molecular methods for the detection and quantification of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus type 1. Int J Infect Dis 2014; 25:145-9. [PMID: 24927665 DOI: 10.1016/j.ijid.2014.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/01/2014] [Accepted: 04/09/2014] [Indexed: 12/11/2022] Open
Abstract
The detection of acute human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) infection is vital for controlling the spread of HIV, HBV, and HCV to uninfected individuals. Considering that these viruses have high replication rates and are undetectable by serological markers, early detection upon transmission is crucial. Various nucleic acid assays have been developed for diagnostics and therapeutic monitoring of infections. In the past decade, rapid and sensitive molecular techniques such as PCR have revolutionized the detection of a variety of infectious viruses, including HIV, HCV, and HBV. Here, we describe two of the most commonly used licensed methods for the detection and quantification of HIV, HCV, and HBV: the cobas TaqScreen MPX (PCR) test and the Tigris System. We used transcription-mediated amplification to review and compare the development and efficiency of these technologies.
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Affiliation(s)
- Guilherme Albertoni
- Federal University of São Paulo (UNIFESP), Department of Medicine, Nephrology Division, Rua Botucatu 740, São Paulo, 04023-900, SP, Brazil; Colsan (Associação Beneficente de Coleta de Sangue), São Paulo, SP, Brazil.
| | | | - Nestor Schor
- Federal University of São Paulo (UNIFESP), Department of Medicine, Nephrology Division, Rua Botucatu 740, São Paulo, 04023-900, SP, Brazil
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Stabilization of biothreat diagnostic samples through vitrification matrices. J Microbiol Methods 2014; 101:81-5. [DOI: 10.1016/j.mimet.2014.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 04/03/2014] [Accepted: 04/03/2014] [Indexed: 11/22/2022]
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Peeling RW, McNerney R. Emerging technologies in point-of-care molecular diagnostics for resource-limited settings. Expert Rev Mol Diagn 2014; 14:525-34. [DOI: 10.1586/14737159.2014.915748] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rigano LA, Malamud F, Orce IG, Filippone MP, Marano MR, do Amaral AM, Castagnaro AP, Vojnov AA. Rapid and sensitive detection of Candidatus Liberibacter asiaticus by loop mediated isothermal amplification combined with a lateral flow dipstick. BMC Microbiol 2014; 14:86. [PMID: 24708539 PMCID: PMC4021466 DOI: 10.1186/1471-2180-14-86] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 03/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Citrus Huanglongbing (HLB) is the most devastating bacterial citrus disease worldwide. Three Candidatus Liberibacter species are associated with different forms of the disease: Candidatus Liberibacter asiaticus, Candidatus Liberibacter americanus and Candidatus Liberibacter africanus. Amongst them, Candidatus Liberibacter asiaticus is the most widespread and economically important. These Gram-negative bacterial plant pathogens are phloem-limited and vectored by citrus psyllids. The current management strategy of HLB is based on early and accurate detection of Candidatus Liberibacter asiaticus in both citrus plants and vector insects. Nowadays, real time PCR is the method of choice for this task, mainly because of its sensitivity and reliability. However, this methodology has several drawbacks, namely high equipment costs, the need for highly trained personnel, the time required to conduct the whole process, and the difficulty in carrying out the detection reactions in field conditions. RESULTS A recent DNA amplification technique known as Loop Mediated Isothermal Amplification (LAMP) was adapted for the detection of Candidatus Liberibacter asiaticus. This methodology was combined with a Lateral Flow Dipstick (LFD) device for visual detection of the resulting amplicons, eliminating the need for gel electrophoresis. The assay was highly specific for the targeted bacterium. No cross-reaction was observed with DNA from any of the other phytopathogenic bacteria or fungi assayed. By serially diluting purified DNA from an infected plant, the sensitivity of the assay was found to be 10 picograms. This sensitivity level was proven to be similar to the values obtained running a real time PCR in parallel. This methodology was able to detect Candidatus Liberibacter asiaticus from different kinds of samples including infected citrus plants and psyllids. CONCLUSIONS Our results indicate that the methodology here reported constitutes a step forward in the development of new tools for the management, control and eradication of this destructive citrus disease. This system constitutes a potentially field-capable approach for the detection of the most relevant HLB-associated bacteria in plant material and psyllid vectors.
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Affiliation(s)
- Luciano A Rigano
- Instituto de Ciencia y Tecnología Dr. Cesar Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand
| | - Florencia Malamud
- Instituto de Ciencia y Tecnología Dr. Cesar Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
- Instituto de investigaciones fisiológicas y ecológicas vinculadas a la Agricultura (IFEVA-FAUBA), Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Ingrid G Orce
- Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- CONICET, Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Las Talitas, Tucumán, Argentina
| | - Maria P Filippone
- Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- CONICET, Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Las Talitas, Tucumán, Argentina
| | - Maria R Marano
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias, Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Atilio P Castagnaro
- Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- CONICET, Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Las Talitas, Tucumán, Argentina
| | - Adrian A Vojnov
- Instituto de Ciencia y Tecnología Dr. Cesar Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
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80
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Inoue S, Becker AL, Kim JH, Shu Z, Soelberg SD, Weigel KM, Hiraiwa M, Cairns A, Lee HB, Furlong CE, Oh K, Lee KH, Gao D, Chung JH, Cangelosi GA. Semi-automated, occupationally safe immunofluorescence microtip sensor for rapid detection of Mycobacterium cells in sputum. PLoS One 2014; 9:e86018. [PMID: 24465845 PMCID: PMC3899086 DOI: 10.1371/journal.pone.0086018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/04/2013] [Indexed: 11/18/2022] Open
Abstract
An occupationally safe (biosafe) sputum liquefaction protocol was developed for use with a semi-automated antibody-based microtip immunofluorescence sensor. The protocol effectively liquefied sputum and inactivated microorganisms including Mycobacterium tuberculosis, while preserving the antibody-binding activity of Mycobacterium cell surface antigens. Sputum was treated with a synergistic chemical-thermal protocol that included moderate concentrations of NaOH and detergent at 60°C for 5 to 10 min. Samples spiked with M. tuberculosis complex cells showed approximately 106-fold inactivation of the pathogen after treatment. Antibody binding was retained post-treatment, as determined by analysis with a microtip immunosensor. The sensor correctly distinguished between Mycobacterium species and other cell types naturally present in biosafe-treated sputum, with a detection limit of 100 CFU/mL for M. tuberculosis, in a 30-minute sample-to-result process. The microtip device was also semi-automated and shown to be compatible with low-cost, LED-powered fluorescence microscopy. The device and biosafe sputum liquefaction method opens the door to rapid detection of tuberculosis in settings with limited laboratory infrastructure.
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Affiliation(s)
- Shinnosuke Inoue
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Annie L. Becker
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jong-Hoon Kim
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Zhiquan Shu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Scott D. Soelberg
- Departments of Medicine-Division of Medical Genetics and Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Morgan Hiraiwa
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Andrew Cairns
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Hyun-Boo Lee
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Clement E. Furlong
- Departments of Medicine-Division of Medical Genetics and Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kieseok Oh
- NanoFacture, Inc., Bellevue, Washington, United States of America
| | - Kyong-Hoon Lee
- NanoFacture, Inc., Bellevue, Washington, United States of America
| | - Dayong Gao
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Jae-Hyun Chung
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
- * E-mail: (GAC); (JHC)
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail: (GAC); (JHC)
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81
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Lemieux B, Li Y, Kong H, Tang YW. Near instrument-free, simple molecular device for rapid detection of herpes simplex viruses. Expert Rev Mol Diagn 2014; 12:437-43. [DOI: 10.1586/erm.12.34] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Bertrand Lemieux
- BioHelix Corporation, 500 Cummings Center, Suite 5550, Beverly, MA 01915, USA
| | - Ying Li
- BioHelix Corporation, 500 Cummings Center, Suite 5550, Beverly, MA 01915, USA
| | - Huimin Kong
- BioHelix Corporation, 500 Cummings Center, Suite 5550, Beverly, MA 01915, USA
| | - Yi-Wei Tang
- Clinical Microbiology Service, Memorial Sloan–Kettering Cancer Center, 1275 York Avenue, S428, New York, NY 10065, USA
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82
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Linnes JC, Fan A, Rodriguez NM, Lemieux B, Kong H, Klapperich CM. Paper-based molecular diagnostic for Chlamydia trachomatis.. RSC Adv 2014; 4:42245-42251. [PMID: 25309740 DOI: 10.1039/c4ra07911f] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein we show the development of a minimally instrumented paper-based molecular diagnostic for point of care detection of sexually transmitted infections caused by Chlamydia trachomatis. This new diagnostic platform incorporates cell lysis, isothermal nucleic acid amplification, and lateral flow visual detection using only a pressure source and heat block, eliminating the need for expensive laboratory equipment. This paper-based test can be performed in less than one hour and has a clinically relevant limit of detection that is 100x more sensitive than current rapid immunoassays used for chlamydia diagnosis.
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Affiliation(s)
| | - Andy Fan
- Biomedical Engineering, Boston University, Boston, MA, 02215
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83
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Loop-mediated isothermal amplification for Rickettsia typhi (the causal agent of murine typhus): problems with diagnosis at the limit of detection. J Clin Microbiol 2013; 52:832-8. [PMID: 24371248 PMCID: PMC3957756 DOI: 10.1128/jcm.02786-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Murine typhus is a flea-borne disease of worldwide distribution caused by Rickettsia typhi. Although treatment with tetracycline antibiotics is effective, treatment is often misguided or delayed due to diagnostic difficulties. As the gold standard immunofluorescence assay is imperfect, we aimed to develop and evaluate a loop-mediated isothermal amplification (LAMP) assay. LAMP assays have the potential to fulfill the WHO ASSURED criteria (affordable, sensitive, specific, user friendly, robust and rapid, equipment free, deliverable to those who need them) for diagnostic methodologies, as they can detect pathogen-derived nucleic acid with low technical expenditure. The LAMP assay was developed using samples of bacterial isolates (n = 41), buffy coat specimens from R. typhi PCR-positive Lao patients (n = 42), and diverse negative controls (n = 47). The method was then evaluated prospectively using consecutive patients with suspected scrub typhus or murine typhus (n = 266). The limit of detection was ∼40 DNA copies/LAMP reaction, with an analytical sensitivity of <10 DNA copies/reaction based on isolate dilutions. Despite these low cutoffs, the clinical sensitivity was disappointing, with 48% (95% confidence interval [95% CI], 32.5 to 62.7%) (specificity, 100% [95% CI, 100 to 100%]) in the developmental phase and 33% (95% CI, 9.2 to 56.8%) (specificity, 98.5% [95% CI, 97.0% to 100%]) in the prospective study. This low diagnostic accuracy was attributed to low patient R. typhi bacterial loads (median, 210 DNA copies/ml blood; interquartile range, 130 to 500). PCR-positive but LAMP-negative samples demonstrated significantly lower bacterial loads than LAMP-positive samples. Our findings highlight the diagnostic challenges for diseases with low pathogen burdens and emphasize the need to integrate pathogen biology with improved template production for assay development strategies.
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84
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Niessen L, Luo J, Denschlag C, Vogel RF. The application of loop-mediated isothermal amplification (LAMP) in food testing for bacterial pathogens and fungal contaminants. Food Microbiol 2013; 36:191-206. [DOI: 10.1016/j.fm.2013.04.017] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
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85
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Byrnes S, Thiessen G, Fu E. Progress in the development of paper-based diagnostics for low-resource point-of-care settings. Bioanalysis 2013; 5:2821-36. [PMID: 24256361 PMCID: PMC4012918 DOI: 10.4155/bio.13.243] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
This Review focuses on recent work in the field of paper microfluidics that specifically addresses the goal of translating the multistep processes that are characteristic of gold-standard laboratory tests to low-resource point-of-care settings. A major challenge is to implement multistep processes with the robust fluid control required to achieve the necessary sensitivity and specificity of a given application in a user-friendly package that minimizes equipment. We review key work in the areas of fluidic controls for automation in paper-based devices, readout methods that minimize dedicated equipment, and power and heating methods that are compatible with low-resource point-of-care settings. We also highlight a focused set of recent applications and discuss future challenges.
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Affiliation(s)
| | | | - Elain Fu
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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86
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87
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Li Y, Kumar N, Gopalakrishnan A, Ginocchio C, Manji R, Bythrow M, Lemieux B, Kong H. Detection and species identification of malaria parasites by isothermal tHDA amplification directly from human blood without sample preparation. J Mol Diagn 2013; 15:634-41. [PMID: 23800575 DOI: 10.1016/j.jmoldx.2013.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 04/05/2013] [Accepted: 05/15/2013] [Indexed: 11/26/2022] Open
Abstract
We report the clinical and analytical performance of an isothermal thermophilic helicase-dependent amplification assay for blood Plasmodium parasite detection and species-level identification. The assay amplifies the 18S rRNA gene fragment of all Plasmodium species and uses a species-specific probe and a pan-malarial probe to definitively identify Plasmodium falciparum from other infectious Plasmodium species. Amplicon-probe hybridization products are detected with a disposable dipstick enclosed in a cassette. With a pan-malarial-positive and P. falciparum-negative result, an additional test is performed to detect if the pan-malarial-positive band was the result of the presence of Plasmodium vivax. The assay uses only 2 μL of human whole blood directly for a 50-μL amplification reaction, without any pre-amplification processing. The clinical performance of the assay was validated using 88 samples from New York patients suspected of malaria or babesiosis. The overall sensitivity of the assay was 96.6% (95% CI, 87.3% to 99.4%), and the specificity was 100% (95% CI, 85.4% to 100%), compared with gold standard microscopy and a laboratory-developed molecular assay, respectively. The analytical sensitivity was 50 copies of DNA per assay or 200 parasites per microliter of blood, and the assay can detect samples with parasitemia levels <1%. This novel molecular diagnostic assay requires minimal laboratory instrumentation and uses un-processed blood as input; it can be readily performed in the field.
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Affiliation(s)
- Ying Li
- BioHelix Corporation, Beverly, Massachusetts, USA.
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88
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Mori Y, Kanda H, Notomi T. Loop-mediated isothermal amplification (LAMP): recent progress in research and development. J Infect Chemother 2013; 19:404-11. [PMID: 23539453 PMCID: PMC7088141 DOI: 10.1007/s10156-013-0590-0] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Indexed: 11/21/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an established technology that continues to attract the attention of researchers in many fields. Research and development efforts on LAMP technology in recent years have focused on two major areas; first, the study of its clinical application as an approved in vitro diagnostics tool in Japan and certain other countries; and second, research aimed at further simplifying the LAMP test process. This review provides an overview of the status of LAMP on these two topics by summarizing research work conducted, in the main, after our previous review article.
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Affiliation(s)
- Yasuyoshi Mori
- Eiken Chemical Co., Ltd, 1381-3 Shimoishigami, Ohtawara, Tochigi, Japan.
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89
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Huang S, Do J, Mahalanabis M, Fan A, Zhao L, Jepeal L, Singh SK, Klapperich CM. Low cost extraction and isothermal amplification of DNA for infectious diarrhea diagnosis. PLoS One 2013; 8:e60059. [PMID: 23555883 PMCID: PMC3610934 DOI: 10.1371/journal.pone.0060059] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/25/2013] [Indexed: 12/18/2022] Open
Abstract
In order to counter the common perception that molecular diagnostics are too complicated to work in low resource settings, we have performed a difficult sample preparation and DNA amplification protocol using instrumentation designed to be operated without wall or battery power. In this work we have combined a nearly electricity-free nucleic acid extraction process with an electricity-free isothermal amplification assay to detect the presence of Clostridium difficile (C. difficile) DNA in the stool of infected patients. We used helicase-dependent isothermal amplification (HDA) to amplify the DNA in a low-cost, thermoplastic reaction chip heated with a pair of commercially available toe warmers, while using a simple Styrofoam insulator. DNA was extracted from known positive and negative stool samples. The DNA extraction protocol utilized an air pressure driven solid phase extraction device run using a standard bicycle pump. The simple heater setup required no electricity or battery and was capable of maintaining the temperature at 65°C±2°C for 55 min, suitable for repeatable HDA amplification. Experiments were performed to explore the adaptability of the system for use in a range of ambient conditions. When compared to a traditional centrifuge extraction protocol and a laboratory thermocycler, this disposable, no power platform achieved approximately the same lower limit of detection (1.25×10(-2) pg of C. difficile DNA) while requiring much less raw material and a fraction of the lab infrastructure and cost. This proof of concept study could greatly impact the accessibility of molecular assays for applications in global health.
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Affiliation(s)
- Shichu Huang
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Jaephil Do
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Madhumita Mahalanabis
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Andy Fan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Lei Zhao
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Lisa Jepeal
- Department of Gastroenterology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Satish K. Singh
- Department of Gastroenterology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Medicine, VA Boston Health Care System, Boston, Massachusetts, United States of America
| | - Catherine M. Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, United States of America
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90
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Singleton J, Zentner C, Buser J, Yager P, LaBarre P, Weigl BH. Instrument-free exothermic heating with phase change temperature control for paper microfluidic devices. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2013; 8615:86150R. [PMID: 25426269 DOI: 10.1117/12.2005928] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Many infectious diseases, as well as some cancers, that affect global health are most accurately diagnosed through nucleic acid amplification and detection. There is a great need to simplify nucleic acid-based assay systems for use in global health in low-resource settings as well as in settings that do not have convenient access to laboratory staff and equipment such as doctors' offices and home care settings. In developing countries, unreliable electric power, inadequate supply chains, and lack of maintenance for complex diagnostic instruments are all common infrastructure shortfalls. Many elements of instrument-free, disposable, nucleic acid amplification assays have been demonstrated in recent years. However, the problem of instrument-free, low-cost, temperature-controlled chemical heating remains unsolved. In this paper we present the current status and results of work towards developing disposable, low-cost, temperature-controlled heaters designed to support isothermal nucleic acid amplification assays that are integrated with a two-dimensional paper network. Our approach utilizes the heat generated through exothermic chemical reactions and controls the heat through use of engineered phase change materials to enable sustained temperatures required for nucleic acid amplification. By selecting appropriate exothermic and phase change materials, temperatures can be controlled over a wide range, suitable for various isothermal amplification methods, and maintained for over an hour at an accuracy of +/- 1°C.
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Affiliation(s)
| | - Chris Zentner
- PATH, 2201 Westlake Ave., Suite 200, Seattle, WA, USA 98121
| | - Josh Buser
- Department of Bioengineering, University of Washington, Seattle, WA, USA 98195, Telephone: (206) 285-3500
| | - Paul Yager
- Department of Bioengineering, University of Washington, Seattle, WA, USA 98195, Telephone: (206) 285-3500
| | - Paul LaBarre
- PATH, 2201 Westlake Ave., Suite 200, Seattle, WA, USA 98121
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91
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KUBOTA R, LABARRE P, WEIGL BH, LI Y, HAYDOCK P, JENKINS DM. Molecular diagnostics in a teacup: Non-Instrumented Nucleic Acid Amplification (NINA) for rapid, low cost detection of Salmonella enterica. ACTA ACUST UNITED AC 2013; 58:1162-1168. [PMID: 25477717 PMCID: PMC4251779 DOI: 10.1007/s11434-012-5634-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report on the use of a novel non-instrumented platform to enable a Loop Mediated isothermal Amplification (LAMP) based assay for Salmonella enterica. Heat energy is provided by addition of a small amount (<150 g) of boiling water, and the reaction temperature is regulated by storing latent energy at the melting temperature of a lipid-based engineered phase change material. Endpoint classification of the reaction is achieved without opening the reaction tube by observing the fluorescence of sequence-specific FRET-based assimilating probes with a simple handheld fluorometer. At or above 22°C ambient temperature the non-instrumented devices could maintain reactions above a threshold temperature of 61°C for over 90 min—significantly longer than the 60 min reaction time. Using the simple format, detection limits were less than 20 genome copies for reactions run at ambient temperatures ranging from 8 to 36°C. When used with a pre-enrichment step and non-instrumented DNA extraction device, trace contaminations of Salmonella in milk close to 1 CFU/mL could be reliably detected. These findings illustrate that the non- instrumented amplification approach is a simple, viable, low-cost alternative for field-based food and agricultural diagnostics or clinical applications in developing countries.
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Affiliation(s)
- Ryo KUBOTA
- Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Diagenetics, Inc, Honolulu, HI 96822, USA
| | - Paul LABARRE
- Program for Appropriate Technologies in Health (PATH), Seattle, WA 98109, USA
| | - Bernhard H WEIGL
- Program for Appropriate Technologies in Health (PATH), Seattle, WA 98109, USA
| | - Yong LI
- Human Nutrition, Food, and Animal Science, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Paul HAYDOCK
- Blood Cell Storage Inc (BCSI), Seattle, WA 98109, USA
| | - Daniel M JENKINS
- Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Corresponding author: ()
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92
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Almassian DR, Cockrell LM, Nelson WM. Portable nucleic acid thermocyclers. Chem Soc Rev 2013; 42:8769-98. [DOI: 10.1039/c3cs60144g] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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93
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Abstract
Determining the microbiologic etiology of enteric infection remains an elusive goal. Conventional approaches, including culture, microscopy, and antigen-based tests have significant limitations such as limit of detection and the need for multiple procedures. Molecular diagnostics, especially PCR based tests, are rapidly changing research and practice in infectious diseases. Diarrheal disease, with its broad range of potential infectious etiologies, is well suited for multiplex molecular testing. This review highlights examples of currently employed molecular tests, as well as ways in which these tests can be applied in the future. The absence of a gold standard for the microbiologic cause of diarrhea means that the clinical significance of detected organisms may not always be clear. Conventional wisdom is that there should be one main pathogen causing diarrhea, however our thinking is challenged by increased detection of mixed infections. Thus, the successful incorporation of molecular diagnostics for diarrheal disease into practice will require both a careful understanding of the technical aspects and research to define their clinical utility.
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94
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Rohrman BA, Leautaud V, Molyneux E, Richards-Kortum RR. A lateral flow assay for quantitative detection of amplified HIV-1 RNA. PLoS One 2012; 7:e45611. [PMID: 23029134 PMCID: PMC3448666 DOI: 10.1371/journal.pone.0045611] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/23/2012] [Indexed: 11/18/2022] Open
Abstract
Although the accessibility of HIV treatment in developing nations has increased dramatically over the past decade, viral load testing to monitor the response of patients receiving therapy is often unavailable. Existing viral load technologies are often too expensive or resource-intensive for poor settings, and there is no appropriate HIV viral load test currently available at the point-of-care in low resource settings. Here, we present a lateral flow assay that employs gold nanoparticle probes and gold enhancement solution to detect amplified HIV RNA quantitatively. Preliminary results show that, when coupled with nucleic acid sequence based amplification (NASBA), this assay can detect concentrations of HIV RNA that match the clinically relevant range of viral loads found in HIV patients. The lateral flow test is inexpensive, simple and rapid to perform, and requires few resources. Our results suggest that the lateral flow assay may be integrated with amplification and sample preparation technologies to serve as an HIV viral load test for low-resource settings.
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Affiliation(s)
- Brittany A. Rohrman
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Veronica Leautaud
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Elizabeth Molyneux
- Paediatric Department, College of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
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95
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Wang S, Sarenac D, Chen MH, Huang SH, Giguel FF, Kuritzkes DR, Demirci U. Simple filter microchip for rapid separation of plasma and viruses from whole blood. Int J Nanomedicine 2012; 7:5019-28. [PMID: 23055720 PMCID: PMC3457680 DOI: 10.2147/ijn.s32579] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sample preparation is a significant challenge for detection and sensing technologies, since the presence of blood cells can interfere with the accuracy and reliability of virus detection at the nanoscale for point-of-care testing. To the best of our knowledge, there is not an existing on-chip virus isolation technology that does not use complex fluidic pumps. Here, we presented a lab-on-a-chip filter device to isolate plasma and viruses from unprocessed whole blood based on size exclusion without using a micropump. We demonstrated that viruses (eg, HIV) can be separated on a filter-based chip (2-μm pore size) from HIV-spiked whole blood at high recovery efficiencies of 89.9% ± 5.0%, 80.5% ± 4.3%, and 78.2% ± 3.8%, for viral loads of 1000, 10,000 and 100,000 copies/mL, respectively. Meanwhile, 81.7% ± 6.7% of red blood cells and 89.5% ± 2.4% of white blood cells were retained on 2 μm pore–sized filter microchips. We also tested these filter microchips with seven HIV-infected patient samples and observed recovery efficiencies ranging from 73.1% ± 8.3% to 82.5% ± 4.1%. These results are first steps towards developing disposable point-of-care diagnostics and monitoring devices for resource-constrained settings, as well as hospital and primary care settings.
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Affiliation(s)
- ShuQi Wang
- Bio-acoustic MEMS in Medicine Laboratory, Department of Medicine, Division of Biomedical Engineering, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Rohrman BA, Richards-Kortum RR. A paper and plastic device for performing recombinase polymerase amplification of HIV DNA. LAB ON A CHIP 2012; 12:3082-8. [PMID: 22733333 PMCID: PMC3569001 DOI: 10.1039/c2lc40423k] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Despite the importance of early diagnosis and treatment of HIV, only a small fraction of HIV-exposed infants in low- and middle-income countries are tested for the disease. The gold standard for early infant diagnosis, DNA PCR, requires resources that are unavailable in poor settings, and no point-of-care HIV DNA test is currently available. We have developed a device constructed of layers of paper, glass fiber, and plastic that is capable of performing isothermal, enzymatic amplification of HIV DNA. The device is inexpensive, small, light-weight, and easy to assemble. The device stores lyophilized enzymes, facilitates mixing of reaction components, and supports recombinase polymerase amplification in five steps of operation. Using commercially available lateral flow strips as a detection method, we demonstrate the ability of our device to amplify 10 copies of HIV DNA to detectable levels in 15 min. Our results suggest that our device, which is designed to be used after DNA extraction from dried-blood spots, may serve in conjunction with lateral flow strips as part of a point-of-care HIV DNA test to be used in low resource settings.
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97
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Design and development of an in-house multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV in plasma samples. IRANIAN JOURNAL OF MICROBIOLOGY 2012; 52:456-63. [PMID: 22783455 DOI: 10.1007/s12088-012-0271-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 04/26/2012] [Indexed: 01/12/2023]
Abstract
BACKGROUND AND OBJECTIVES HIV-1 and HCV infections are life threatening problems in patients who receive blood products. Serological methods have proven useful in detecting these infections, but there are setbacks that make it challenging to detect these infectious agents. By the advent of Nucleic Acid Testing (NAT) methods, especially in multiplex format, more precise detection is possible. MATERIALS AND METHODS We have developed a multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV. Primers were designed for highly conserved region of genome of each virus. Using these primers and standard plasmids, we determined the limit of detection, clinical and analytical specificity and sensitivity of the assay. Monoplex and multiplex RT-PCR were performed. RESULTS Analytical sensitivity was considered to be 100 and 200 copies/ml for HIV-1 and HCV, respectively. High concentration of one virus had no significant effect on the detection of the other one with low concentration. By analysis of 40 samples, clinical sensitivity of the assay was determined to be 97.5%. Using different viral and human genome samples, the specificity of the assay was evaluated to be 100%. CONCLUSIONS The aim of this study was to develop a reliable, rapid and cost effective method to detect HIV-1 and HCV simultaneously. Results showed that this simple and rapid method is perfectly capable of detecting two viruses in clinical samples.
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98
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Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: A review. Anal Chim Acta 2012; 733:1-15. [DOI: 10.1016/j.aca.2012.04.031] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 04/10/2012] [Accepted: 04/24/2012] [Indexed: 12/19/2022]
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99
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Abstract
PURPOSE OF REVIEW To provide evidence that HIV-1 RNA load can guide treatment-for-prevention interventions to mitigate the HIV epidemic. RECENT FINDINGS Some HIV-infected individuals maintain increased levels of HIV-1 RNA load after acute infection for an extended period of time, and can disproportionately contribute to the spread of HIV in the community. The recent HIV Prevention Trials Network 052 study has demonstrated 96% efficacy for initiation of early antiretroviral treatment (ART) in HIV-1 serodiscordant couples. SUMMARY The level of HIV-1 RNA load in plasma is the major biological predictor of virus transmission. HIV-infected individuals who maintain increased levels of HIV-1 RNA load, extended high viremics, can transmit virus at higher rates. Combinatorial ART decreases HIV replication, thus reducing rates of virus transmission. Identifying high viremics and placing them on ART seems an attractive strategy that has the potential to achieve both individual benefits by lowering risk for early onset of clinical AIDS and public health benefits by reducing HIV transmission. A key logistical challenge is to screen for high viremics among HIV-positive individuals. Efficacy of the modified treatment-for-prevention approach focused on high viremics is being evaluated in ongoing and upcoming clinical trials. If efficacious, such an approach could be used widely to mitigate and control the HIV epidemic.
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100
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Fu E, Yager P, Floriano PN, Christodoulides N, McDevitt JT. Perspective on diagnostics for global health. IEEE Pulse 2012; 2:40-50. [PMID: 22147068 DOI: 10.1109/mpul.2011.942766] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Elain Fu
- Department of Bioengineering, University of Washington, Washington, USA.
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