Optimization of Reverse Transcription Loop-Mediated Isothermal Amplification for In Situ Detection of SARS-CoV-2 in a Micro-Air-Filtration Device Format

The Coronavirus disease 2019 (COVID-19) pandemic has supercharged innovation in the field of molecular diagnostics and led to the exploration of systems that permit the autonomous identification of airborne infectious agents. Airborne virus detection is an emerging approach for determining exposure risk, although current methods limit intervention timeliness. Here, we explore reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for one-pot detection of Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) (SCV2) run on membrane filters suitable for micro-air-filtration of airborne viruses. We use a design of experiments statistical framework to establish the optimal additive composition for running RT-LAMP on membrane filters. Using SCV2 liquid spike-in experiments and fluorescence detection, we show that single-pot RT-LAMP on glass fiber filters reliably detected 0.10 50% tissue culture infectious dose (TCID50) SCV2 per reaction (3600 E-gene copies) and is an order of magnitude more sensitive than conventional RT-LAMP.

PicoGreen assay for nucleic acid quantification - Applications, challenges, and solutions

Various analytical methods and reagents have been employed for nucleic acid analysis in cells, biological fluids, and formulations. Standard techniques like gel electrophoresis and qRT-PCR are widely used for qualitative and quantitative nucleic acid analysis. However, these methods can be time-consuming and labor-intensive, with limitations such as inapplicability to small RNA at low concentrations and high costs associated with qRT-PCR reagents and instruments. As an alternative, PicoGreen (PG) has emerged as a valuable method for the quantitative analysis of nucleic acids. PG, a fluorescent dye, enables the quantitation of double-stranded DNA (dsDNA) or double-stranded RNA, including miRNA mimic and siRNA, in solution. It is also applicable to DNA and RNA analysis within cells using techniques like FACS and fluorescence microscopy. Despite its advantages, PG's fluorescence intensity is affected by various experimental conditions, such as pH, salts, and chemical reagents. This review explores the recent applications of PG as a rapid, cost-effective, robust, and accurate assay tool for nucleic acid quantification. We also address the limitations of PG and discuss approaches to overcome these challenges, recognizing the expanding range of its applications.

An Integrated Paper Microfluidic Device Based on Isothermal Amplification for Simple Sample-to-Answer Detection of Campylobacter jejuni

Campylobacter jejuni is recognized as the most common species in the genus Campylobacter that causes foodborne diseases. The main reservoirs harboring C. jejuni are poultry products, which are associated with most illnesses, creating a demand for effective detection methods to achieve point-of-need diagnostics. We developed an easy-to-use, hybrid paper/polymer-based microfluidic device that integrates paper-based DNA extraction, isothermal nucleic acid amplification, and lateral flow detection. Overall, the recombinase polymerase amplification (RPA) reaction was completed in 20 min and demonstrated 100% specificity to C. jejuni, including 2 reference strains and 6 wild strains isolated from the agroecosystem, 9 other Campylobacter subspecies strains, and 11 non-Campylobacter strains. The limit of detection (LOD) was 46 CFU/mL with DNA extracted on the cellulose paper. The sensitivity was reduced to 460 CFU/mL on the integrated hybrid paper/polymer-based microfluidic device. This device could detect C. jejuni spiked at concentrations ranging from 101 to 102 CFU/g in chicken meat after an enrichment of 5 to 10 h. For C. jejuni levels of >102 CFU/g, it managed to confirm positive results immediately, without bacterial enrichment. RPA reagents and primers remained stable on the paper platform at 22°C for 12 h. After lyophilization and storage on paper, the RPA reaction showed consistent sensitivity for 3 days, and the LOD was reduced to 103 CFU/mL when storage was extended to 25 days. The use of this hybrid paper/polymer-based microfluidic device enabled detection of Campylobacter in foods with high specificity and sensitivity, demonstrating its potential as a reliable point-of-need diagnostic platform for on-site conditions due to its low cost, portability, and simplicity. IMPORTANCE The global health and economic burden of Campylobacter prompts the development of novel detection techniques that can be implemented in resource-limited and on-site settings. This study described point-of-need identification of C. jejuni using a hybrid paper/polymer-based microfluidic device that is easy to operate. This device had high specificity and sensitivity toward C. jejuni and significantly reduced the total analysis time compared to conventional culture-based methods. Nucleic acid extraction was simplified from intensive pipetting to a paper dipstick, making it more convenient for use in the field as a promising tool for future routine surveillance and outbreak investigation.

A Multicomponent Nucleic Acid Enzyme-Cleavable Quantum Dot Nanobeacon for Highly Sensitive Diagnosis of Tuberculosis with the Naked Eye

Clinical tuberculosis (TB) screening and diagnosis are crucial for controlling the spread of this life-threatening infectious disease. In this work, a novel, rapid, and simple colorimetric detection platform for TB was developed based on a quantum dot-based nanobeacon (QD-NB) and multicomponent nucleic acid enzyme (MNAzyme). In the presence of target DNA (IS1081 gene fragment), the recombinase polymerase amplification (RPA) was performed and the amplicons were chemically DNA-denatured and then subjected to MNAzyme reaction. RNA-cleaving MNAzyme assembly included the recognition of target DNA and hybridization with a QD-NB fluorescence probe. Under the addition of Mg²⁺, the RNA-containing QD-NB as a cleavable substrate could be broken into two DNA fragments, leading to green fluorescence release due to their departure from a black hole quencher (BHQ2). The TB detection could be achieved with the naked eye under a portable and inexpensive UV flashlight. Our results demonstrated that QD-NB-based MNAzyme colorimetric assays improved the detection sensitivity by 1 order of magnitude compared with the detection using RPA. The limit of detection (LOD) of the visual reading was as low as 2 copies/μL (3.3 amol/L). Excellent specificity and reproducibility could also be achieved. Furthermore, the practical application of the colorimetric method for TB diagnosis was verified by 36 clinical TB patients and 20 healthy individuals. The developed QD-NB-based MNAzyme colorimetric assays provided a rapid, convenient, sensitive, and accurate alternative for clinical TB screening and diagnosis.

Point-of-care diagnostic tests for tuberculosis disease

Rapid diagnosis is one key pillar to end tuberculosis (TB). Point-of-care tests (POCTs) facilitate early detection, immediate treatment, and reduced transmission of TB disease. This Review evaluates current diagnostic assays endorsed by the World Health Organization and identifies the gaps between existing conventional tests and the ideal POCT. We discuss the commercial development of new rapid tests and research studies on nonsputum-based diagnostic biomarkers from both pathogen and host. Last, we highlight advances in integrated microfluidics technology that may aid the development of new POCTs.

Paper based microfluidics: A forecast toward the most affordable and rapid point-of-care devices

The microfluidic industry has evolved through years with acquired scientific knowledge from different, and already developed industries. Consequently, a wide range of materials like silicon from the electronic industry to all the way, silicone, from the chemical engineering industry, has been spotted to solve similar challenges. Although a typical microfluidic chip, fabricated from glass or polymer substrates offers definite benefits, however, paper-based microfluidic analytical devices (μPADs) possess numerous special benefits for practical implementation at a lower price. Owing to these features, in recent years, paper microfluidics has drawn immense interest from researchers in industry and academia alike. These devices have wider applications with advantages like lower cost, speedy detection, user-easiness, biocompatibility, sensitivity, and specificity etc. when compared to other microfluidic devices. Therefore, these sensitive but affordable devices fit themselves into point-of-care (POC) testing with features in demand like natural disposability, situational flexibility, and the capability to store and analyze the target at the point of requirement. Gradually, advancements in fabrication technologies, assay development techniques, and improved packaging capabilities, have contributed significantly to the real-time identification and health investigation through paper microfluidics; however, the growth has not been limited to the biomedical field; industries like electronics, energy storage and many more have expanded substantially. Here, we represent an overall state of the paper-based microfluidic technology by covering the fundamentals, working principles, different fabrication procedures, applications for various needs and then to make things more practical, the real-life scenario and practical challenges involved in launching a device into the market have been revealed. To conclude, recent contribution of μPADs in the 2020 pandemic and potential future possibilities have been reviewed.

A finger-driven disposable micro-platform based on isothermal amplification for the application of multiplexed and point-of-care diagnosis of tuberculosis

Tuberculosis (TB) remains the high-risk infectious pathogen that caused global pandemic and high mortality, particularly in the areas lack in health resources. Clinical TB screening and diagnosis are so far mainly conducted on limited types of commercial platforms, which are expensive and require skilled personnel. In this work, we introduced a low-cost and portable finger-driven microfluidic chip (named Fd-MC) based on recombinase polymerase amplification (RPA) for rapid on-site detection of TB. After injection of the pre-treated sample solution, the pre-packaged buffer was driven by the pressure generated by the finger-actuated operation to accomplish sequential processes of diagnosis in a fully isolated microchannel. An in-situ fluorescence strategy based on FAM-probe was implemented for on-chip results read-out though a hand-held UV lamp. Hence, the Fd-MC proved unique advantageous for avoiding the risk of infection or environmental contamination. In addition, the Fd-MC was designed for multiplexed detection, which is able to not only identify TB/non-TB infection, but also differentiate between human Mycobacterium tuberculosis and Mycobacterium bovis. The platform was verified in 37 clinical samples, statistically with 100% specificity and 95.2% sensitivity as compared to commercial real-time RPA. Overall, the proposed platform eliminates the need on external pumps and skilled personnel, holding promise to POC testing in the resource-limited area.

Fluorescent Semiconductor Nanorods for the Solid-Phase Polymerase Chain Reaction-Based, Multiplexed Gene Detection of Mycobacterium tuberculosis

The spread of infectious diseases with significantly high mortality rates can wreak devastating damage on global health systems and economies, underscoring the need for better disease diagnostic platforms. Solid-phase polymerase chain reaction (SP-PCR) potentially combines the advantages of conventional PCR-based diagnostics with the capability of multiplexed detection, given that the spatial separation between primers circumvents unwanted primer-primer interactions. However, the generally low efficiency of solid-phase amplification results in poor sensitivity and limits its use in detection schemes. We present an SP-PCR-based, multiplexed pulldown fluorescence assay for the detection of Mycobacterium tuberculosis (MTB), utilizing highly fluorescent oligonucleotide-functionalized CdSe/CdS and CdSe_1-xS_x/CdS nanorods (NRs) as multicolor hybridization probes. The large surface area of the NRs allows for their easy capture and pulldown, but without contributing significantly to the interparticle photon reabsorption when clustered at the pulldown sites. The NR nanoprobes were specifically designed to target the hotspot regions of the rpoB gene of MTB, which have been implicated in resistance to standard rifampicin treatment. The implementation of the semiconductor NRs as photostable multicolor fluorophores in a multiplexed SP-PCR-based detection scheme allowed for the identification of multiple hotspot regions with sub-picomolar levels of sensitivity and high specificity in artificial sputum. While this work demonstrates the utility of semiconductor NRs as highly fluorescent chromophores that can enable SP-PCR as a sensitive and accurate technique for multipathogen diagnostics, the flexible surface chemistry of the NRs should allow them to be applicable to a wide variety of detection motifs.

Long-term dry storage of enzyme-based reagents for isothermal nucleic acid amplification in a porous matrix for use in point-of-care diagnostic devices

Nucleic acid amplification test (NAAT)-based point-of-care (POC) devices are rapidly growing for use in low-resource settings. However, key challenges are the ability to store the enzyme-based reagents in dry form in the device and the long-term stability of those reagents at elevated temperatures, especially where ambient temperatures could be as high as 45 °C. Here, we describe a set of excipients including a combination of trehalose, polyethylene glycol and dextran, and a method for using them that allows long-term dry storage of enzyme-based reagents for an isothermal strand displacement amplification (iSDA) reaction in a porous matrix. Various porous materials, including nitrocellulose, cellulose, and glass fiber, were tested. Co-dried reagents for iSDA always included those that amplified the ldh1 gene in Staphylococcus aureus (a polymerase and a nicking enzyme, 4 primers, dNTPs and a buffer). Reagents also either included a capture probe and a streptavidin-Au label required for lateral flow (LF) detection after amplification, or a fluorescent probe used for real-time detection. The reagents showed the best stability in a glass fiber matrix when stored in the presence of 10% trehalose and 2.5% dextran. The reagents were stable for over a year at ∼22 °C as determined by lateral flow detection and gel electrophoresis. The reagents also exhibited excellent stability after 360 h at 45 °C; the assay still detected as few as 10 copies of ldh1 gene target by lateral flow detection, and 50 copies with real-time fluorescence detection. These results demonstrate the potential for incorporation of amplification reagents in dry form in point-of-care devices for use in a wide range of settings.

Loop-mediated isothermal amplification technique: principle, development and wide application in food safety

Food safety is a major and enduring challenge and has a profound impact on the quality of human life. Loop-mediated isothermal amplification (LAMP) is a relatively novel gene amplification method under isothermal conditions with rapidity, simplicity and high specificity. This review will describe the principles and development of the LAMP technique along with its advantages and disadvantages, such as LAMP integrated on classical microfluidic chips, paper-chips, electrochemical devices, nanomaterials and digital devices. Moreover, we will systematically and comprehensively review its applications in the field of food safety, such as in the detection of foodborne pathogens, allergens and organophosphorus pesticides and genetically modified organisms; finally its development trends in food safety will be discussed.

Developing a Point-of-Care Molecular Test to Detect SARS-CoV-2

There is a need for widespread testing in India to stop the spread of the novel coronavirus in the population. While RT-PCR is the recommended diagnostic technique, its use is limited to well-equipped laboratories due to the need for specialized instrumentation, reagents and trained personnel. Immunodiagnostic tests are not yet recommended by the WHO for diagnosing active infections. There is a strong need for developing point-of-care molecular tests. Based on our past experience with paperfluidic devices for diagnosing bacterial infections by molecular tests, we propose the development of a diagnostic test for COVID-19. As a platform technology, it could be adapted to other viral outbreaks in future.

Paper Stacks for Uniform Rehydration of Dried Reagents in Paper Microfluidic Devices

Spatially uniform reconstitution of dried reagents is critical to the function of paper microfluidic devices. Advancing fluid fronts in paper microfluidic devices drive (convect) and concentrate rehydrated reagents to the edges, causing steep chemical gradients and imperfect mixing. This largely unsolved problem in paper microfluidics is exacerbated by increasing device dimensions. In this article, we demonstrate that mixing of dried reagents with a rehydrating fluid in paper microfluidics may be significantly enhanced by stacking paper layers having different wicking rates. Compared to single-layer paper membranes, stacking reduced the “non-reactive area”, i.e. area in which the reconstituted reagents did not interact with the rehydrating fluid, by as much as 97% in large (8 cm × 2 cm) paper membranes. A paper stack was designed to collect ~0.9 ml liquid sample and uniformly mix it with dried reagents. Applications of this technology are demonstrated in two areas: (i) collection and dry storage of sputum samples for tuberculosis testing, and (ii) salivary glucose detection using an enzymatic assay and colorimetric readout. Maximizing the interaction of liquids with dried reagents is central to enhancing the performance of all paper microfluidic devices; this technique is therefore likely to find important applications in paper microfluidics.

A modular paper-and-plastic device for tuberculosis nucleic acid amplification testing in limited-resource settings

We present a prototype for conducting rapid, inexpensive and point-of-care-compatible nucleic acid amplification tests (NAATs) for tuberculosis (TB). The fluorescent isothermal paper-and-plastic NAAT (FLIPP-NAAT) uses paper-based loop mediated isothermal amplification (LAMP) for DNA detection. The cost of materials required to build a 12-test-zone device is $0.88 and the cost of reagents per reaction is $0.43. An inexpensive imaging platform enables filter-free fluorescence detection of amplified DNA using a cell-phone camera. FLIPP-NAAT can be operated by an untrained user and only requires a regular laboratory incubator as ancillary equipment. All reagents can be dry-stored in the device, facilitating storage and transportation without cold chains. The device design is modular and the assay demonstrated high specificity to Mycobacterium tuberculosis (Mtb), analytical sensitivity of the order of 10 copies of Mtb gDNA, and tolerance to complex samples. The clinical sensitivity and specificity of sputum-based FLIPP NAAT tests were 100% (zero false negatives) and 68.75% (five false positives), respectively (N = 30), using Xpert MTB/RIF assay as the reference standard. FLIPP-NAAT has the potential to provide affordable and accessible molecular diagnostics for TB in low- and middle-income countries, when used in conjunction with an appropriate sample preparation technique. Although demonstrated for the detection of TB, FLIPP-NAAT is a platform technology for amplification of any nucleic acid sequence.

Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing

In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.

LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification

Nucleic acid amplification for the detection of infectious diseases, food pathogens, or assessment of genetic disorders require a laboratory setting with specialized equipment and technical expertise. Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Other key advantages of LAMP are robustness and the production of pyrophosphate in the presence of the target gene, enabling to detect the reaction products using the naked eye. Polymerase inhibitors, presented in clinical samples, do not affect the amplification process, making LAMP suitable for a simple sample-to-answer diagnostic systems with simplified sample preparation. In this review, we discuss the trends in miniaturized LAMP techniques, such as microfluidic, paper-based, and digital with their advantages and disadvantages, especially for POC applications alongside our opinion of the future development of miniaturized LAMP.

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Introduction of loop mediated isothermal amplification (LAMP) and its principle.

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Classical microfluidics-based LAMP for DNA/RNA detection.

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Paper-based LAMP.

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Microfluidic-based digital LAMP.

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Future of microfluidic LAMP development.

Paper-based nucleic acid amplification tests for point-of-care diagnostics

There has been a recent resurgence in the use of paper as a substrate for developing point-of-care medical diagnostic tests, possibly triggered by expiring patents published in the 1990s. A hallmark of this resurgence has been the development of advanced shapes and structures made from paper to conduct multi-step fluidic operations using the wicking action of porous materials. Such devices indicate a distinct improvement over lateral flow immunoassays, which are restricted to conducting one-step operations. New developments in paper-based diagnostic devices have triggered interest in the development of paper-based point-of-care nucleic acid amplification tests (NAATs). NAATs can identify extremely low levels of specific nucleic acid sequences from clinical samples and are the most sensitive of all available tests for infectious disease diagnosis. Because traditional PCR-based NAATs require expensive instruments, the development of portable paper-based NAAT's has become an exciting field of research. This article aims to review and analyse the current state of development of paper-based NAATs. We project paper-based NAATs as miniaturized chemical processes and shed light on various schemes of operation used for converting the multiple steps of the chemical processes into paper microfluidic devices. We conclude by elaborating on the challenges that must be overcome in the near future so that progress can be made towards the development of fully functional and commercial paper-based NAATs.

A Paper Sensor Printed with Multifunctional Bio/Nano Materials

We report a paper-based aptasensor platform that uses two reaction zones and a connecting bridge along with printed multifunctional bio/nano materials to achieve molecular recognition and signal amplification. Upon addition of analyte to the first zone, a fluorescently labelled DNA or RNA aptamer is desorbed from printed graphene oxide, rapidly producing an initial fluorescence signal. The released aptamer then flows to the second zone where it reacts with printed reagents to initiate rolling circle amplification, generating DNA amplicons containing a peroxidase-mimicking DNAzyme, which produces a colorimetric readout that can be read in an equipment-free manner or with a smartphone. The sensor was demonstrated using an RNA aptamer for adenosine triphosphate (a bacterial marker) and a DNA aptamer for glutamate dehydrogenase (Clostridium difficile marker) with excellent sensitivity and specificity. These targets could be detected in spiked serum or feacal samples, demonstrating the potential for testing clinical samples.

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection

Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed.

Graphical Abstract

Thermal lysis and isothermal amplification of Mycobacterium tuberculosis H37Rv in one tube

Tuberculosis (TB) is a leading cause of high mortality rates in developing countries. Sample preparation is one of the major challenges in developing an inexpensive point-of-care device for rapid and confirmed detection of tuberculosis. Existing chemical and mechanical lysis methods are unsuitable for field applications, as they require intermediate wash steps, manual intervention or separate lysis equipment. We report a one-step reaction protocol (65°C and 60min) for the H37Rv strain of Mycobacterium tuberculosis that (i) completely disinfects the mycobacteria culture, (ii) lyses the cells and (iii) performs helicase dependent amplification on the extracted DNA. Our assay combines multiple functions in a single step, uses a dry heat bath and does not require any intermediate user intervention, which makes it suitable for use by minimally trained health workers at the point of care.