Integration of sample preparation with RNA-Amplification in a hand-held device for airborne virus detection

Research advances in microfluidic collection and detection of virus, bacterial, and fungal bioaerosols

Bioaerosols are airborne suspensions of fine solid or liquid particles containing biological substances such as viruses, bacteria, cellular debris, fungal spores, mycelium, and byproducts of microbial metabolism. The global Coronavirus disease 2019 (COVID-19) pandemic and the previous emergence of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and influenza have increased the need for reliable and effective monitoring tools for bioaerosols. Bioaerosol collection and detection have aroused considerable attention. Current bioaerosol sampling and detection techniques suffer from long response time, low sensitivity, and high costs, and these drawbacks have forced the development of novel monitoring strategies. Microfluidic technique is considered a breakthrough for high performance analysis of bioaerosols. In recent years, several emerging methods based on microfluidics have been developed and reported for collection and detection of bioaerosols. The unique advantages of microfluidic technique have enabled the integration of bioaerosol collection and detection, which has a higher efficiency over conventional methods. This review focused on the research progress of bioaerosol collection and detection methods based on microfluidic techniques, with special attention on virus aerosols and bacterial aerosols. Different from the existing reviews, this work took a unique perspective of the targets to be collected and detected in bioaerosols, which would provide a direct index of bioaerosol categories readers may be interested in. We also discussed integrated microfluidic monitoring system for bioaerosols. Additionally, the application of bioaerosol detection in biomedicine was presented. Finally, the current challenges in the field of bioaerosol monitoring are presented and an outlook given of future developments.

An all-in-one platform to deplete pathogenic bacteria for rapid and safe enrichment of plant-derived extracellular vesicles

Plant-derived extracellular vesicles (PDEVs) have exhibited several advantages, such as high biocompatibility, improvement of skin conditions, and the prevention of skin aging. However, traditional methods of extraction for plant substances, such as heating under reflux or solvent extraction, are complicated, time-consuming, and low in purity. Accordingly, a simple and efficient platform is necessary for purely isolating natural substances from plants. In this study, we report a newly designed platform for removing impurities to purify PDEVs. The proposed platform comprises three parts: (i) inflow of samples, (ii) depletion of impurities, and (iii) collection of PDEVs. The platform is designed to flow from top to bottom using gravity without the need for electric components. The platform allows the delimitation of impurities, such as the pathogenic bacteria in PDEVs, by capturing magnetic beads coated with Concanavalin A (Con A). We validate the practicality of our platform using extracellular vesicles derived from liquorice (LdEVs). Notably, the LdEVs purified using the Con A-coated magnetic beads provide better cell uptake and wound recovery than the commercialized extract LdEVs. This highlights the therapeutic potential of fresh LdEVs purified using our platform, particularly in preventing skin aging. The findings of this study hold significant practical implications for the cosmeceutical and therapeutic field, providing a promising approach for the extraction and purification of natural substances from plants to harness their benefits effectively.

Celebrating the 30th anniversary of a pioneering microfluidics paper

We mark the 30th anniversary of the Science paper by Harrison et al. that is often credited for helping establish microfluidics as a research field.

Sensitive and highly rapid electrochemical measurement of airborne coronaviruses through condensation-based direct impaction onto carbon nanotube-coated porous paper working electrodes

Rapid detection of indoor airborne viruses is critical to prevent the spread of respiratory diseases. Herein, we present sensitive, highly rapid electrochemical measurement of airborne coronaviruses through condensation-based direct impaction onto antibody-immobilized, carbon nanotube-coated porous paper working electrodes (PWEs). Carboxylated carbon nanotubes are drop-cast on paper fibers to make three-dimensional (3D) porous PWEs. These PWEs have higher active surface area-to-volume ratios and electron transfer characteristics than conventional screen-printed electrodes. The limit of detection and detection time of the PWEs for liquid-borne coronaviruses OC43 are 65.7 plaque-forming units (PFU)/mL and 2 min, respectively. The PWEs showed sensitive and rapid detection of whole coronaviruses, which can be ascribed to the 3D porous electrode structure of the PWEs. Moreover, water molecules condense on airborne virus particles during air sampling, and these water-encapsulated virus particles (<4 µm) are impacted on the PWE for direct measurement without virus lysis and elution. The whole detection takes ∼10 min, including air sampling, at virus concentrations of 1.8 and 11.5 PFU/L of air, which can be due to the highly enriching and minimally damaging virus capture on a soft and porous PWE, demonstrating the potential for the rapid and low-cost airborne virus monitoring system.

Mayaro virus detection by integrating sample preparation with isothermal amplification in portable devices

Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus that causes clinical symptoms similar to those caused by Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV). To differentiate MAYV from these viruses diagnostically, we have developed a portable device that integrates sample preparation with real-time, reverse-transcription, loop-mediated isothermal amplification (rRT-LAMP). First, we designed a rRT-LAMP assay targeting MAYV's non-structural protein (NS1) gene and determined the limit of detection of at least 10 viral genome equivalents per reaction. The assay was specific for MAYV, without cross-reactions with CHIKV, DENV, or ZIKV. The rRT-LAMP assay was integrated with a sample preparation device (SPD) wherein virus lysis and RNA enrichment/purification were carried out on the spot, without requiring pipetting, while subsequent real-time amplification device (RAD) enables virus detection at the point of care (POC). The functions of our platform were demonstrated using purified MAYV RNA or blood samples containing viable viruses. We have used the devices for detection of MAYV in as short as 13 min, with limit of detection to as low as 10 GEs/reaction.

Molecular testing devices for on-site detection of E. coli in water samples

Escherichia coli (E. coli) cells are present in fecal materials that can be the main source for disease-causing agents in water. As a result, E. coli is recommended as a water quality indicator. We have developed an innovative platform to detect E. coli for monitoring water quality on-site by integrating paper-based sample preparation with nucleic acid isothermal amplification. The platform carries out bacterial lysis and DNA enrichment onto a paper pad through ball-based valves for fluid control, with no need of laboratory equipment, followed by loop-mediated isothermal amplification (LAMP) in a battery-operated coffee mug, and colorimetric detection. We have used the platform to detect E. coli in environmental water samples in about 1 h, with a limit of quantitation of 0.2 CFU/mL, and 3 copies per reaction. The platform was confirmed for detecting multiple E. coli strains, and for water samples of different salt concentrations. We validated the functions of the platform by analyzing recreational water samples collected near the Atlantic Ocean that contain different concentrations of salt and bacteria.

Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens

From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.

High enrichment and near real-time quantification of airborne viruses using a wet-paper-based electrochemical immunosensor under an electrostatic field

Conventional airborne virus measurement usually requires appreciable sampling and detection times. Viral aerosols should also be collected or prepared in a liquid medium whose volume typically ranges from milliliters to tens of milliliters; hence, many sampling and detection steps need to be taken with the unit horizontal or immobile. Moreover, viral aerosols need to be sufficiently enriched, which makes real-time monitoring difficult. Herein, we present a near real-time enrichment and quantification system of airborne viruses that consists of a wet-paper-based electrochemical immunosensor with a gel electrolyte and a modified electrostatic particle concentrator. A small amount of phosphate-buffered saline flowed on the electrode, which resulted in sensor electrodes that are barely wet (covered in a thin buffer film measuring several micrometers) to ensure antigen-antibody interaction and the removal of non-target particles on the electrode surface. This system ensures that airborne viruses are highly enriched on the working electrode of the immunosensor, and it is possible to measure the MS2 virus particle concentrations every 10 min for 60 min stably and selectively against non-target airborne viruses and bacteria at horizontal and tilted measurement configurations. This system thus has the potential to be used in the real-time mobile monitoring of airborne microorganisms.

Efficient measurement of airborne viable viruses using the growth-based virus aerosol concentrator with high flow velocities

Growth tube collectors (GTCs) are used to sample virus aerosols because of their superior viable virus recovery among air samplers. However, a major limitation of such samplers is that they operate at low flow rates compared to many inertia-based air samplers. Herein, we demonstrated efficient measurements of airborne MS2 and T3 viruses using a GTC that can implement high flow velocities for higher flow rates per tube, which we refer to as the growth-based virus aerosol concentrator (GVC), via qPCR and the plaque assay technique. The GVC exhibited a flow rate of up to 6 L/min, where the average sampling flow velocity was 5.09 m/s, 22 times higher than those used in the GTCs, for a single tube with a diameter of 5 mm. The count median diameter of the size-increased particles at the exit of the initiator was measured to be 1.44 µm at 6 L/min, considerably smaller than those observed in conventional GTCs. Nevertheless, the measurement of airborne MS2 and T3 viruses using the GVC showed a high concentration (high enrichment ratio of 109,458 at 10-min sampling) of viruses in a sampling medium, with a high viable virus percentage (> 90%) and physical collection efficiency (> 90%) at 6 L/min, which shows the potential for rapid on-site detection of airborne viruses.

Label- and enzyme-free plasmon-enhanced single molecule fluorescence detection of HIV DNA fragments based on a catalytic hairpin assembly

We developed a label- and enzyme-free single molecule fluorescence counting strategy for HIV DNA fragments detection. The nucleic acid biosensor consists of a 5' terminal connected with a triangular gold nanoplate, 3' terminal rich in guanine hairpin probe (HP1) and a hairpin probe HP2 complementary to the partial sequence of HP1. Without the existence of the target DNA, the DNA fragment rich in the guanine region is locked in a hairpin structure and cannot form a G-quadruplex, hence NMM exhibits a low fluorescence signal. When the target DNA exists, the hairpin assembly will trigger a strand displacement amplification reaction that produces a great number of G-quadruplexes, and the fluorescence brightness of NMM will be enhanced. The plasmon resonance effect of the triangular gold nanoplates will further amplify the fluorescence signal. This method can analyze the target DNA with high sensitivity and selectivity, and the detection limit is 0.83 fM. The analysis of the HIV DNA fragments in diluted human serum samples was successfully achieved, and the recovery rate was 92%-104%. Because of its easy operation and low cost, it has broad development potential in biochemical analysis and clinical applications.

A Valve-Enabled Sample Preparation Device with Isothermal Amplification for Multiplexed Virus Detection at the Point-of-Care

Early and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses at the point-of-care is crucial for reducing disease transmission during the current pandemic and future flu seasons. To prepare for potential cocirculation of these two viruses, we report a valve-enabled, paper-based sample preparation device integrated with isothermal amplification for their simultaneous detection. The device incorporates (1) virus lysis and RNA enrichment, enabled by ball-based valves for sequential delivery of reagents with no pipet requirement, (2) reverse transcription loop-mediated isothermal amplification, carried out in a coffee mug, and (3) colorimetric detection. We have used the device for simultaneously detecting inactivated SARS-CoV-2 and influenza A H1N1 viruses in 50 min, with limits of detection at 2 and 6 genome equivalents, respectively. The device was further demonstrated to detect both viruses in environmental samples.

Recent advancements in the measurement of pathogenic airborne viruses

Air-transmissible pathogenic viruses, such as influenza viruses and coronaviruses, are some of the most fatal strains and spread rapidly by air, necessitating quick and stable measurements from sample air volumes to prevent further spread of diseases and to take appropriate steps rapidly. Measurements of airborne viruses generally require their collection into liquids or onto solid surfaces, with subsequent hydrosolization and then analysis using the growth method, nucleic-acid-based techniques, or immunoassays. Measurements can also be performed in real time without sampling, where species-specific determination is generally disabled. In this review, we introduce some recent advancements in the measurement of pathogenic airborne viruses. Air sampling and measurement technologies for viral aerosols are reviewed, with special focus on the effects of air sampling on damage to the sampled viruses and their measurements. Measurement of pathogenic airborne viruses is an interdisciplinary research area that requires understanding of both aerosol technology and biotechnology to effectively address the issues. Hence, this review is expected to provide some useful guidelines regarding appropriate air sampling and virus detection methods for particular applications.