Smartphone-based multiplex 30-minute nucleic acid test of live virus from nasal swab extract

Updated ACVIM consensus statement on equine herpesvirus-1

Equine herpesvirus-1 (EHV-1) is a highly prevalent and frequently pathogenic infection of equids. The most serious clinical consequences of infection are abortion and equine herpesvirus myeloencephalopathy (EHM). The previous consensus statement was published in 2009 and considered pathogenesis, strain variation, epidemiology, diagnostic testing, vaccination, outbreak prevention and control, and treatment. A recent survey of American College of Veterinary Internal Medicine large animal diplomates identified the need for a revision to this original consensus statement. This updated consensus statement is underpinned by 4 systematic reviews that addressed key questions concerning vaccination, pharmaceutical treatment, pathogenesis, and diagnostic testing. Evidence for successful vaccination against, or effective treatment of EHV-1 infection was limited, and improvements in experimental design and reporting of results are needed in future studies of this important disease. This consensus statement also updates the topics considered previously in 2009.

Advancements in magnetic nanoparticle-based biosensors for point-of-care testing

The significance of point-of-care testing (POCT) in early clinical diagnosis and personalized patient care is increasingly recognized as a crucial tool in reducing disease outbreaks and improving patient survival rates. Within the realm of POCT, biosensors utilizing magnetic nanoparticles (MNPs) have emerged as a subject of substantial interest. This review aims to provide a comprehensive evaluation of the current landscape of POCT, emphasizing its growing significance within clinical practice. Subsequently, the current status of the combination of MNPs in the Biological detection has been presented. Furthermore, it delves into the specific domain of MNP-based biosensors, assessing their potential impact on POCT. By combining existing research and spotlighting pivotal discoveries, this review enhances our comprehension of the advancements and promising prospects offered by MNP-based biosensors in the context of POCT. It seeks to facilitate informed decision-making among healthcare professionals and researchers while also promoting further exploration in this promising field of study.

Fast detection of bacterial gut pathogens on miniaturized devices: an overview

INTRODUCTION

Gut microbes pose challenges like colon inflammation, deadly diarrhea, antimicrobial resistance dissemination, and chronic disease onset. Development of early, rapid and specific diagnosis tools is essential for improving infection control. Point-of-care testing (POCT) systems offer rapid, sensitive, low-cost and sample-to-answer methods for microbe detection from various clinical and environmental samples, bringing the advantages of portability, automation, and simple operation.

AREAS COVERED

Rapid detection of gut microbes can be done using a wide array of techniques including biosensors, immunological assays, electrochemical impedance spectroscopy, mass spectrometry and molecular biology. Inclusion of Internet of Things, machine learning, and smartphone-based point-of-care applications is an important aspect of POCT. In this review, the authors discuss various fast diagnostic platforms for gut pathogens and their main challenges.

EXPERT OPINION

Developing effective assays for microbe detection can be complex. Assay design must consider factors like target selection, real-time and multiplex detection, sample type, reagent stability and storage, primer/probe design, and optimizing reaction conditions for accuracy and sensitivity. Mitigating these challenges requires interdisciplinary collaboration among scientists, clinicians, engineers, and industry partners. Future efforts are essential to enhance sensitivity, specificity, and versatility of POCT systems for gut microbe detection and quantification, advancing infectious disease diagnostics and management.

Mobile Apps for COVID-19 Detection and Diagnosis for Future Pandemic Control: Multidimensional Systematic Review

BACKGROUND

In the modern world, mobile apps are essential for human advancement, and pandemic control is no exception. The use of mobile apps and technology for the detection and diagnosis of COVID-19 has been the subject of numerous investigations, although no thorough analysis of COVID-19 pandemic prevention has been conducted using mobile apps, creating a gap.

OBJECTIVE

With the intention of helping software companies and clinical researchers, this study provides comprehensive information regarding the different fields in which mobile apps were used to diagnose COVID-19 during the pandemic.

METHODS

In this systematic review, 535 studies were found after searching 5 major research databases (ScienceDirect, Scopus, PubMed, Web of Science, and IEEE). Of these, only 42 (7.9%) studies concerned with diagnosing and detecting COVID-19 were chosen after applying inclusion and exclusion criteria using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) protocol.

RESULTS

Mobile apps were categorized into 6 areas based on the content of these 42 studies: contact tracing, data gathering, data visualization, artificial intelligence (AI)-based diagnosis, rule- and guideline-based diagnosis, and data transformation. Patients with COVID-19 were identified via mobile apps using a variety of clinical, geographic, demographic, radiological, serological, and laboratory data. Most studies concentrated on using AI methods to identify people who might have COVID-19. Additionally, symptoms, cough sounds, and radiological images were used more frequently compared to other data types. Deep learning techniques, such as convolutional neural networks, performed comparatively better in the processing of health care data than other types of AI techniques, which improved the diagnosis of COVID-19.

CONCLUSIONS

Mobile apps could soon play a significant role as a powerful tool for data collection, epidemic health data analysis, and the early identification of suspected cases. These technologies can work with the internet of things, cloud storage, 5th-generation technology, and cloud computing. Processing pipelines can be moved to mobile device processing cores using new deep learning methods, such as lightweight neural networks. In the event of future pandemics, mobile apps will play a critical role in rapid diagnosis using various image data and clinical symptoms. Consequently, the rapid diagnosis of these diseases can improve the management of their effects and obtain excellent results in treating patients.

Microfluidic-assisted integrated nucleic acid test strips for POCT

Numerous diseases have posed significant threats to public health, notably the global pandemic of COVID-19, resulting in widespread devastation due to its high infectivity and severity. The nucleic acid lateral flow assay (NALFA) addresses challenges of complexity, cost, and time associated with traditional assays, offering a reliable platform for rapid and precise nucleic acid target detection. NALFA is gaining prominence as a point-of-care testing (POCT) technique, thanks to its user-friendly operation and rapid results. Nevertheless, conventional NALFA relies on specialized technicians and involves labor-intensive steps like DNA extraction and PCR processes, impeding its efficiency. To overcome these limitations, integrating NALFA with microfluidic technology, widely employed in rapid field detection, holds promise. This review comprehensively outlines prevailing strategies for integrating NALFA, encompassing both research initiatives and commercial applications. Addressing the bottleneck of nucleic acid amplification as a rate-limiting step, the review delves into progress in amplification-free NALFA and highlights prevalent signal amplification techniques. Ultimately, the review outlines the future prospect of integrated NALFA development, capturing the technology's evolution and providing valuable insights for academic and commercial endeavors.

A Point-of-Care Testing Device Utilizing Graphene-Enhanced Fiber Optic SPR Sensor for Real-Time Detection of Infectious Pathogens

Timely detection of highly infectious pathogens is essential for preventing and controlling public health risks. However, most traditional testing instruments require multiple tedious steps and ultimately testing in hospitals and third-party laboratories. The sample transfer process significantly prolongs the time to obtain test results. To tackle this aspect, a portable fiber optic surface plasmon resonance (FO-SPR) device was developed for the real-time detection of infectious pathogens. The portable device innovatively integrated a compact FO-SPR sensing component, a signal acquisition and processing system, and an embedded power supply unit. A gold-plated fiber is used as the FO-SPR sensing probe. Compared with traditional SPR sensing systems, the device is smaller size, lighter weight, and higher convenience. To enhance the detection capacity of pathogens, a monolayer graphene was coated on the sensing region of the FO-SPR sensing probe. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was used to evaluate the performance of the portable device. The device can accurately detect the SARS-CoV-2 spike S1 protein in phosphate-buffered saline (PBS) and artificial saliva within just 20 min, and the device successfully detected cultured SARS-CoV-2 virus. Furthermore, the FO-SPR probe has long-term stability, remaining stable for up to 8 days. It could distinguish between the SARS-CoV-2 spike protein and the MERS-CoV spike protein. Hence, this FO-SPR device provides reliable, rapid, and portable access to test results. It provides a promising point-of-care testing (POCT) tool for on-site screening of infectious pathogens.

An immobilization-free electrochemical biosensor based on CRISPR/Cas13a and FAM-RNA-MB for simultaneous detection of multiple pathogens

To better respond to biosecurity issues, we need to build good technology and material reserves for pathogenic microorganism screening. Here, we designed an electrochemical/optical signal probe with a common fluorophore and an electrochemically active group, breaking the previous perception that the signal probe is composed of a fluorophore and a quenching group and realizing the response of three signals: electrochemistry, fluorescence, and direct observation. Then, we proposed a homogeneous electrochemical nucleic acid detection system based on CRISPR/Cas named "HELEN-CR" by integrating free electrochemical/optical signal probes and Cas13a cleavage, achieving a limit of detection of 1 pM within 25 min. To improve the detection sensitivity, we applied recombinase polymerase amplification to amplify the target nucleic acid, achieving a limit of detection of 30 zM within 45 min. Complemented by our self-developed multi-chamber microfluidic chip and portable electrochemical instrument, simultaneous detection of multiple pathogens can be achieved within 50 min, facilitating minimally trained personnel to obtain detection results quickly in a difficult environment. This study proposes a simple, scalable, and general idea and solution for the rapid detection of pathogenic microorganisms and biosecurity monitoring.

Investigation of DNA Hybridization on Nano-Structured Plasmonic Surfaces for Identifying Nasopharyngeal Viruses

Recently, studies have revealed that human herpesvirus 4 (HHV-4), also known as the Epstein-Barr virus, might be associated with the severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Compared to SARS-CoV-2 infection alone, patients coinfected with SARS-CoV-2 and HHV-4 had higher risks of fever, inflammation, and even death, thus, confirming that HHV-4/SARS-CoV-2 coinfection in patients could benefit from clinical investigation. Although several intelligent devices can simultaneously discern multiple genes related to SARS-CoV-2, most operate via label-based detection, which restricts them from directly measuring the product. In this study, we developed a device that can replicate and detect SARS-CoV-2 and HHV-4 DNA. This device can conduct a duplex polymerase chain reaction (PCR) in a microfluidic channel and detect replicates in a non-labeled manner through a plasmonic-based sensor. Compared to traditional instruments, this device can reduce the required PCR time by 55% while yielding a similar amount of amplicon. Moreover, our device's limit of detection (LOD) reached 100 fg/mL, while prior non-labeled sensors for SARS-CoV-2 detection were in the range of ng/mL to pg/mL. Furthermore, the device can detect desired genes by extracting cells artificially infected with HHV-4/SARS-CoV-2. We expect that this device will be able to help verify HHV-4/SARS-CoV-2 coinfected patients and assist in the evaluation of practical treatment approaches.

Multiplex solid-phase RPA coupled CRISPR-based visual detection of SARS-CoV-2

The COVID-19 pandemic has presented a significant challenge to the world's public health and led to over 6.9 million deaths reported to date. A rapid, sensitive, and cost-effective point-of-care virus detection device is essential for the control and surveillance of the contagious severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. The study presented here aimed to demonstrate a solid-phase isothermal recombinase polymerase amplification coupled CRISPR-based (spRPA-CRISPR) assay for on-chip multiplexed, sensitive and visual COVID-19 DNA detection. The assay targets the SARS-CoV-2 structure protein encoded genomes and can simultaneously detect two specific genes without cross-interaction. The amplified target sequences were immobilized on the one-pot device surface and detected using the mixed Cas12a-crRNA collateral cleavage of reporter-released fluorescent signal when specific genes were recognized. The endpoint signal can be directly visualized for rapid detection of COVID-19. The system was tested with samples of a broad range of concentrations (20 to 2 × 104 copies) and showed analytical sensitivity down to 20 copies per microliter. Furthermore, a low-cost blue LED flashlight (~$12) was used to provide a visible SARS-CoV-2 detection signal of the spRPA-CRISPR assay which could be purchased online easily. Thus, our platform provides a sensitive and easy-to-read multiplexed gene detection method that can specifically identify low concentration genes.

Engineering Materials and Devices for the Prevention, Diagnosis, and Treatment of COVID-19 and Infectious Diseases

Following the global spread of COVID-19, scientists and engineers have adapted technologies and developed new tools to aid in the fight against COVID-19. This review discusses various approaches to engineering biomaterials, devices, and therapeutics, especially at micro and nano levels, for the prevention, diagnosis, and treatment of infectious diseases, such as COVID-19, serving as a resource for scientists to identify specific tools that can be applicable for infectious-disease-related research, technology development, and treatment. From the design and production of equipment critical to first responders and patients using three-dimensional (3D) printing technology to point-of-care devices for rapid diagnosis, these technologies and tools have been essential to address current global needs for the prevention and detection of diseases. Moreover, advancements in organ-on-a-chip platforms provide a valuable platform to not only study infections and disease development in humans but also allow for the screening of more effective therapeutics. In addition, vaccines, the repurposing of approved drugs, biomaterials, drug delivery, and cell therapy are promising approaches for the prevention and treatment of infectious diseases. Following a comprehensive review of all these topics, we discuss unsolved problems and future directions.

Rapid On-Site Detection of SARS-CoV-2 Using RT-LAMP Assay with a Portable Low-Cost Device

Emerging infectious diseases pose a serious threat to human health and affect social stability. In recent years, the epidemic situation of emerging infectious diseases is very serious; among these infectious diseases, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected many countries and regions in a short time. The prevention and treatment of these diseases require rapid on-site detection methods. However, the common detection method, RT-PCR, requires expensive instruments, complex operations, and professional operators. Here, we developed a portable low-cost assay for rapid on-site detection of viral nucleic acid using reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The SARS-CoV-2 RNA can be successfully amplified within 15 min in a thermos, and the detection result is read rapidly in a portable low-cost device with a sensitivity of 10⁰ copies/µL. The portable low-cost device consists of a black box, a laser or LED and a filter, costing only a few cents. The rapid on-site detection method can provide strong support for the control of biological threats such as infectious diseases. It is also an emergency detection method for low-resource settings, relieving the huge pressure on health care.

Nanotechnology-Based Diagnostics for Diseases Prevalent in Developing Countries: Current Advances in Point-of-Care Tests

The introduction of point-of-care testing (POCT) has revolutionized medical testing by allowing for simple tests to be conducted near the patient's care point, rather than being confined to a medical laboratory. This has been especially beneficial for developing countries with limited infrastructure, where testing often involves sending specimens off-site and waiting for hours or days for results. However, the development of POCT devices has been challenging, with simplicity, accuracy, and cost-effectiveness being key factors in making these tests feasible. Nanotechnology has played a crucial role in achieving this goal, by not only making the tests possible but also masking their complexity. In this article, recent developments in POCT devices that benefit from nanotechnology are discussed. Microfluidics and lab-on-a-chip technologies are highlighted as major drivers of point-of-care testing, particularly in infectious disease diagnosis. These technologies enable various bioassays to be used at the point of care. The article also addresses the challenges faced by these technological advances and interesting future trends. The benefits of point-of-care testing are significant, especially in developing countries where medical care is shifting towards prevention, early detection, and managing chronic conditions. Infectious disease tests at the point of care in low-income countries can lead to prompt treatment, preventing infections from spreading.

Moving toward smart biomedical sensing

The development of novel biomedical sensors as highly promising devices/tools in early diagnosis and therapy monitoring of many diseases and disorders has recently witnessed unprecedented growth; more and faster than ever. Nonetheless, on the eve of Industry 5.0 and by learning from defects of current sensors in smart diagnostics of pandemics, there is still a long way to go to achieve the ideal biomedical sensors capable of meeting the growing needs and expectations for smart biomedical/diagnostic sensing through eHealth systems. Herein, an overview is provided to highlight the importance and necessity of an inevitable transition in the era of digital health/Healthcare 4.0 towards smart biomedical/diagnostic sensing and how to approach it via new digital technologies including Internet of Things (IoT), artificial intelligence, IoT gateways (smartphones, readers), etc. This review will bring together the different types of smartphone/reader-based biomedical sensors, which have been employing for a wide variety of optical/electrical/electrochemical biosensing applications and paving the way for future eHealth diagnostic devices by moving towards smart biomedical sensing. Here, alongside highlighting the characteristics/criteria that should be met by the developed sensors towards smart biomedical sensing, the challenging issues ahead are delineated along with a comprehensive outlook on this extremely necessary field.

Multiplexed Ultrasensitive Sample-to-Answer RT-LAMP Chip for the Identification of SARS-CoV-2 and Influenza Viruses

Prompt on-site diagnosis of SARS-CoV-2 with other respiratory infections will have minimized the global impact of the COVID-19 pandemic through rapid, effective management. However, no such multiplex point-of-care (POC) chip has satisfied a suitable sensitivity of gold-standard nucleic acid amplification tests (NAATs). Here, a rapid multiplexed ultrasensitive sample-to-answer loop-mediated isothermal amplification (MUSAL) chip operated by simple LED-driven photothermal amplification to detect six targets from single-swab sampling is presented. First, the MUSAL chip allows ultrafast on-chip sample preparation with ≈500-fold preconcentration at a rate of 1.2 mL min^-1 . Second, the chip enables contamination-free amplification using autonomous target elution into on-chip reagents by photothermal activation. Finally, the chip accomplishes multiplexed on-chip diagnostics of SARS-CoV-2 and influenza viruses with a limit of detection (LoD) of 0.5 copies µL^-1 . The rapid, ultrasensitive, cost-effective sample-to-answer chip with a multiplex capability will allow timely management of various pandemics situations that may be faced shortly.

Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems

As nucleic acid testing is playing a vital role in increasingly many research fields, the need for rapid on-site testing methods is also increasing. The test procedure often consists of three steps: Sample preparation, amplification, and detection. This review covers recent advances in on-chip methods for each of these three steps and explains the principles underlying related methods. The sample preparation process is further divided into cell lysis and nucleic acid purification, and methods for the integration of these two steps on a single chip are discussed. Under amplification, on-chip studies based on PCR and isothermal amplification are covered. Three isothermal amplification methods reported to have good resistance to PCR inhibitors are selected for discussion due to their potential for use in direct amplification. Chip designs and novel strategies employed to achieve rapid extraction/amplification with satisfactory efficiency are discussed. Four detection methods providing rapid responses (fluorescent, optical, and electrochemical detection methods, plus lateral flow assay) are evaluated for their potential in rapid on-site detection. In the final section, we discuss strategies to improve the speed of the entire procedure and to integrate all three steps onto a single chip; we also comment on recent advances, and on obstacles to reducing the cost of chip manufacture and achieving mass production. We conclude that future trends will focus on effective nucleic acid extraction via combined methods and direct amplification via isothermal methods.

Ferrobotic swarms enable accessible and adaptable automated viral testing

Expanding our global testing capacity is critical to preventing and containing pandemics^1–9. Accordingly, accessible and adaptable automated platforms that in decentralized settings perform nucleic acid amplification tests resource-efficiently are required^10–14. Pooled testing can be extremely efficient if the pooling strategy is based on local viral prevalence^15–20; however, it requires automation, small sample volume handling and feedback not available in current bulky, capital-intensive liquid handling technologies^21–29. Here we use a swarm of millimetre-sized magnets as mobile robotic agents (‘ferrobots’) for precise and robust handling of magnetized sample droplets and high-fidelity delivery of flexible workflows based on nucleic acid amplification tests to overcome these limitations. Within a palm-sized printed circuit board-based programmable platform, we demonstrated the myriad of laboratory-equivalent operations involved in pooled testing. These operations were guided by an introduced square matrix pooled testing algorithm to identify the samples from infected patients, while maximizing the testing efficiency. We applied this automated technology for the loop-mediated isothermal amplification and detection of the SARS-CoV-2 virus in clinical samples, in which the test results completely matched those obtained off-chip. This technology is easily manufacturable and distributable, and its adoption for viral testing could lead to a 10–300-fold reduction in reagent costs (depending on the viral prevalence) and three orders of magnitude reduction in instrumentation cost. Therefore, it is a promising solution to expand our testing capacity for pandemic preparedness and to reimagine the automated clinical laboratory of the future.

A handheld printed circuit board-based programmable platform using ferrobots can perform the complex, laboratory-equivalent procedures involved in multiplexed and pooled nucleic acid amplification testing, allowing for the decentralization of viral diagnostics.

Laboratory detection of SARS-CoV-2: A review of the current literature and future perspectives

Nowadays, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), whose infectivity is awfully strong, has been a major global threat to the public health. Since lung is the major target of SARS-CoV-2, the infection can lead to respiratory distress syndrome (RDS), multiple organ failure (MOF), and even death. The studies on viral structure and infection mechanism have found that angiotensin-converting enzyme 2 (ACE2), a pivotal enzyme affecting the organ-targeting in the RAS system, is the receptor of the SARS-CoV-2 virus. Currently, the detection of SARSCoV-2 is mainly achieved using open plate real-time reverse-transcription polymerase chain reaction (RT-PCR). While open plate method has some limitations, such as a high false-negative rate, cumbersome manual operation, aerosol pollution and leakage risks. Therefore, a convenient method to rapidly detect SARS-CoV-2 virus is urgently and extremely required for timely epidemic control with the limited resources. In this review, the current real-time methods and principles for novel coronavirus detection are summarized, with the aim to provide a reference for real-time screening of coronavirus in areas with insufficient detection capacity and inadequate medical resources. The development and establishment of a rapid, simple, sensitive and specific system to detect SARS-CoV-2 is of vital importance for distinct diagnosis and effective treatment of the virus, especially in the flu season.

Photothermal-Reagent-Triggered Visual Thermoresponsive and Quantized Photoelectrochemical Dual-Signal Assay

In vitro biosensing chips are urgently needed for early-stage diagnosis and real-time surveillance of epidemic diseases. Herein, a versatile zone with photothermal effects is implanted in the miniature space of a collapsible lab-on-paper photoelectrochemical biosensor for on-site detection of microRNA-141 in body fluids, which can flexibly interconnect the traditional photocurrent signal with functional temperature response. The visualized thermoresponsive results are enhanced by the exciton energy conversion between Fe₃O₄ nanoparticles (Fe₃O₄ NPs) and formed Prussian blue nanoparticles under near-infrared irradiation, which not only presents heat energy gradient variations but also generates color changes. Significantly, the controlled release of Fe₃O₄ NPs is actuated by a target-triggered enzyme assist strand displacement cycle strategy to efficiently improve the accuracy of target temperature signal prediction, which can concurrently mediate photoelectric signal attenuation via promoting the rapid recombination of photoexcited charge carriers on the CuInS₂/CoIn₂S₄ electrode surface, affording dependable ultrasensitive detection results. Benefitting from the ingenious design of the versatile thermoresponsive-photoelectric sensing platform, the preliminary screening and ultrasensitive quantitative analysis can be simultaneously achieved in a single-drop sample. As a consequence, speedy prediction results and satisfied monitoring data are acquired in the ranges of 0.5 pM to 2 nM and 0.001 pM to 5 nM by measuring the temperature change and photocurrent intensity. By right of these advantages, such research paves a prospective paradigm for the manufacture of a visual, rapid, broad-spectrum, and reliable real-time surveillance platform, which allows it to be a promising candidate for epidemic disease home diagnosis and intelligent diagnosis.

Smartphone clip-on instrument and microfluidic processor for rapid sample-to-answer detection of Zika virus in whole blood using spatial RT-LAMP

Rapid, simple, inexpensive, accurate, and sensitive point-of-care (POC) detection of viral pathogens in bodily fluids is a vital component of controlling the spread of infectious diseases. The predominant laboratory-based methods for sample processing and nucleic acid detection face limitations that prevent them from gaining wide adoption for POC applications in low-resource settings and self-testing scenarios. Here, we report the design and characterization of an integrated system for rapid sample-to-answer detection of a viral pathogen in a droplet of whole blood comprised of a 2-stage microfluidic cartridge for sample processing and nucleic acid amplification, and a clip-on detection instrument that interfaces with the image sensor of a smartphone. The cartridge is designed to release viral RNA from Zika virus in whole blood using chemical lysis, followed by mixing with the assay buffer for performing reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) reactions in six parallel microfluidic compartments. The battery-powered handheld detection instrument uniformly heats the compartments from below, and an array of LEDs illuminates from above, while the generation of fluorescent reporters in the compartments is kinetically monitored by collecting a series of smartphone images. We characterize the assay time and detection limits for detecting Zika RNA and gamma ray-deactivated Zika virus spiked into buffer and whole blood and compare the performance of the same assay when conducted in conventional PCR tubes. Our approach for kinetic monitoring of the fluorescence-generating process in the microfluidic compartments enables spatial analysis of early fluorescent "bloom" events for positive samples, in an approach called "Spatial LAMP" (S-LAMP). We show that S-LAMP image analysis reduces the time required to designate an assay as a positive test, compared to conventional analysis of the average fluorescent intensity of the entire compartment. S-LAMP enables the RT-LAMP process to be as short as 22 minutes, resulting in a total sample-to-answer time in the range of 17-32 minutes to distinguish positive from negative samples, while demonstrating a viral RNA detection as low as 2.70 × 102 copies per μl, and a gamma-irradiated virus of 103 virus particles in a single 12.5 μl droplet blood sample.

Modular micro-PCR system for the onsite rapid diagnosis of COVID-19

Effective containment of the COVID-19 pandemic requires rapid and accurate detection of the pathogen. Polymerase chain reaction (PCR) remains the gold standard for COVID-19 confirmation. In this article, we report the performance of a cost-effective modular microfluidic reverse transcription (RT)-PCR and RT-loop mediated isothermal amplification (RT-LAMP) platform, Epidax®, for the point-of-care testing and confirmation of SARS-CoV-2. This platform is versatile and can be reconfigured either for screening using endpoint RT-PCR or RT-LAMP tests or for confirmatory tests using real-time RT-PCR. Epidax® is highly sensitive and detects as little as 1 RNA copy per µL for real-time and endpoint RT-PCR, while using only half of the reagents. We achieved comparable results with those of a commercial platform when detecting SARS-CoV-2 viruses from 81 clinical RNA extracts. Epidax® can also detect SARS-CoV-2 from 44 nasopharyngeal samples without RNA extraction by using a direct RT-PCR assay, which shortens the sample-to-answer time to an hour with minimal user steps. Furthermore, we validated the technology using an RT-LAMP assay on 54 clinical RNA extracts. Overall, our platform provides a sensitive, cost-effective, and accurate diagnostic solution for low-resource settings.

Micro/nano biomedical devices for point-of-care diagnosis of infectious respiratory diseases

Corona Virus Disease 2019 (COVID-19) has developed into a global pandemic in the last two years, causing significant impacts on our daily life in many countries. Rapid and accurate detection of COVID-19 is of great importance to both treatments and pandemic management. Till now, a variety of point-of-care testing (POCT) approaches devices, including nucleic acid-based test and immunological detection, have been developed and some of them has been rapidly ruled out for clinical diagnosis of COVID-19 due to the requirement of mass testing. In this review, we provide a summary and commentary on the methods and biomedical devices innovated or renovated for the quick and early diagnosis of COVID-19. In particular, some of micro and nano devices with miniaturized structures, showing outstanding analytical performances such as ultra-sensitivity, rapidness, accuracy and low cost, are discussed in this paper. We also provide our insights on the further implementation of biomedical devices using advanced micro and nano technologies to meet the demand of point-of-care diagnosis and home testing to facilitate pandemic management. In general, our paper provides a comprehensive overview of the latest advances on the POCT device for diagnosis of COVID-19, which may provide insightful knowledge for researcher to further develop novel diagnostic technologies for rapid and on-site detection of pathogens including SARS-CoV-2.

A free customizable tool for easy integration of microfluidics and smartphones

The integration of smartphones and microfluidics is nowadays the best possible route to achieve effective point-of-need testing (PONT), a concept increasingly demanded in the fields of human health, agriculture, food safety, and environmental monitoring. Nevertheless, efforts are still required to integrally seize all the advantages of smartphones, as well as to share the developments in easily adoptable formats. For this purpose, here we present the free platform appuente that was designed for the easy integration of microfluidic chips, smartphones, and the cloud. It includes a mobile app for end users, which provides chip identification and tracking, guidance and control, processing, smart-imaging, result reporting and cloud and Internet of Things (IoT) integration. The platform also includes a web app for PONT developers, to easily customize their mobile apps and manage the data of administered tests. Three application examples were used to validate appuente: a dummy grayscale detector that mimics quantitative colorimetric tests, a root elongation assay for pesticide toxicity assessment, and a lateral flow immunoassay for leptospirosis detection. The platform openly offers fast prototyping of smartphone apps to the wide community of lab-on-a-chip developers, and also serves as a friendly framework for new techniques, IoT integration and further capabilities. Exploiting these advantages will certainly help to enlarge the use of PONT with real-time connectivity in the near future.

Minimization of MEDA Biochip-Size in Droplet Routing

With the increasing demand for fast, accurate, and reliable biological sensor systems, miniaturized systems have been aimed at droplet-based sensor systems and have been promising. A micro-electrode dot array (MEDA) biochip, which is one kind of the miniaturized systems for biochemical protocols such as dispensing, dilutions, mixing, and so on, has become widespread due to enabling dynamical control of the droplets in microfluidic manipulations. In MEDA biochips, the electrowetting-on-dielectric (EWOD) technique stands out since it can actuate droplets with nano/picoliter volumes. Microelectrode cells on MEDA actuate multiple droplets simultaneously to route locations for the purpose of the biochemical operations. Taking advantage of the feature, droplets are often routed in parallel to achieve high-throughput outcomes. Regarding parallel manipulation of multiple droplets, however, the droplets are known to be initially placed at a distant position to avoid undesirable mixing. The droplets thus result in traveling a long way for a manipulation, and the required biochip size for routing is also enlarged. This paper proposes a routing method for droplets to reduce the biochip size on a MEDA biochip with the allowance of splitting during routing operations. We mathematically derive the routing problem, and the experiments demonstrate that our proposal can significantly reduce the biochip size by 70.8% on average, compared to the state-of-the-art method.

Microfluidic point-of-care device for detection of early strains and B.1.1.7 variant of SARS-CoV-2 virus

Since the beginning of the COVID-19 pandemic, several mutations of the SARS-CoV-2 virus have emerged. Current gold standard detection methods for detecting the virus and its variants are based on PCR-based diagnostics using complex laboratory protocols and time-consuming steps, such as RNA isolation and purification, and thermal cycling. These steps limit the translation of technology to the point-of-care and limit accessibility to under-resourced regions. While PCR-based assays currently offer the possibility of multiplexed gene detection, and commercial products of single gene PCR and isothermal LAMP at point-of-care are also now available, reports of isothermal assays at the point-of-care with detection of multiple genes are lacking. Here, we present a microfluidic assay and device to detect and differentiate the Alpha variant (B.1.1.7) from the SARS-CoV-2 virus early strains in saliva samples. The detection assay, which is based on isothermal RT-LAMP amplification, takes advantage of the S-gene target failure (SGTF) to differentiate the Alpha variant from the SARS-CoV-2 virus early strains using a binary detection system based on spatial separation of the primers specific to the N- and S-genes. We use additively manufactured plastic cartridges in a low-cost optical reader system to successfully detect the SARS-CoV-2 virus from saliva samples (positive amplification is detected with concentration ≥10 copies per μL) within 30 min. We demonstrate that our platform can discriminate the B.1.1.7 variant (USA/CA_CDC_5574/2020 isolate) from SARS-CoV-2 negative samples, but also from the SARS-CoV-2 USA-WA1/2020 isolate. The reliability of the developed point-of-care device was confirmed by testing 38 clinical saliva samples, including 20 samples positive for Alpha variant (sensitivity > 90%, specificity = 100%). This study highlights the current relevance of binary-based testing, as the new Omicron variant also exhibits S-gene target failure and could be tested by adapting the approach presented here.

Microfluidics-based strategies for molecular diagnostics of infectious diseases

Traditional diagnostic strategies for infectious disease detection require benchtop instruments that are inappropriate for point-of-care testing (POCT). Emerging microfluidics, a highly miniaturized, automatic, and integrated technology, are a potential substitute for traditional methods in performing rapid, low-cost, accurate, and on-site diagnoses. Molecular diagnostics are widely used in microfluidic devices as the most effective approaches for pathogen detection. This review summarizes the latest advances in microfluidics-based molecular diagnostics for infectious diseases from academic perspectives and industrial outlooks. First, we introduce the typical on-chip nucleic acid processes, including sample preprocessing, amplification, and signal read-out. Then, four categories of microfluidic platforms are compared with respect to features, merits, and demerits. We further discuss application of the digital assay in absolute nucleic acid quantification. Both the classic and recent microfluidics-based commercial molecular diagnostic devices are summarized as proof of the current market status. Finally, we propose future directions for microfluidics-based infectious disease diagnosis.

On-board smartphone micromotor-based fluorescence assays

Herein, we describe the design of a portable device integrated with micromotors for real-time fluorescence sensing of (bio)markers. The system comprises a universal 3D printed platform to hold a commercial smartphone, which is equipped with an external magnification optical lens (20-400×) and tailor-made emission filters directly attached to the camera, an adjustable sample holder to accommodate a glass slide and laser excitation sources. On a first approach, we illustrate the suitability of the platform using magnetic Janus micromotors modified with fluorescent ZnS@Cd_xSe_1-x quantum dots for real-time ON-OFF mercury detection. On a second approach, graphdiyne tubular catalytic micromotors modified with a rhodamine labelled affinity peptide are used for the OFF-ON detection of cholera toxin B. The micromotor-based smartphone for fluorescence sensing approach was compared to a high-performance optical microscope, and similar analytical features were obtained. This versatility allows for easy integration of micromotor fluorescence sensing strategies based on different propulsion mechanisms, allowing for its future use with a myriad of biomarkers and even multiplexed schemes.

A scalable framework for smart COVID surveillance in the workplace using Deep Neural Networks and cloud computing

A smart and scalable system is required to schedule various machine learning applications to control pandemics like COVID-19 using computing infrastructure provided by cloud and fog computing. This paper proposes a framework that considers the use case of smart office surveillance to monitor workplaces for detecting possible violations of COVID effectively. The proposed framework uses deep neural networks, fog computing and cloud computing to develop a scalable and time-sensitive infrastructure that can detect two major violations: wearing a mask and maintaining a minimum distance of 6 feet between employees in the office environment. The proposed framework is developed with the vision to integrate multiple machine learning applications and handle the computing infrastructures for pandemic applications. The proposed framework can be used by application developers for the rapid development of new applications based on the requirements and do not worry about scheduling. The proposed framework is tested for two independent applications and performed better than the traditional cloud environment in terms of latency and response time. The work done in this paper tries to bridge the gap between machine learning applications and their computing infrastructure for COVID-19.

A wearable AIEgen-based lateral flow test strip for rapid detection of SARS-CoV-2 RBD protein and N protein

Accurate and rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is significant for early tracing, isolation, and treatment of infected individuals, which will efficiently prevent large-scale transmission of coronavirus disease 2019 (COVID-19). Here, two kinds of test strips for receptor binding domain (RBD) and N antigens of SARS-CoV-2 are established with high sensitivity and specificity, in which AIE luminogens (AIEgens) are utilized as reporters. Because of the high brightness and resistance to quenching in aqueous solution, the limit of detection can be as low as 6.9 ng/mL for RBD protein and 7.2 ng/mL for N protein. As an antigen collector, an N95 mask equipped with a test strip with an excellent enrichment effect would efficiently simplify the sampling procedures. Compared with a test strip based on Au nanoparticles or fluorescein isothiocyanate (FITC), the AIEgen-based test strip shows high anti-interference capacity in complex biosamples. Therefore, an AIEgen-based test strip assay could be built as a promising platform for emergency use during the pandemic.

A rapid and label-free DNA-based interference reduction nucleic acid amplification strategy for viral RNA detection

Common reference methods for COVID-19 diagnosis include thermal cycling amplification (e.g. RT-PCR) and isothermal amplification methods (e.g. LAMP and RPA). However, they may not be suitable for direct detection in environmental and biological samples due to background signal interference. Here, we report a rapid and label-free interference reduction nucleic acid amplification strategy (IR-NAAS) that exploits the advantages of luminescent iridium(III) probes, time-resolved emission spectroscopy (TRES) and multi-branch rolling circle amplification (mbRCA). Using IR-NAAS, we established a luminescence approach for diagnosing COVID-19 RNAs sequences RdRp, ORF1ab and N with a linear range of 0.06-6.0 × 10⁵ copies/mL and a detection limit of down to 7.3 × 10⁴ copies/mL. Moreover, the developed method was successfully applied to detect COVID-19 RNA sequences from various environmental and biological samples, such as domestic sewage, and mice urine, blood, feces, lung tissue, throat and nasal secretions. Apart from COVID-19 diagnosis, IR-NAAS was also demonstrated for detecting other RNA viruses, such as H1N1 and CVA10, indicating that this approach has great potential approach for routine preliminary viral detection.

Isothermal nucleic acid amplification technology for rapid detection of virus

While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.

Recombinase polymerase amplification integrated with microfluidics for nucleic acid testing at point of care

Nucleic acid testing (NAT) implemented on a portable, miniaturized, and integrated device with rapid and sensitive results readout is highly demanded for pathogen detection or genetic screening at resource-limited settings, especially after the outbreak of coronavirus disease 2019 (COVID-19). The integration of recombinase polymerase amplification (RPA) with emerging microfluidics, classified by paper-based microfluidics and chip-based microfluidics, shows great potential to perform laboratory independent NAT assays at point of care with minimal labor, time and energy consumption. This review summarizes the state-of-the-art of RPA integrated with paper-based microfluidics and chip-based microfluidics, and discusses their pros and cons. Finally, existing challenges and possible ways for optimization of microfluidics-based RPA are proposed.

New approach in SARS-CoV-2 surveillance using biosensor technology: a review

Biosensors are analytical tools that transform the bio-signal into an observable response. Biosensors are effective for early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection because they target viral antigens to assess clinical development and provide information on the severity and critical trends of infection. The biosensors are capable of being on-site, fast, and extremely sensitive to the target viral antigen, opening the door for early detection of SARS-CoV-2. They can screen individuals in hospitals, airports, and other crowded locations. Microfluidics and nanotechnology are promising cornerstones for the development of biosensor-based techniques. Recently, due to high selectivity, simplicity, low cost, and reliability, the production of biosensor instruments have attracted considerable interest. This review article precisely provides the extensive scientific advancement and intensive look of basic principles and implementation of biosensors in SARS-CoV-2 surveillance, especially for human health. In this review, the importance of biosensors including Optical, Electrochemical, Piezoelectric, Microfluidic, Paper-based biosensors, Immunosensors, and Nano-Biosensors in the detection of SARS-CoV-2 has been underscored. Smartphone biosensors and calorimetric strips that target antibodies or antigens should be developed immediately to combat the rapidly spreading SARS-CoV-2. Wearable biosensors can constantly monitor patients, which is a highly desired feature of biosensors. Finally, we summarized the literature, outlined new approaches and future directions in diagnosing SARS-CoV-2 by biosensor-based techniques.

COVID-19: Clinical laboratory diagnosis and monitoring of novel coronavirus infected patients using molecular, serological and biochemical markers: A review

COVID-19, a novel coronavirus disease, has provoked a variety of health and safety concerns, and socioeconomic challenges around the globe. The laboratory diagnosis of SARS-CoV-2 was quickly established utilizing nucleic acid amplification techniques (NAAT) after the disease causing virus has been identified, and its genetic sequence has been determined. In addition to NAAT, serological tests based on antibodies testing against SARS-CoV-2 were introduced for diagnostic and epidemiologic studies. Other biochemical investigations include monitoring of peripheral blood cells count, platelets/lymphocyte ratio, coagulation profile, cardiac, and inflammatory markers such as cytokines storm are also crucial in combating COVID-19 pandemic. Further, accurate and reliable laboratory results for SARS-CoV-2 play very important role in the initiation of early treatment and timely management of COVID-19 patients, provide support in clinical decision-making process to control infection, and detection of asymptomatic cases. The Task Force on Coronavirus-19 constituted by International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) has recognized informational framework for epidemiology, pathogenesis, and recommended the PCR-based analysis, serological and biochemical assays for analysis, monitoring, and management of disease. This literature review provides an overview of the currently used diagnostic techniques in clinical laboratories for the diagnosis, treatment monitoring, and management of COVID-19 patients. We concluded that each assays differ in their performance characteristics and the utilization of multiple techniques is necessary for the accurate diagnosis and management of SARS-CoV-2 infection.

Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection

The ever-growing global threats to human life caused by the human acute respiratory virus (RV) infections have cost billions of lives, created a significant economic burden, and shaped society for centuries. The timely response to emerging RVs could save human lives and reduce the medical care burden. The development of RV detection technologies is essential for potentially preventing RV pandemic and epidemics. However, commonly used detection technologies lack sensitivity, specificity, and speed, thus often failing to provide the rapid turnaround times. To address this problem, new technologies are devised to address the performance inadequacies of the traditional methods. These emerging technologies offer improvements in convenience, speed, flexibility, and portability of point-of-care test (POCT). Herein, recent developments in POCT are comprehensively reviewed for eight typical acute respiratory viruses. This review discusses the challenges and opportunities of various recognition and detection strategies and discusses these according to their detection principles, including nucleic acid amplification, optical POCT, electrochemistry, lateral flow assays, microfluidics, enzyme-linked immunosorbent assays, and microarrays. The importance of limits of detection, throughput, portability, and specificity when testing clinical samples in resource-limited settings is emphasized. Finally, the evaluation of commercial POCT kits for both essential RV diagnosis and clinical-oriented practices is included.

Smartphone-Based Janus Micromotors Strategy for Motion-Based Detection of Glutathione

Herein, we describe a Janus micromotor smartphone platform for the motion-based detection of glutathione. The system compromises a universal three-dimensional (3D)-printed platform to hold a commercial smartphone, which is equipped with an external magnification optical lens (20-400×) directly attached to the camera, an adjustable sample holder to accommodate a glass slide, and a light-emitting diode (LED) source. The presence of glutathione in peroxide-rich sample media results in the decrease in the speed of 20 μm graphene-wrapped/PtNPs Janus micromotors due to poisoning of the catalytic layer by a thiol bond formation. The speed can be correlated with the concentration of glutathione, achieving a limit of detection of 0.90 μM, with percent recoveries and excellent selectivity under the presence of interfering amino acids and proteins. Naked-eye visualization of the speed decrease allows for the design of a test strip for fast glutathione detection (30 s), avoiding previous amplification strategies or sample preparation steps. The concept can be extended to other micromotor approaches relying on fluorescence or colorimetric detection for future multiplexed schemes.

A method of sequential liquid dispensing for the multiplexed genetic diagnosis of viral infections in a microfluidic device

In this study, we introduce polydimethylsiloxane (PDMS)-based microfluidic devices capable of sequential dispensing of samples into multiple reaction microchambers in a single operation to provide a fast and easy sample-to-answer platform for multiplexed genetic diagnosis of multiple viral infectious diseases. This approach utilizes the loop-mediated isothermal amplification (LAMP) method to amplify and detect specific nucleic acid (DNA/RNA) targets. We present a microfluidic flow control theory for sequential liquid dispensing phenomena, which provides design guidelines for device optimization. The device specifications, such as the possible dispensing number and maximal allowable flow rate, can be theoretically designed by optimizing the geometric dimensions of the microchannels and a pair of passive stop valves integrated into each microchamber together with the water contact angles of the materials used to fabricate the microfluidic devices. In addition, a passive stop valve with a vertical-type phaseguide structure was designed to improve device performance. We could simultaneously diagnose coronavirus disease 2019 (COVID-19) and other infectious diseases, such as severe acute respiratory syndrome (SARS), seasonal influenza A, and pandemic influenza A (H1N1) 2009. The colorimetric reverse transcription LAMP (RT-LAMP) assay suggests that the four viral infectious diseases can be detected within 30 min using a hue-based quantitative analysis, and the naked eye using our microfluidic devices.

A Cross-Disciplinary View of Testing and Bioinformatic Analysis of SARS-CoV-2 and Other Human Respiratory Viruses in Pandemic Settings

The SARS-Coronavirus-2 (SARS-CoV-2) infectious disease, COVID-19, has spread rapidly, resulting in a global pandemic with significant mortality. The combination of early diagnosis via rapid screening, contact tracing, social distancing and quarantine has helped to control the pandemic. The absence of real time response and diagnosis is a crucial technology shortfall and is a key reason why current contact tracing methods are inadequate to control spread. In contrast, current information technology combined with a new generation of near-real time tests offers consumer-engaged smartphone-based "lab-in-a-phone" internet-of-things (IoT) connected devices that provide increased pandemic monitoring. This review brings together key aspects required to create an entire global diagnostic ecosystem. Cross-disciplinary understanding and integration of both mechanisms and technologies for effective detection, incidence mapping and disease containment in near real-time is summarized. Available measures to monitor and/or sterilize surfaces, next-generation laboratory and smartphone-based diagnostic approaches can be brought together and networked for instant global monitoring that informs Public Health policy. Cloud-based analysis enabling real-time mapping will enable future pandemic control, drive the suppression and elimination of disease spread, saving millions of lives globally. A new paradigm is introduced - scaled and multiple diagnostics for mapping and spreading of a pandemic rather than traditional accumulation of individual measurements. This can do away with the need for ultra-precise and ultra-accurate analysis by taking mass measurements that can relax tolerances and build resilience through networked analytics and informatics, the basis for novel swarm diagnostics. These include addressing ethical standards, local, national and international collaborative engagement, multidisciplinary and analytical measurements and standards, and data handling and storage protocols.

Rapid detection of novel coronavirus SARS-CoV-2 by RT-LAMP coupled solid-state nanopores

The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the disease spread. Here, we present an RT-LAMP coupled glass nanopore digital counting method for rapid detection of SARS-CoV-2. We validated and compared two one-pot RT-LAMP assays targeting nucleocapsid (N) and envelop (E) genes. The nucleocapsid assay was adopted due to its quick time to positive and better copy number sensitivity. For qualitative positive/negative classification of a testing sample, we used the glass nanopore to digitally count the RT-LAMP amplicons and benchmarked the event rate with a threshold. Due to its intrinsic single molecule sensitivity, nanopore sensors could capture the amplification dynamics more rapidly (quick time to positive). We validated our RT-LAMP coupled glass nanopore digital counting method for SARS-CoV-2 detection by using both spiked saliva samples and COVID-19 clinical nasopharyngeal swab samples. The results obtained showed excellent agreement with the gold standard RT-PCR assay. With its integration capability, the electronic nanopore digital counting platform has significant potential to provide a rapid, sensitive, and specific point-of-care assay for SARS-CoV-2.

Loop-mediated isothermal amplification (LAMP): An effective molecular point-of-care technique for the rapid diagnosis of coronavirus SARS-CoV-2

The novel coronavirus disease-2019 (Covid-19) public health emergency has caused enormous loss around the world. This pandemic is a concrete example of the existing gap between availability of advanced diagnostics and current need for cost-effective methodology. The advent of the loop-mediated isothermal amplification (LAMP) assay provided an innovative tool for establishing a rapid diagnostic technique based on the molecular amplification of pathogen RNA or DNA. In this review, we explore the applications, diagnostic effectiveness of LAMP test for molecular diagnosis and surveillance of severe acute respiratory syndrome coronavirus 2. Our results show that LAMP can be considered as an effective point-of-care test for the diagnosis of Covid-19 in endemic areas, especially for low- and middle-income countries.

Nucleic Acids Analytical Methods for Viral Infection Diagnosis: State-of-the-Art and Future Perspectives

The analysis of viral nucleic acids (NA), DNA or RNA, is a crucial issue in the diagnosis of infections and the treatment and prevention of related human diseases. Conventional nucleic acid tests (NATs) require multistep approaches starting from the purification of the pathogen genetic material in biological samples to the end of its detection, basically performed by the consolidated polymerase chain reaction (PCR), by the use of specialized instruments and dedicated laboratories. However, since the current NATs are too constraining and time and cost consuming, the research is evolving towards more integrated, decentralized, user-friendly, and low-cost methods. These will allow the implementation of massive diagnoses addressing the growing demand of fast and accurate viral analysis facing such global alerts as the pandemic of coronavirus disease of the recent period. Silicon-based technology and microfluidics, in this sense, brought an important step up, leading to the introduction of the genetic point-of-care (PoC) systems. This review goes through the evolution of the analytical methods for the viral NA diagnosis of infection diseases, highlighting both advantages and drawbacks of the innovative emerging technologies versus the conventional approaches.

Passively driven microfluidic device with simple operation in the development of nanolitre droplet assay in nucleic acid detection

Since nucleic acid amplification technology has become a vital tool for disease diagnosis, the development of precise applied nucleic acid detection technologies in point-of care testing (POCT) has become more significant. The microfluidic-based nucleic acid detection platform offers a great opportunity for on-site diagnosis efficiency, and the system is aimed at user-friendly access. Herein, we demonstrate a microfluidic system with simple operation that provides reliable nucleic acid results from 18 uniform droplets via LAMP detection. By using only micropipette regulation, users are able to control the nanoliter scale of the droplets in this valve-free and pump-free microfluidic (MF) chip. Based on the oil enclosure method and impermeable fabrication, we successfully preserved the reagent inside the microfluidic system, which significantly reduced the fluid loss and condensation. The relative standard deviation (RSD) of the fluorescence intensity between the droplets and during the heating process was < 5% and 2.0%, respectively. Additionally, for different nucleic acid detection methods, the MF-LAMP chip in this study showed good applicability to both genome detection and gene expression analysis.

Conventional and microfluidic methods for airborne virus isolation and detection

With the COVID-19 pandemic, the threat of infectious diseases to public health and safety has become much more apparent. Viral, bacterial and fungal diseases have led to the loss of millions of lives, especially in the developing world. Diseases caused by airborne viruses like SARS-CoV-2 are difficult to control, as these viruses are easily transmissible and can circulate in the air for hours. To contain outbreaks of viruses such as SARS-CoV-2 and institute targeted precautions, it is important to detect them in air and understand how they infect their targets. Point-of-care (PoC) diagnostics and point-of-need (PoN) detection methods are necessary to rapidly test patient and environmental samples, so precautions can immediately be applied. Traditional benchtop detection methods such as ELISA, PCR and culture are not suitable for PoC and PoN monitoring, because they can take hours to days and require specialized equipment. Microfluidic devices can be made at low cost to perform such assays rapidly and at the PoN. They can also be integrated with air- and liquid-based sampling technologies to capture and analyze viruses from air and body fluids. Here, conventional and microfluidic virus detection methods are reviewed and compared. The use of air sampling devices to capture and concentrate viruses is discussed first, followed by a review of analysis methods such as immunoassays, RT-PCR and isothermal amplification in conventional and microfluidic platforms. This review provides an overview of the capabilities of microfluidics in virus handling and detection, which will be useful to infectious disease researchers, biomedical engineers, and public health agencies.

Real-Time Fluorometric Isothermal LAMP Assay for Detection of Chlamydia pecorum in Rapidly Processed Ovine Abortion Samples: A Veterinary Practitioner's Perspective

Traditional methods of detecting Chlamydia pecorum in tissue samples such as polymerase chain reaction or cell culture are laborious and costly. We evaluated the use of a previously developed C. pecorum LAMP assay using minimally processed ovine samples. Cotyledon (n = 16), foetal liver (n = 22), foetal lung (n = 2), and vaginal (n = 6) swabs, in addition to cotyledon (n = 6) and foetal liver (n = 8) tissue samples, were rapidly processed and used for LAMP testing without DNA extraction. Overall, LAMP test results were highly congruent with the in-house reference qPCR, with 80.43% (37/46; 72.73% positive agreement (PA); 84.75% negative agreement (NA)) overall agreeance for swab samples, and 85.71% (12/14; 80% PA; 88.89% NA) overall agreeance for tissue samples. Out of the 11 total discrepant results, discrepancy was mainly observed in samples (n = 10) with less than 100 copies/µL C. pecorum DNA. While sensitivity could be improved, the simplicity, low cost, and accuracy of detection makes this test amenable for use at point-of-care for detecting C. pecorum in sheep.

CASE-CF: Context Aware Smart Epidemic Control Framework

Novel Coronavirus (COVID-19) has become one of the deadliest pandemics that has affected almost all the nations in the world. Lockdown and systematic re-opening of shopping malls, offices, etc. is still one of the major weapons against this virus. However, the government and medical agencies take long time to reopen the places due to risks involved in this deadly virus. The delay to reopen places has resulted in sharp decline in the growth of economy. In this paper a current context aware framework is proposed which uses multiple inputs for a specific region to decide whether to open it or not. The proposed framework used series of deep neural network models to generate recommendations specific to a particular region. Most of the inputs are real-time and readily available with the government. The main aim is to develop framework which can be used in any kind of pandemic even in small region to easily contain it. However, it has been tested using opensource data available for COVID-19. Data was crawled from web for 22 districts of Haryana state of India. Experimental result proved the efficiency of proposed framework.

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.

Real-time fluorometric and end-point colorimetric isothermal assays for detection of equine pathogens C. psittaci and equine herpes virus 1: validation, comparison and application at the point of care

Background

C. psittaci has recently emerged as an equine abortigenic pathogen causing significant losses to the Australian Thoroughbred industry, while Equine herpesvirus-1 (EHV-1) is a well-recognized abortigenic agent. Diagnosis of these agents is based on molecular assays in diagnostic laboratories.

In this study, we validated C. psittaci and newly developed EHV-1 Loop Mediated Isothermal Amplification (LAMP) assays performed in a real-time fluorometer (rtLAMP) against the reference diagnostic assays. We also evaluated isothermal amplification using commercially available colorimetric mix (cLAMP), and SYBR Green DNA binding dye (sgLAMP) for “naked eye” end-point detection when testing ‘real-world’ clinical samples. Finally, we applied the C. psittaci LAMP assays in two pilot Point-of-Care (POC) studies in an equine hospital.

Results

The analytical sensitivity of C. psittaci and EHV-1 rt-, and colorimetric LAMPs was determined as one and 10 genome equivalents per reaction, respectively. Compared to reference diagnostic qPCR assays, the C. psittaci rtLAMP showed sensitivity of 100%, specificity of 97.5, and 98.86% agreement, while EHV-1 rtLAMP showed 86.96% sensitivity, 100% specificity, and 91.43% agreement.

When testing rapidly processed clinical samples, all three C. psittaci rt-, c-, sg-LAMP assays were highly congruent with each other, with Kappa values of 0. 906 for sgLAMP and 0. 821 for cLAMP when compared to rtLAMP. EHV-1 testing also revealed high congruence between the assays, with Kappa values of 0.784 for cLAMP and 0.638 for sgLAMP when compared to rtLAMP. The congruence between LAMP assays and the C. psittaci or EHV-1 qPCR assays was high, with agreements ranging from 94.12 to 100% for C. psittaci, and 88.24 to 94.12% for EHV-1, respectively.

At the POC, the C. psittaci rt- and c-LAMP assays using rapidly processed swabs were performed by technicians with no prior molecular experience, and the overall congruence between the POC C. psittaci LAMPs and the qPCR assays ranged between 90.91–100%.

Conclusions

This study describes reliable POC options for the detection of the equine pathogens: C. psittaci and EHV-1. Testing ‘real-world’ samples in equine clinical setting, represents a proof-of-concept that POC isothermal diagnostics can be applied to rapid disease screening in the equine industry.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02986-8.

Lab on a Chip: Bioreactors miniaturization for rapid optimization of biomedical processes and its impact on SARS-CoV-2 diagnosis

Lab on a Chip (LoC) as part of Microbioreactors (MBRs) constitute an emergent technology to carry out micro-bioprocesses based on microfluidics research. In this review, the usefulness of LoCs is exposed since its inception, demonstrating that it is a multidisciplinary research field, gathering different science branches to develop this technology. As a result, a beneficial point of advancement is reached, producing useful consumables for humanity. Some of the described LoCs throughout this work are also used to detect infectious diseases caused by bacteria or viruses, allowing accelerated studies on emerging or high-impact diseases, such as COVID-19. Here are also displayed with an updated panorama, different strategies to improve the use, applications in the biomedical field, and spread of these devices aimed at their availability to solve social problems.