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1.
Sci Rep ; 11(1): 14961, 2021 07 22.
Article in English | MEDLINE | ID: covidwho-1322501

ABSTRACT

Influenza and other respiratory viruses present a significant threat to public health, national security, and the world economy, and can lead to the emergence of global pandemics such as from COVID-19. A barrier to the development of effective therapeutics is the absence of a robust and predictive preclinical model, with most studies relying on a combination of in vitro screening with immortalized cell lines and low-throughput animal models. Here, we integrate human primary airway epithelial cells into a custom-engineered 96-device platform (PREDICT96-ALI) in which tissues are cultured in an array of microchannel-based culture chambers at an air-liquid interface, in a configuration compatible with high resolution in-situ imaging and real-time sensing. We apply this platform to influenza A virus and coronavirus infections, evaluating viral infection kinetics and antiviral agent dosing across multiple strains and donor populations of human primary cells. Human coronaviruses HCoV-NL63 and SARS-CoV-2 enter host cells via ACE2 and utilize the protease TMPRSS2 for spike protein priming, and we confirm their expression, demonstrate infection across a range of multiplicities of infection, and evaluate the efficacy of camostat mesylate, a known inhibitor of HCoV-NL63 infection. This new capability can be used to address a major gap in the rapid assessment of therapeutic efficacy of small molecules and antiviral agents against influenza and other respiratory viruses including coronaviruses.


Subject(s)
Antiviral Agents/pharmacology , Coronavirus Infections/virology , Influenza, Human/virology , Microbial Sensitivity Tests/instrumentation , Microfluidic Analytical Techniques/instrumentation , Respiratory Mucosa/cytology , Bronchi/cytology , Bronchi/virology , COVID-19/drug therapy , COVID-19/virology , Cell Culture Techniques/instrumentation , Cell Line , Coronavirus/drug effects , Coronavirus Infections/drug therapy , Equipment Design , High-Throughput Screening Assays/instrumentation , Humans , Influenza A virus/drug effects , Influenza, Human/drug therapy , Respiratory Mucosa/virology , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/virology , SARS-CoV-2/drug effects
2.
Biotechnol Bioeng ; 118(9): 3559-3568, 2021 09.
Article in English | MEDLINE | ID: covidwho-1245365

ABSTRACT

Molecular diagnosis is an essential means to detect pathogens. The portable nucleic acid detection chip has excellent prospects in places where medical resources are scarce, and it is also of research interest in the field of microfluidic chips. Here, the article developed a new type of microfluidic chip for nucleic acid detection where stretching acts as the driving force. The sample entered the chip by applying capillary force. The strain valve was opened under the action of tensile force, and the spring pump generated the power to drive the fluid to flow to the detection chamber in a specific direction. The detection of coronavirus disease 2019 (COVID-19) was realized on the chip. The RT-LAMP amplification system was adopted to observe the liquid color in the detection chamber to decide whether the sample tested positive or negative qualitatively.


Subject(s)
COVID-19/virology , Microfluidic Analytical Techniques/instrumentation , Nucleic Acids/analysis , SARS-CoV-2/isolation & purification , Humans
3.
Clin Chem ; 67(4): 672-683, 2021 03 31.
Article in English | MEDLINE | ID: covidwho-1165392

ABSTRACT

BACKGROUND: Infectious disease outbreaks such as the COVID-19 (coronavirus disease 2019) pandemic call for rapid response and complete screening of the suspected community population to identify potential carriers of pathogens. Central laboratories rely on time-consuming sample collection methods that are rarely available in resource-limited settings. METHODS: We present a highly automated and fully integrated mobile laboratory for fast deployment in response to infectious disease outbreaks. The mobile laboratory was equipped with a 6-axis robot arm for automated oropharyngeal swab specimen collection; virus in the collected specimen was inactivated rapidly using an infrared heating module. Nucleic acid extraction and nested isothermal amplification were performed by a "sample in, answer out" laboratory-on-a-chip system, and the result was automatically reported by the onboard information platform. Each module was evaluated using pseudovirus or clinical samples. RESULTS: The mobile laboratory was stand-alone and self-sustaining and capable of on-site specimen collection, inactivation, analysis, and reporting. The automated sampling robot arm achieved sampling efficiency comparable to manual collection. The collected samples were inactivated in as short as 12 min with efficiency comparable to a water bath without damage to nucleic acid integrity. The limit of detection of the integrated microfluidic nucleic acid analyzer reached 150 copies/mL within 45 min. Clinical evaluation of the onboard microfluidic nucleic acid analyzer demonstrated good consistency with reverse transcription quantitative PCR with a κ coefficient of 0.979. CONCLUSIONS: The mobile laboratory provides a promising solution for fast deployment of medical diagnostic resources at critical junctions of infectious disease outbreaks and facilitates local containment of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) transmission.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Laboratories , Mobile Health Units , Pathology, Molecular/methods , RNA, Viral/analysis , Adult , Automobiles , COVID-19/epidemiology , COVID-19 Nucleic Acid Testing/instrumentation , Female , Humans , Lab-On-A-Chip Devices , Male , Microfluidic Analytical Techniques/instrumentation , Microfluidic Analytical Techniques/methods , Middle East Respiratory Syndrome Coronavirus/chemistry , Molecular Diagnostic Techniques/instrumentation , Molecular Diagnostic Techniques/methods , Pandemics , Pathology, Molecular/instrumentation , Robotics , SARS-CoV-2/chemistry
4.
Biotechniques ; 69(4): 317-325, 2020 10.
Article in English | MEDLINE | ID: covidwho-1067502

ABSTRACT

PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.


Subject(s)
Polymerase Chain Reaction/methods , Animals , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques/instrumentation , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Equipment Design , Humans , Microfluidic Analytical Techniques/instrumentation , Microfluidic Analytical Techniques/methods , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Point-of-Care Systems , Polymerase Chain Reaction/instrumentation , SARS-CoV-2
5.
Nature ; 582(7811): 277-282, 2020 06.
Article in English | MEDLINE | ID: covidwho-980299

ABSTRACT

The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples1-3 while simultaneously testing for many pathogens4-6. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents7 self-organize in a microwell array8 to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health9-11.


Subject(s)
CRISPR-Associated Proteins/metabolism , CRISPR-Cas Systems/genetics , Microfluidic Analytical Techniques/methods , Virus Diseases/diagnosis , Virus Diseases/virology , Animals , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Drug Resistance, Viral/genetics , Genome, Viral/genetics , HIV/classification , HIV/genetics , HIV/isolation & purification , Humans , Influenza A virus/classification , Influenza A virus/genetics , Influenza A virus/isolation & purification , Microfluidic Analytical Techniques/instrumentation , RNA, Guide/genetics , SARS-CoV-2 , Sensitivity and Specificity
6.
Anal Chem ; 92(21): 14297-14302, 2020 11 03.
Article in English | MEDLINE | ID: covidwho-872628

ABSTRACT

With the global outbreak of the coronavirus disease 2019 (COVID-19), the highly infective, highly pathogenic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted great attention. Currently, a method to simultaneously diagnose the seven known types human coronaviruses remains lacking and is urgently needed. In this work, we successfully developed a portable microfluidic system for the rapid, accurate, and simultaneous detection of SARS-CoV, middle east respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2, and four other human coronaviruses (HCoVs) including HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1. The disk-like microfluidic platform integrated with loop-mediated isothermal amplification provides highly accurate, sensitive, and specific results with a wide linear range within 40 min. The diagnostic tool achieved 100% consistency with the "gold standard" polymerase chain reaction in detecting 54 real clinical samples. The integrated system, with its simplicity, is urgently needed for the diagnosis of SARS-CoV-2 during the COVID-19 pandemic.


Subject(s)
Coronavirus Infections/diagnostic imaging , DNA, Viral/analysis , Lab-On-A-Chip Devices , Microfluidic Analytical Techniques/methods , Pneumonia, Viral/diagnostic imaging , Betacoronavirus , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , Coronavirus 229E, Human , Coronavirus Infections/diagnosis , Coronavirus NL63, Human , Diagnosis, Differential , Humans , Microfluidic Analytical Techniques/instrumentation , Nucleic Acid Amplification Techniques/methods , Pandemics , SARS-CoV-2
8.
Biosens Bioelectron ; 169: 112572, 2020 Dec 01.
Article in English | MEDLINE | ID: covidwho-741059

ABSTRACT

Convalescent serum with a high abundance of neutralization IgG is a promising therapeutic agent for rescuing COVID-19 patients in the critical stage. Knowing the concentration of SARS-CoV-2 S1-specific IgG is crucial in selecting appropriate convalescent serum donors. Here, we present a portable microfluidic ELISA technology for rapid (15 min), quantitative, and sensitive detection of anti-SARS-CoV-2 S1 IgG in human serum with only 8 µL sample volume. We first identified a humanized monoclonal IgG that has a high binding affinity and a relatively high specificity towards SARS-CoV-2 S1 protein, which can subsequently serve as the calibration standard of anti-SARS-CoV-2 S1 IgG in serological analyses. We then measured the abundance of anti-SARS-CoV-2 S1 IgG in 16 convalescent COVID-19 patients. Due to the availability of the calibration standard and the large dynamic range of our assay, we were able to identify "qualified donors" for convalescent serum therapy with only one fixed dilution factor (200 ×). Finally, we demonstrated that our technology can sensitively detect SARS-CoV-2 antigens (S1 and N proteins) with pg/mL level sensitivities in 40 min. Overall, our technology can greatly facilitate rapid, sensitive, and quantitative analysis of COVID-19 related markers for therapeutic, diagnostic, epidemiologic, and prognostic purposes.


Subject(s)
Antibodies, Viral/blood , Betacoronavirus/immunology , Coronavirus Infections/virology , Enzyme-Linked Immunosorbent Assay/instrumentation , Immunoglobulin G/blood , Microfluidic Analytical Techniques/instrumentation , Pneumonia, Viral/virology , Adolescent , Adult , Antibodies, Viral/immunology , Antigens, Viral/blood , Antigens, Viral/immunology , Biosensing Techniques/economics , Biosensing Techniques/instrumentation , COVID-19 , Coronavirus Infections/therapy , Enzyme-Linked Immunosorbent Assay/economics , Equipment Design , Humans , Immunization, Passive , Immunoglobulin G/immunology , Limit of Detection , Luminescent Measurements/economics , Luminescent Measurements/instrumentation , Microfluidic Analytical Techniques/economics , Middle Aged , Pandemics , Pneumonia, Viral/therapy , SARS-CoV-2 , Time Factors , Young Adult
9.
Biosens Bioelectron ; 153: 112041, 2020 Apr 01.
Article in English | MEDLINE | ID: covidwho-156

ABSTRACT

The global risk of viral disease outbreaks emphasizes the need for rapid, accurate, and sensitive detection techniques to speed up diagnostics allowing early intervention. An emerging field of microfluidics also known as the lab-on-a-chip (LOC) or micro total analysis system includes a wide range of diagnostic devices. This review briefly covers both conventional and microfluidics-based techniques for rapid viral detection. We first describe conventional detection methods such as cell culturing, immunofluorescence or enzyme-linked immunosorbent assay (ELISA), or reverse transcription polymerase chain reaction (RT-PCR). These methods often have limited speed, sensitivity, or specificity and are performed with typically bulky equipment. Here, we discuss some of the LOC technologies that can overcome these demerits, highlighting the latest advances in LOC devices for viral disease diagnosis. We also discuss the fabrication of LOC systems to produce devices for performing either individual steps or virus detection in samples with the sample to answer method. The complete system consists of sample preparation, and ELISA and RT-PCR for viral-antibody and nucleic acid detection, respectively. Finally, we formulate our opinions on these areas for the future development of LOC systems for viral diagnostics.


Subject(s)
DNA, Viral/analysis , Lab-On-A-Chip Devices , Microfluidic Analytical Techniques/instrumentation , Nucleic Acids/analysis , Virus Diseases/diagnosis , Biosensing Techniques , Enzyme-Linked Immunosorbent Assay , Equipment Design , Humans , Point-of-Care Systems , Real-Time Polymerase Chain Reaction
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