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Rapid Differential Diagnosis of Seven Human Respiratory Coronaviruses Based on Centrifugal Microfluidic Nucleic Acid Assay.

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.

SUBMITTER: Xiong H

PROVIDER: S-EPMC7586455 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Rapid Differential Diagnosis of Seven Human Respiratory Coronaviruses Based on Centrifugal Microfluidic Nucleic Acid Assay.

Xiong Huiwen H Ye Xin X Li Yang Y Wang Lijuan L Zhang Jin J Fang Xueen X Kong Jilie J

Analytical chemistry 20201019 21

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 ...[more]

PMID: 33073982

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Project description:The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently creating a global health emergency. This crisis is driving a worldwide effort to develop effective vaccines, prophylactics, and therapeutics. Nucleic acid (NA)-based treatments hold great potential to combat outbreaks of coronaviruses (CoVs) due to their rapid development, high target specificity, and the capacity to increase druggability. Here, we review key anti-CoV NA-based technologies, including antisense oligonucleotides (ASOs), siRNAs, RNA-targeting clustered regularly interspaced short palindromic repeats-CRISPR-associated protein (CRISPR-Cas), and mRNA vaccines, and discuss improved delivery methods and combination therapies with other antiviral drugs. Highlights Nucleic-acid based therapies are worth developing against coronavirus (CoV) outbreaks because of their high specificity and rapid development. Several key therapeutic nucleic acid (TNA) strategies, including antisense oligonucleotides (ASOs), siRNA, and RNA-targeting clustered regularly interspaced short palindromic repeats-CRISPR-associated protein (CRISPR-Cas) technologies targeting the viral genome are potentially applicable to combat CoVs. mRNA vaccines are attractive candidates to control CoV outbreaks with rapid/easy manufacturing, high potency, and safety. Optimal therapeutic cocktails comprising different TNAs or TNAs with other antiviral agents could act on multiple targets simultaneously, thereby enhancing antiviral effects and reducing risk of drug resistance. Lipid-ASO (LASO) nanomicelles enable cellular self-uptake and can be conjugated with antiviral molecules, providing promising anti-CoV combinational therapeutics that can be delivered directly to the lungs by aerosol. Advancement in chemical modifications and delivery vehicles remarkably enhance stability and pharmacokinetic profile of TNAs, facilitating clinical application of numerous TNAs; however, more studies on optimal chemical manufacturing and delivery methods improving safety and efficiency for TNAs are needed.

Project description:Global pandemics such as COVID-19 have resulted in significant global social and economic disruption. Although polymerase chain reaction (PCR) is recommended as the standard test for identifying the SARS-CoV-2, conventional assays are time-consuming. In parallel, although artificial intelligence (AI) has been employed to contain the disease, the implementation of AI in PCR analytics, which may enhance the cognition of diagnostics, is quite rare. The information that the amplification curve reveals can reflect the dynamics of reactions. Here, we present a novel AI-aided on-chip approach by integrating deep learning with microfluidic paper-based analytical devices (µPADs) to detect synthetic RNA templates of the SARS-CoV-2 ORF1ab gene. The µPADs feature a multilayer structure by which the devices are compatible with conventional PCR instruments. During analysis, real-time PCR data were synchronously fed to three unsupervised learning models with deep neural networks, including RNN, LSTM, and GRU. Of these, the GRU is found to be most effective and accurate. Based on the experimentally obtained datasets, qualitative forecasting can be made as early as 13 cycles, which significantly enhances the efficiency of the PCR tests by 67.5% (∼40 min). Also, an accurate prediction of the end-point value of PCR curves can be obtained by GRU around 20 cycles. To further improve PCR testing efficiency, we also propose AI-aided dynamic evaluation criteria for determining critical cycle numbers, which enables real-time quantitative analysis of PCR tests. The presented approach is the first to integrate AI for on-chip PCR data analysis. It is capable of forecasting the final output and the trend of qPCR in addition to the conventional end-point Cq calculation. It is also capable of fully exploring the dynamics and intrinsic features of each reaction. This work leverages methodologies from diverse disciplines to provide perspectives and insights beyond the scope of a single scientific field. It is universally applicable and can be extended to multiple areas of fundamental research. Graphical abstract Image, graphical abstract

Dataset Information

Rapid Differential Diagnosis of Seven Human Respiratory Coronaviruses Based on Centrifugal Microfluidic Nucleic Acid Assay.

Publications

Rapid Differential Diagnosis of Seven Human Respiratory Coronaviruses Based on Centrifugal Microfluidic Nucleic Acid Assay.

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