Rapid detection of influenza A virus in clinical samples using an ion channel switch biosensor

This report describes the fabrication and successful use of the ion channel switch biosensor (ICSB) for rapid point-of-care detection of influenza A in different types of respiratory specimens. Virus culture -- regarded as the "gold standard" -- and an immunochromatographic rapid point-of-care test for influenza A virus were compared with the biosensor. The ICSB rapid test provided an objective readout within 10 min of specimen inoculation into the ICSB chamber wells, without the need for chemical or other pretreatments. Construction of the ICSB with specific antibodies also enables rapid detection and identification of appropriate influenza A subtypes.     

基于CRISPR/Cas生物传感原理的病原菌检测技术研究进展*

病原菌的快速准确检测是实现疫情高效防控、疾病精准治疗、污染环境及时处置的关键。而现有的病原菌现场快速检测技术,主要以定性分析为主,假阳性/假阴性受到诟病,检测准确性仍有待提升,亟待发展基于新原理、新方法的病原菌快速检测技术。基于CRISPR(clustered regularly interspaced short palindromic repeats)的生物传感技术因具有高灵活性(对不同的基因靶点只需改变crRNA序列)、高特异性(单碱基分辨)、高灵敏(优于10^-18 mol/L浓度)、可编程、可模块化、低成本、可在各种体外介质中高效稳定运行等独特优势,打破了传统分子诊断与检测技术的局限性,正在成为下一代病原菌检测技术的引领者。在该技术中,Cas效应蛋白被用作高特异性的序列识别元件,结合不同的生物传感机制,即可用于病原菌的高特异性快速灵敏检测。在总结CRISPR/Cas生物传感技术原理的基础上,综述了用于病原菌检测的CRISPR/Cas12和CRISPR/Cas13生物传感技术研究进展。通过阐述CRISPR/Cas生物传感技术在实际应用中面临的挑战,展望其未来的发展前景。     

拉曼光谱技术在病原菌感染诊断中的应用进展

快速准确诊断感染性疾病病原体是遏制超级细菌传播和抗生素滥用的重要防线。目前,临床病原菌感染诊断十分依赖于培养手段,导致检测周期长达数日,不但影响了患者的及时诊治,还间接导致抗生素的滥用。拉曼光谱技术是一种无损、高灵敏的分子指纹图谱检测技术,近年来在生物学领域得到广泛应用,其具有的免培养、快速、高特异性、低成本等优点为病原菌感染的诊断提供了新方案。本文阐述了拉曼光谱技术的原理和特点,综述了其在病原菌鉴定和抗菌药物敏感性试验方面的应用进展。     

Rapid and sensitive point-of-care detection of Leptospira by RPA-CRISPR/Cas12a targeting lipL32

BackgroundOne of the key barriers preventing rapid diagnosis of leptospirosis is the lack of available sensitive point-of-care testing. This study aimed to develop and validate a clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 12a (CRISPR/Cas12a) platform combined with isothermal amplification to detect leptospires from extracted patient DNA samples.Methodology/Principal findingsA Recombinase Polymerase Amplification (RPA)-CRISPR/Cas12a-fluorescence assay was designed to detect the lipL32 gene of pathogenic Leptospira spp. The assays demonstrated a limit of detection (LOD) of 100 cells/mL, with no cross-reactivity against several other acute febrile illnesses. The clinical performance of the assay was validated with DNA extracted from 110 clinical specimens and then compared to results from qPCR detection of Leptospira spp. The RPA-CRISPR/Cas12a assay showed 85.2% sensitivity, 100% specificity, and 92.7% accuracy. The sensitivity increased on days 4–6 after the fever onset and decreased after day 7. The specificity was consistent for several days after the onset of fever. The overall performance of the RPA-CRISPR/Cas12a platform was better than the commercial rapid diagnostic test (RDT). We also developed a lateral flow detection assay (LFDA) combined with RPA-CRISPR/Cas12a to make the test more accessible and easier to interpret. The combined LFDA showed a similar LOD of 100 cells/mL and could correctly distinguish between known positive and negative clinical samples in a pilot study.Conclusions/SignificanceThe RPA-CRISPR/Cas12 targeting the lipL32 gene demonstrated acceptable sensitivity and excellent specificity for detection of leptospires. This assay might be an appropriate test for acute leptospirosis screening in limited-resource settings.     

Detection of Mycoplasma pneumoniae in simulated and true clinical throat swab specimens by nanorod array-surface-enhanced Raman spectroscopy

The prokaryote Mycoplasma pneumoniae is a major cause of respiratory disease in humans, accounting for 20% of all community-acquired pneumonia and the leading cause of pneumonia in older children and young adults. The limitations of existing options for mycoplasma diagnosis highlight a critical need for a new detection platform with high sensitivity, specificity, and expediency. Here we evaluated silver nanorod arrays (NA) as a biosensing platform for detection and differentiation of M. pneumoniae in culture and in spiked and true clinical throat swab samples by surface-enhanced Raman spectroscopy (SERS). Three M. pneumoniae strains were reproducibly differentiated by NA-SERS with 95%-100% specificity and 94-100% sensitivity, and with a lower detection limit exceeding standard PCR. Analysis of throat swab samples spiked with M. pneumoniae yielded detection in a complex, clinically relevant background with >90% accuracy and high sensitivity. In addition, NA-SERS correctly classified with >97% accuracy, ten true clinical throat swab samples previously established by real-time PCR and culture to be positive or negative for M. pneumoniae. Our findings suggest that the unique biochemical specificity of Raman spectroscopy, combined with reproducible spectral enhancement by silver NA, holds great promise as a superior platform for rapid and sensitive detection and identification of M. pneumoniae, with potential for point-of-care application.     

基于纳米信号标签的表面增强拉曼散射在病原菌检测中的应用

表面增强拉曼散射(surface-enhanced Ranan scattering,SERS)技术由于其灵敏度高、检测速度快、高特异性和无损等优点,在病原菌检测领域受到了广泛的关注.主要总结了近年来基于纳米信号标签的SERS方法在检测病原菌领域中的研究进展,并介绍了多功能SERS检测平台的构建及在病原菌检测中的应用....     

禽流感病毒最新研究进展

本文针对2004年爆发的禽流感疫病,回顾了2004年至2005年期间禽流感病毒的研究进展。逆转录聚合酶链式反应技术为禽流感病毒的分型提供了一种快速、可靠、准确的方法。对H5N1禽流感病毒致病机制的研究发现,其强致病性在于它可以躲避人类抗病毒细胞因子的作用,NS1基因编码蛋白的92位谷氨酸在其中发挥了关键作用。由于禽流感疾病多引起结膜炎,并与病毒细胞受体的研究结果相结合,有科学家认为眼部特异性是禽流感病毒的一个总体特征。社会普遍关注禽流感疫苗的研制,人类和禽类流感A型病毒M2蛋白胞外区域的序列比对工作为疫苗研制提供了一条新的思路,依据神经氨酸酶抑制剂抑制病毒的出芽繁殖原理的疫苗正在研制过程中,而利用siRNA预防和治疗禽流感也是很有潜力的一种方法。禽流感病毒研究的另一个热点是病毒基因节段的重配问题。     

Influenza A Virus Encoding Secreted Gaussia Luciferase as Useful Tool to Analyze Viral Replication and Its Inhibition by Antiviral Compounds and Cellular Proteins

Reporter genes inserted into viral genomes enable the easy and rapid quantification of virus replication, which is instrumental to efficient in vitro screening of antiviral compounds or in vivo analysis of viral spread and pathogenesis. Based on a published design, we have generated several replication competent influenza A viruses carrying either fluorescent proteins or Gaussia luciferase. Reporter activity could be readily quantified in infected cultures, but the virus encoding Gaussia luciferase was more stable than viruses bearing fluorescent proteins and was therefore analyzed in detail. Quantification of Gaussia luciferase activity in the supernatants of infected culture allowed the convenient and highly sensitive detection of viral spread, and enzymatic activity correlated with the number of infectious particles released from infected cells. Furthermore, the Gaussia luciferase encoding virus allowed the sensitive quantification of the antiviral activity of the neuraminidase inhibitor (NAI) zanamivir and the host cell interferon-inducible transmembrane (IFITM) proteins 1–3, which are known to inhibit influenza virus entry. Finally, the virus was used to demonstrate that influenza A virus infection is sensitive to a modulator of endosomal cholesterol, in keeping with the concept that IFITMs inhibit viral entry by altering cholesterol levels in the endosomal membrane. In sum, we report the characterization of a novel influenza A reporter virus, which allows fast and sensitive detection of viral spread and its inhibition, and we show that influenza A virus entry is sensitive to alterations of endosomal cholesterol levels.     

Influenza A Neuraminidase Antibody Assay with Sensitized Erythrocytes

Erythrocytes sensitized with purified neuraminidase (Hong Kong) antigens were used for assay of influenza A neuraminidase antibodies. The neuraminidase indirect hemagglutination test was equal to the neuraminidase hemagglutination-inhibition (enhancement) test and appeared to be better than the neuraminidase inhibition test for detection of fourfold or greater antibody rises in paired sera from influenza patients or vaccinees. It was better than both tests for detection of neuraminidase antibody. The neuraminidase indirect hemagglutination test is simple to perform and has the advantage of direct antigen-antibody assay.     

Genosensor for rapid,sensitive, specific point-of-care detection of H1N1 influenza (swine flu)

A 5′ amine group-linked haemagglutinin (HA) gene-specific probe was attached over the surface of a working electrode to develop a rapid, specific, and sensitive point of care detection assay for H1N1 (swine flu) in human respiratory nasal swabs. The probe was attached with a cysteine covered screen-printed gold electrode via 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS). The electrochemical assay was performed using differential pulse voltammetry with the use of the redox indicator methylene blue for the detection of different concentrations of the single-stranded viral genome. The developed genosensor showed high sensitivity for H1N1 influenza virus with a detection limit of 0.002 ng/6 μL of viral nucleic acid in the sample. Samples were analysed by quantitative real-time Polymerase Chain Reaction as well as by conventional PCR. The genosensor showed high specificity, as no cross-reaction was observed with the heterologous nucleic acid of different pathogens (Salmonella typhi, Neisseria meningitides, and Streptococcus pyogenes) and human DNA, and it was specific for H1N1 with a sensitivity of ∼49 μA cm⁻² ng^-1. Genosensor is based on a very simple methodology that can be followed based on its easy-to-access approach. It is quick and could be used as a point-of-care test for the detection of influenza virus within 30 min.     

Engineering a chemical implementation device and an imaging device for detecting chemiluminescence with a Polaroid™ high‐speed detector film: application to influenza diagnostics with the ZstatFlu®‐II test

We describe the engineering and product development of the chemiluminescent ZstatFlu®‐II Test kit for influenza diagnostics. The reaction vessel is a chemical implementation device with a polystyrene bottom chamber and a polypropylene top chamber that screw together. The patient's specimen is dispersed in a proprietary diluent and mixed inside the bottom chamber with the influenza viral neuraminidase‐specific substrate, 1,2‐dioxetane‐4,7‐dimethoxy‐Neu5Ac. Neuraminidase catalysis releases the dioxetane. The top chamber contains 40% NaOH and is sealed at the top with an ABS plastic plug‐crush pin assembly. The top chamber floor is 85% thinner at the centre, forming a frangible flap. An automated imaging device serves as an incubator for the chemical implementation devices and also facilitates the piercing of the flap by the crush pin. This action results in NaOH flushing into the bottom chamber, initiating chemiluminescence. The imaging device also exposes the Polaroid? high‐speed detector film to chemiluminescence. At the end of exposure, the film is automatically processed and ejected. Chemiluminescence from an influenza virus‐positive specimen produces a ‘+’‐shaped white image, archiving the diagnostic outcome. The modular ZstatFlu®‐II test kit components are easily adaptable for the chemiluminescent detection of a wide range of analytes. Copyright © 2003 John Wiley & Sons, Ltd.     

Rapid detection of SARS-CoV-2 with CRISPR-Cas12a

The recent outbreak of betacoronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is responsible for the Coronavirus Disease 2019 (COVID-19) global pandemic, has created great challenges in viral diagnosis. The existing methods for nucleic acid detection are of high sensitivity and specificity, but the need for complex sample manipulation and expensive machinery slow down the disease detection. Thus, there is an urgent demand to develop a rapid, inexpensive, and sensitive diagnostic test to aid point-of-care viral detection for disease monitoring. In this study, we developed a clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated proteins (Cas) 12a-based diagnostic method that allows the results to be visualized by the naked eye. We also introduced a rapid sample processing method, and when combined with recombinase polymerase amplification (RPA), the sample to result can be achieved in 50 minutes with high sensitivity (1–10 copies per reaction). This accurate and portable detection method holds a great potential for COVID-19 control, especially in areas where specialized equipment is not available.

The outbreak of SARS-CoV-2 has caused great damage to human society, and early detection of this virus is important to contain its spread and save lives. Existing diagnostic methods are complex and require well-trained personnel, but this study describes a fast and accurate method which can be operated by lay-users and whose results can be visualized by the naked eye.     

Ultrasensitive detection of rare mutations using next-generation targeted resequencing

With next-generation DNA sequencing technologies, one can interrogate a specific genomic region of interest at very high depth of coverage and identify less prevalent, rare mutations in heterogeneous clinical samples. However, the mutation detection levels are limited by the error rate of the sequencing technology as well as by the availability of variant-calling algorithms with high statistical power and low false positive rates. We demonstrate that we can robustly detect mutations at 0.1% fractional representation. This represents accurate detection of one mutant per every 1000 wild-type alleles. To achieve this sensitive level of mutation detection, we integrate a high accuracy indexing strategy and reference replication for estimating sequencing error variance. We employ a statistical model to estimate the error rate at each position of the reference and to quantify the fraction of variant base in the sample. Our method is highly specific (99%) and sensitive (100%) when applied to a known 0.1% sample fraction admixture of two synthetic DNA samples to validate our method. As a clinical application of this method, we analyzed nine clinical samples of H1N1 influenza A and detected an oseltamivir (antiviral therapy) resistance mutation in the H1N1 neuraminidase gene at a sample fraction of 0.18%.     

Quantum dot-based immunochromatography test strip for rapid, quantitative and sensitive detection of alpha fetoprotein

Rapid, quantitative detection of tumor markers with high sensitivity and specificity is critical to clinical diagnosis and treatment of cancer. We describe here a novel portable fluorescent biosensor that integrates quantum dot (QD) with an immunochromatography test strip (ICTS) and a home-made test strip reader for detection of tumor markers in human serum. Alpha fetoprotein (AFP), which is valuable for diagnosis of primary hepatic carcinoma, is used as a model tumor marker to demonstrate the performance of the proposed immunosensor. The principle of this sensor is on the basis of a sandwich immunoreaction that was performed on an ICTS. The fluorescence intensity of captured QD labels on the test line and control line served as signals was determined by the home-made test strip reader. The strong luminescence and robust photostability of QDs combined with the promising advantages of an ICTS and sensitive detection with the test strip reader result in good performance. Under optimal conditions, this biosensor is capable of detecting as low as 1 ng/mL AFP standard analyte in 10 min with only 50 μL sample volume. Furthermore, 1000 clinical human serum samples were tested by both the QD-based ICTS and a commercial electrochemiluminescence immunoassay AFP kit simultaneously to estimate the sensitivity, specificity and concordance of the assays. Results showed high consistency except for 24 false positive cases (false positive rate 3.92%) and 17 false negative cases (false negative rate 4.38%); the error rate was 4.10% in all. This demonstrates that the QD-based ICTS is capable of rapid, sensitive, and quantitative detection of AFP and shows a great promise for point-of-care testing of other tumor markers.     

Multiplexed detection and differentiation of the DNA strains for influenza A (H1N1 2009) using a silicon-based microfluidic system

Pandemic influenza by the swine-origin influenza virus (H1N1 2009) has attracted considerable concern worldwide. A convenient and accurate diagnostic approach that can be deployed at the point of care, such as in a doctor's office or at an airport, is critical for disease control. Here we report the development of a silicon-based microfluidic system for subtype differentiation of the novel H1N1 2009 strain vs. the seasonal influenza A (FluA) strain. The proposed system included two functional modules: a multiplexed PCR module for amplification of nucleic acid targets and a multiplexed silicon nanowire (SiNW) module for sequence determination. The PCR module consisted of a microfluidic PCR chamber and an electrical controller to perform a multiplexed protocol that simultaneously enriched specific segments of both H1N1 and FluA strains (if present), with 10(4)-10(5) amplification efficiency. The PCR amplicon was subsequently denatured and transferred to the SiNW sensing module for a label-free, multiplexed detection. A control SiNW was implemented, for the first time, in order to eliminate background interference. The detection module demonstrated a 10× change in the magnitude of differential current when the target DNA was injected. Overall, the system achieved a sensitivity of 20-30 fg/μl for H1N1 and seasonal FluA nucleic acids in a 10 μl sample. The low sample consumption, high sensitivity and high specificity render it a potential point-of-care (POC) platform to help doctors reach a yes/no decision for infectious diseases.     

Identification of upper respiratory tract pathogens using electrochemical detection on an oligonucleotide microarray

Bacterial and viral upper respiratory infections (URI) produce highly variable clinical symptoms that cannot be used to identify the etiologic agent. Proper treatment, however, depends on correct identification of the pathogen involved as antibiotics provide little or no benefit with viral infections. Here we describe a rapid and sensitive genotyping assay and microarray for URI identification using standard amplification and hybridization techniques, with electrochemical detection (ECD) on a semiconductor-based oligonucleotide microarray. The assay was developed to detect four bacterial pathogens (Bordetella pertussis, Streptococcus pyogenes, Chlamydia pneumoniae and Mycoplasma pneumoniae) and 9 viral pathogens (adenovirus 4, coronavirus OC43, 229E and HK, influenza A and B, parainfluenza types 1, 2, and 3 and respiratory syncytial virus. This new platform forms the basis for a fully automated diagnostics system that is very flexible and can be customized to suit different or additional pathogens. Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation. Because ECD uses an enzymatic reaction to create electrical signals that can be read directly from the array, there is no need for image analysis or for expensive and delicate optical scanning equipment. We show assay sensitivity and specificity that are excellent for a multiplexed format.     

To Test or to Treat? An Analysis of Influenza Testing and Antiviral Treatment Strategies Using Economic Computer Modeling

Background

Due to the unpredictable burden of pandemic influenza, the best strategy to manage testing, such as rapid or polymerase chain reaction (PCR), and antiviral medications for patients who present with influenza-like illness (ILI) is unknown.

Methodology/Principal Findings

We developed a set of computer simulation models to evaluate the potential economic value of seven strategies under seasonal and pandemic influenza conditions: (1) using clinical judgment alone to guide antiviral use, (2) using PCR to determine whether to initiate antivirals, (3) using a rapid (point-of-care) test to determine antiviral use, (4) using a combination of a point-of-care test and clinical judgment, (5) using clinical judgment and confirming the diagnosis with PCR testing, (6) treating all with antivirals, and (7) not treating anyone with antivirals. For healthy younger adults (<65 years old) presenting with ILI in a seasonal influenza scenario, strategies were only cost-effective from the societal perspective. Clinical judgment, followed by PCR and point-of-care testing, was found to be cost-effective given a high influenza probability. Doubling hospitalization risk and mortality (representing either higher risk individuals or more virulent strains) made using clinical judgment to guide antiviral decision-making cost-effective, as well as PCR testing, point-of-care testing, and point-of-care testing used in conjunction with clinical judgment. For older adults (≥65 years old), in both seasonal and pandemic influenza scenarios, employing PCR was the most cost-effective option, with the closest competitor being clinical judgment (when judgment accuracy ≥50%). Point-of-care testing plus clinical judgment was cost-effective with higher probabilities of influenza. Treating all symptomatic ILI patients with antivirals was cost-effective only in older adults.

Conclusions/Significance

Our study delineated the conditions under which different testing and antiviral strategies may be cost-effective, showing the importance of accuracy, as seen with PCR or highly sensitive clinical judgment.     

Optimization and clinical validation of a pathogen detection microarray

DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.     

Polymeric LabChip Real-Time PCR as a Point-of-Care-Potential Diagnostic Tool for Rapid Detection of Influenza A/H1N1 Virus in Human Clinical Specimens

It is clinically important to be able to detect influenza A/H1N1 virus using a fast, portable, and accurate system that has high specificity and sensitivity. To achieve this goal, it is necessary to develop a highly specific primer set that recognizes only influenza A viral genes and a rapid real-time PCR system that can detect even a single copy of the viral gene. In this study, we developed and validated a novel fluidic chip-type real-time PCR (LabChip real-time PCR) system that is sensitive and specific for the detection of influenza A/H1N1, including the pandemic influenza strain A/H1N1 of 2009. This LabChip real-time PCR system has several remarkable features: (1) It allows rapid quantitative analysis, requiring only 15 min to perform 30 cycles of real-time PCR. (2) It is portable, with a weight of only 5.5 kg. (3) The reaction cost is low, since it uses disposable plastic chips. (4) Its high efficiency is equivalent to that of commercially available tube-type real-time PCR systems. The developed disposable LabChip is an economic, heat-transferable, light-transparent, and easy-to-fabricate polymeric chip compared to conventional silicon- or glass-based labchip. In addition, our LabChip has large surface-to-volume ratios in micro channels that are required for overcoming time consumed for temperature control during real-time PCR. The efficiency of the LabChip real-time PCR system was confirmed using novel primer sets specifically targeted to the hemagglutinin (HA) gene of influenza A/H1N1 and clinical specimens. Eighty-five human clinical swab samples were tested using the LabChip real-time PCR. The results demonstrated 100% sensitivity and specificity, showing 72 positive and 13 negative cases. These results were identical to those from a tube-type real-time PCR system. This indicates that the novel LabChip real-time PCR may be an ultra-fast, quantitative, point-of-care-potential diagnostic tool for influenza A/H1N1 with a high sensitivity and specificity.