scholarly journals Rapid functionalisation and detection of viruses via a novel Ca2+-mediated virus-DNA interaction

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nicole C. Robb ◽  
Jonathan M. Taylor ◽  
Amy Kent ◽  
Oliver J. Pambos ◽  
Barak Gilboa ◽  
...  
Keyword(s):  
Virus Detection ◽  
Dna Interaction ◽  
Single Particle Tracking ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Intact Virus ◽  
Wide Range ◽  
Particle Size Determination ◽  
Pathogenic Viruses ◽  
Chemical Groups

Abstract Current virus detection methods often take significant time or can be limited in sensitivity and specificity. The increasing frequency and magnitude of viral outbreaks in recent decades has resulted in an urgent need for diagnostic methods that are facile, sensitive, rapid and inexpensive. Here, we describe and characterise a novel, calcium-mediated interaction of the surface of enveloped viruses with DNA, that can be used for the functionalisation of intact virus particles via chemical groups attached to the DNA. Using DNA modified with fluorophores, we have demonstrated the rapid and sensitive labelling and detection of influenza and other viruses using single-particle tracking and particle-size determination. With this method, we have detected clinical isolates of influenza in just one minute, significantly faster than existing rapid diagnostic tests. This powerful technique is easily extendable to a wide range of other enveloped pathogenic viruses and holds significant promise as a future diagnostic tool.

scholarly journals Rapid functionalisation and detection of viruses via a novel Ca2+-mediated virus-DNA interaction

2019 ◽  
Author(s):  
Nicole C. Robb ◽  
Jonathan M. Taylor ◽  
Amy Kent ◽  
Oliver J. Pambos ◽  
Barak Gilboa ◽  
...  
Keyword(s):  
Virus Detection ◽  
Dna Interaction ◽  
Single Particle Tracking ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Intact Virus ◽  
Wide Range ◽  
Particle Size Determination ◽  
Pathogenic Viruses ◽  
Chemical Groups

ABSTRACTCurrent virus detection methods often take significant time or can be limited in sensitivity and specificity. The increasing frequency and magnitude of viral outbreaks in recent decades has resulted in an urgent need for diagnostic methods that are facile, sensitive, rapid and inexpensive. Here, we describe and characterise a novel, calcium-mediated interaction of the surface of enveloped viruses with DNA, that can be used for the functionalisation of intact virus particles via chemical groups attached to the DNA. Using DNA modified with fluorophores, we have demonstrated the rapid and sensitive labelling and detection of influenza and other viruses using single-particle tracking and particle-size determination. With this method, we have detected clinical isolates of influenza in just one minute, significantly faster than existing rapid diagnostic tests. This powerful technique is easily extendable to a wide range of other enveloped pathogenic viruses and holds significant promise as a future diagnostic tool.

scholarly journals The virome of German bats: comparing virus discovery approaches

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Claudia Kohl ◽  
Annika Brinkmann ◽  
Aleksandar Radonić ◽  
Piotr Wojtek Dabrowski ◽  
Kristin Mühldorfer ◽  
...  
Keyword(s):  
Virus Detection ◽  
Detection Methods ◽  
Single Type ◽  
Metagenomic Sequencing ◽  
Virus Discovery ◽  
Highly Pathogenic ◽  
Pcr Screening ◽  
Specific Pcr ◽  
Pathogenic Viruses ◽  
Viral Sequences

AbstractBats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.

Detection of the influenza virus yesterday and now.

2014 ◽  
Vol 61 (3) ◽  
Author(s):  
Agnieszka Woźniak-Kosek ◽  
Bogumiła Kempińska-Mirosławska ◽  
Grażyna Hoser
Keyword(s):  
Influenza Virus ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Clinical Samples ◽  
Serological Tests ◽  
Human Influenza Virus ◽  
Rapid Spread ◽  
Influenza Virus Detection

Demographic changes and the development of transportation contribute to the rapid spread of influenza. Before an idea of a 'person to person' spread appeared, divergent theories were developed to explain influenza epidemics in the past. Intensified virological and serological tests became possible after isolation of the human influenza virus in 1933. The first influenza virus detection methods were based on its isolation in egg embryos or cell lines and on demonstration of the presence of the viral antigens. Molecular biology techniques associated with amplification of RNA improved the quality of tests as well as sensitivity of influenza virus detection in clinical samples. It became possible to detect mixed infections caused by influenza types A and B and to identify the strain of the virus. Development of reliable diagnostic methods enabled fast diagnosis of influenza which is important for choosing an appropriate medical treatment.

scholarly journals Microfluidic-based virus detection methods for respiratory diseases

2021 ◽  
Author(s):  
E. Alperay Tarim ◽  
Betul Karakuzu ◽  
Cemre Oksuz ◽  
Oyku Sarigil ◽  
Melike Kizilkaya ◽  
...  
Keyword(s):  
Direct Detection ◽  
Genetic Material ◽  
Treatment Strategies ◽  
Virus Detection ◽  
Respiratory Viruses ◽  
Detection Methods ◽  
Novel Technologies ◽  
Detection Techniques ◽  
Specificity And Sensitivity ◽  
Intact Virus

AbstractWith the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid–based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.

scholarly journals Study of Silicon Nitride Waveguide Platform for On-Chip Virus Detection: Prospects for COVID-19

2021 ◽  
Author(s):  
Raghi S. El Shamy ◽  
Mohamed A. Swillam ◽  
Xun Li
Keyword(s):  
Silicon Nitride ◽  
Optical Sensors ◽  
Virus Detection ◽  
High Sensitivity ◽  
Single Mode ◽  
Mass Scale ◽  
Detection Methods ◽  
Slot Waveguide ◽  
Wide Range ◽  
Strip Waveguide

Abstract This work presents a rigorous sensitivity analysis of silicon nitride on silicon dioxide strip waveguide for virus detection, focusing on COVID-19. In general, by functionalizing the waveguide surface with specific antibodies layer, we make the optical sensor sensitive only to a particular virus. Unlike conventional virus detection methods such as polymerase chain reaction (PCR), integrated refractive index (RI) optical sensors offer cheap and mass-scale fabrication of compact devices for fast and straightforward detection with high sensitivity and selectivity. Our analysis includes a wide range of wavelengths from visible to mid-infrared. We determined the strip waveguide's single-mode dimensions and the optimum dimensions that maximize the sensitivity to the virus layer attached to its surface at each wavelength. We also compared the strip waveguide to the widely used slot waveguide. Our study shows that silicon nitride strip waveguide working at lower wavelengths is the optimum choice for virus detection as it maximizes both the waveguide sensitivity (Swg) and the figure of merit (FOM) of the sensor. Furthermore, the optimized waveguide can work for a range of viruses. Balanced Mach-Zehnder interferometer (MZI) sensors were designed at different wavelengths showing high FOM at λ = 450nm ranging from 500 RIU-1 up to 1231 RIU-1 with LMZI=500 µm. Different MZI configurations were also studied and compared. Finally, edge coupling from the fiber to the sensor was designed, showing insertion loss (IL) at λ = 450nm of 4.1 dB for the design with FOM = 500 RIU-1. The obtained coupling efficiencies are higher than recently proposed fiber couplers.

scholarly journals Diagnostics of Grapevine fanleaf virus

Biljni lekar ◽  
2021 ◽  
Vol 49 (1) ◽  
pp. 54-64
Author(s):  
Đina Konstantin ◽  
Goran Barać ◽  
Renata Iličić ◽  
Ferenc Bagi
Keyword(s):  
Visual Inspection ◽  
Virus Detection ◽  
Plant Viruses ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Economic Losses ◽  
Rt Pcr ◽  
Grapevine Fanleaf Virus ◽  
Qrt Pcr ◽  
Propagation Material

Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. Due to the multiple possibilities of infection, they have become widespread. The use of healthy propagation material, free of viroids, viruses and bacteria, is an important strategy in disease control in viticulture. The early and accurate detection of plant viruses is an essential component of their control. Due to the widespread of Grapevine fanleaf virus (GFLV) and its devastating potential, various diagnostic methods are being used. GFLV detection methods based on the specificity of the protein cover (ELISA) and nucleic acid-based virus detection methods (RT-PCR, qRT-PCR). Symptoms of viral diseases are often not distinct and can be confused with those of abiotic stresses, so visual inspection is not reliable enough.

scholarly journals Application of Oxford Nanopore Technology to Plant Virus Detection

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1424
Author(s):  
Lia W. Liefting ◽  
David W. Waite ◽  
Jeremy R. Thompson
Keyword(s):  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Plant Virus Detection ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Virus Diagnostics ◽  
Post Entry ◽  
Read Accuracy

The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.

scholarly journals Detectivity optimization to detect of ultraweak light fluxes with an EM-CCD as binary photon counter array

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ibtissame Khaoua ◽  
Guillaume Graciani ◽  
Andrey Kim ◽  
François Amblard
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Photon Counting ◽  
Detection Methods ◽  
Strong Nonlinearity ◽  
Wide Range ◽  
Depth Analysis ◽  
Spatially Extended ◽  
Extended Sources ◽  
Photon Counting Mode

AbstractFor a wide range of purposes, one faces the challenge to detect light from extremely faint and spatially extended sources. In such cases, detector noises dominate over the photon noise of the source, and quantum detectors in photon counting mode are generally the best option. Here, we combine a statistical model with an in-depth analysis of detector noises and calibration experiments, and we show that visible light can be detected with an electron-multiplying charge-coupled devices (EM-CCD) with a signal-to-noise ratio (SNR) of 3 for fluxes less than $$30\,{\text{photon}}\,{\text{s}}^{ - 1} \,{\text{cm}}^{ - 2}$$ 30 photon s - 1 cm - 2 . For green photons, this corresponds to 12 aW $${\text{cm}}^{ - 2}$$ cm - 2 ≈ $$9{ } \times 10^{ - 11}$$ 9 × 10 - 11 lux, i.e. 15 orders of magnitude less than typical daylight. The strong nonlinearity of the SNR with the sampling time leads to a dynamic range of detection of 4 orders of magnitude. To detect possibly varying light fluxes, we operate in conditions of maximal detectivity $${\mathcal{D}}$$ D rather than maximal SNR. Given the quantum efficiency $$QE\left( \lambda \right)$$ Q E λ of the detector, we find $${ \mathcal{D}} = 0.015\,{\text{photon}}^{ - 1} \,{\text{s}}^{1/2} \,{\text{cm}}$$ D = 0.015 photon - 1 s 1 / 2 cm , and a non-negligible sensitivity to blackbody radiation for T > 50 °C. This work should help design highly sensitive luminescence detection methods and develop experiments to explore dynamic phenomena involving ultra-weak luminescence in biology, chemistry, and material sciences.

scholarly journals Application of the Dehydration Homogeneous Liquid–Liquid Extraction (DHLLE) Sample Preparation Method for Fingerprinting of Honey Volatiles

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2277
Author(s):  
Piotr M. Kuś ◽  
Igor Jerković
Keyword(s):  
Carboxylic Acid ◽  
Sample Preparation ◽  
Preparation Method ◽  
Liquid Extraction ◽  
Sample Preparation Method ◽  
Phenyllactic Acid ◽  
Homogeneous Liquid ◽  
Liquid Liquid Extraction ◽  
Wide Range ◽  
Chemical Groups

Recently, we proposed a new sample preparation method involving reduced solvent and sample usage, based on dehydration homogeneous liquid–liquid extraction (DHLLE) for the screening of volatiles and semi-volatiles from honey. In the present research, the method was applied to a wide range of honeys (21 different representative unifloral samples) to determine its suitability for detecting characteristic honey compounds from different chemical classes. GC-FID/MS disclosed 130 compounds from different structural and chemical groups. The DHLLE method allowed the extraction and identification of a wide range of previously reported specific and nonspecific marker compounds belonging to different chemical groups (including monoterpenes, norisoprenoids, benzene derivatives, or nitrogen compounds). For example, DHLLE allowed the detection of cornflower honey chemical markers: 3-oxo-retro-α-ionols, 3,4-dihydro-3-oxoedulan, phenyllactic acid; coffee honey markers: theobromine and caffeine; linden honey markers: 4-isopropenylcyclohexa-1,3-diene-1-carboxylic acid and 4-(2-hydroxy-2-propanyl)cyclohexa-1,3-diene-1-carboxylic acid, as well as furan derivatives from buckwheat honey. The obtained results were comparable with the previously reported data on markers of various honey varieties. Considering the application of much lower volumes of very common reagents, DHLLE may provide economical and ecological advantages as an alternative sample preparation method for routine purposes.

scholarly journals Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

2021 ◽  
Vol 9 (4) ◽  
pp. 862
Author(s):  
Vittoria Catara ◽  
Jaime Cubero ◽  
Joël F. Pothier ◽  
Eran Bosis ◽  
Claude Bragard ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Bacterial Species ◽  
Management Strategies ◽  
Diagnostic Methods ◽  
Plant Diseases ◽  
Wild Plants ◽  
Future Climate Change ◽  
Climate Change Scenarios ◽  
Wide Range ◽  
Diversity Studies

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

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