Label-Free Analysis of Single Viruses with a Resolution Comparable to That of Electron Microscopy and the Throughput of Flow Cytometry

Printed Nanochain-Based Colorimetric Assay for Quantitative Virus Detection

Fast and ultrasensitive detection of pathogens is very important for efficient monitoring and prevention of viral infections. Here, we demonstrate a label-free optical detection approach that uses a printed nanochain assay for colorimetric quantitative testing of viruses. The antibody-modified nanochains have high activity and specificity which can rapidly identify target viruses directly from biofluids in 15 min, as well as differentiate their subtypes. Arising from the resonance induced near-field enhancement, the color of nanochains changes with the binding of viruses that are easily observed by a smartphone. We achieve the detection limit of 1 PFU μL^-1 through optimizing the optical response of nanochains in visible region. Besides, it allows for real-time response to virus concentrations ranging from 0 to 1.0×10⁵  PFU mL^-1 . This low-cost and portable platform is also applicable to rapid detection of other biomarkers, making it attractive for many clinical applications.

Quantitative Assessment of the Physical Virus Titer and Purity by Ultrasensitive Flow Virometry

Rapid quantification of viruses is vital for basic research on viral diseases as well as biomedical application of virus-based products. Here, we report the development of a high-throughput single-particle method to enumerate intact viral particles by ultrasensitive flow virometry, which detects single viruses as small as 27 nm in diameter. The nucleic acid dye SYTO 82 was used to stain the viral (or vector) genome, and a laboratory-built nano-flow cytometer (nFCM) was employed to simultaneously detect the side-scatter and fluorescence signals of individual viral particles. Using the bacteriophage T7 as a model system, intact virions were completely discriminated from empty capsids and naked viral genomes. Successful measurement of the physical virus titer and purity was demonstrated for recombinant adenoviruses, which could be used for gene delivery, therapeutic products derived from phage cocktails, and infected cell supernatants for veterinary vaccine production.

Inhibition of Mitochondrial ATP Synthesis and Regulation of Oxidative Stress Based on {SbW8 O30 } Determined by Single-Cell Proteomics Analysis

The 10-nuclear heteroatom cluster modified {SbW₈ O₃₀ } was successfully synthesized and exhibited inhibitory activity (IC₅₀ =0.29 μM). Based on proteomics analysis, Na₄ Ni₂ Sb₂ W₂ -SbW₈ inhibited ATP production by affecting the expression of 16 related proteins, hindering metabolic functions in vivo and cell proliferation due to reactive oxygen species (ROS) stress. In particular, the low expression of FAD/FMN-binding redox enzymes (relative expression ratio of the experimental group to the control=0.43843) could be attributed to the redox mechanism of Na₄ Ni₂ Sb₂ W₂ -SbW₈ , which was consistent with the effect of polyoxometalates (POMs) and FMN-binding proteins on ATP formation. An electrochemical study showed that Na₄ Ni₂ Sb₂ W₂ -SbW₈ combined with FMN to form Na₄ Ni₂ Sb₂ W₂ -SbW₈ -2FMN complex through a one-electron process of the W atoms. Na₄ Ni₂ Sb₂ W₂ -SbW₈ acted as catalase and glutathione peroxidase to protect the cell from ROS stress, and the inhibition rates were 63.3 % at 1.77 μM of NADPH and 86.06 % at 10.62 μM of 2-hydroxyterephthalic acid. Overall, our results showed that POMs can be specific oxidative/antioxidant regulatory agents.

ENVirT: inference of ecological characteristics of viruses from metagenomic data

Background

Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases.

Results

In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses.

Conclusions

These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2398-5) contains supplementary material, which is available to authorized users.

Electron-Beam-Lithographed Nanostructures as Reference Materials for Label-Free Scattered-Light Biosensing of Single Filoviruses

Optical biosensors based on scattered-light measurements are being developed for rapid and label-free detection of single virions captured from body fluids. Highly controlled, stable, and non-biohazardous reference materials producing virus-like signals are valuable tools to calibrate, evaluate, and refine the performance of these new optical biosensing methods. To date, spherical polymer nanoparticles have been the only non-biological reference materials employed with scattered-light biosensing techniques. However, pathogens like filoviruses, including the Ebola virus, are far from spherical and their shape strongly affects scattered-light signals. Using electron beam lithography, we fabricated nanostructures resembling individual filamentous virions attached to a biosensing substrate (silicon wafer overlaid with silicon oxide film) and characterized their dimensions with scanning electron and atomic force microscopes. To assess the relevance of these nanostructures, we compared their signals across the visible spectrum to signals recorded from Ebola virus-like particles which exhibit characteristic filamentous morphology. We demonstrate the highly stable nature of our nanostructures and use them to obtain new insights into the relationship between virion dimensions and scattered-light signal.