Nanotraps based on multifunctional materials for trapping and enrichment

Progress in diagnostic methods and vaccines for lumpy skin disease virus: a path towards understanding the disease

Lumpy skin disease (LSD) is caused by Lumpy Skin disease virus (LSDV) belonging to the genus Capripoxvirus (CaPV). The disease is widespread in Africa, the Middle East and Asia and has been present in Egypt since 1988. LSD is mainly transmitted by blood-sucking insects. LSD is clinically distinguished by a high fever, skin nodules, and swollen Lymph nodes. Detecting sub-clinical disease can be challenging however, prompt laboratory investigations are vital. Skin lesions are the main source of infection, although the virus is shed through many excretions and discharges including semen. Disease confirmation in clinical laboratories includes detection of viral nucleic acid, antigen and antibody levels. Simple, adaptable, and quick assays for detecting LSDV are required for control measures. Vaccination, together with controlled quarantine and vector control measures, may be beneficial for preventing disease spread. Presently, a range of live attenuated vaccines, have been used in the field with different levels of protection and side effects. With high levels of vaccination coverage, attenuated Neethling vaccines have successfully eradicated of LSDV in Europe. Inactivated LSDV vaccines have also been demonstrated effective in experimental infections. Furthermore, due to its large genome, LSDV is being exploited as a vaccine delivery element, generating an innovative composite with additional viral genes by DNA recombination. Vaccines developed on this basis have the potential to prevent a wide range of diseases and have been demonstrated to be effective in experimental settings. In this review, we emphasizethe advances in diagnostic methods and vaccines developed last decade, thereby providing a basis for future research into various aspects of LSDV and providing information for possibility of disease elimination.

An ingenious electrochemical system based on naphthalenediimide derivatives for ultrasensitive immunosensing of alpha-fetoprotein

It is crucial to develop highly efficient electrochemistry systems for sensitive detection of tumour markers. In this work, naphthalenediimide derivatives with electrochemical application potential were successfully synthesized and characterized. Electrochemistry and calculation of density functional theory (DFT) showed that 2,7-bis(4-(dimethylamino)phenyl)benzo[lmn] [3,8]phenanthroline-1,3,6,8(2H,7H)-tetraone (NDI-1) was an ideal candidate for electrochemical probe construction. Subsequently, based on the cyclic catalytic effect between NDI-1 and K2S2O8, a satisfying composite of GO/NDI-1/AuNPs was prepared and used to construct electrochemical probe for the design of ingenious sandwiched electrochemical immunosensor. Taking alpha-fetoprotein (AFP) as the model target biomarker, the designed immunosensor showed good detection performance for AFP, which exhibited wide range of linear response (10 fg/mL - 10 ng/mL), low detection limit (3.3 fg/mL). Moreover, the proposed immunosensor has been successfully applied to AFP detection in human serum, which provides the possibility for clinical applications. The designed electrochemical system provides a new electrochemical probe for the construction of immunosensors and may be extended to the electroanalysis of other biomolecules with recognition units.

Enhanced Recovery and Detection of Highly Infectious Animal Disease Viruses by Virus Capture Using Nanotrap® Microbiome A Particles

This study reports the use of Nanotrap® Microbiome A Particles (NMAPs) to capture and concentrate viruses from diluted suspensions to improve their recovery and sensitivity to detection by real-time PCR/RT-PCR (qPCR/RT-qPCR). Five highly infectious animal disease viruses including goatpox virus (GTPV), sheeppox virus (SPPV), lumpy skin disease virus (LSDV), peste des petits ruminants virus (PPRV), and African swine fever virus (ASFV) were used in this study. After capture, the viruses remained viable and recoverable by virus isolation (VI) using susceptible cell lines. To assess efficacy of recovery, the viruses were serially diluted in phosphate-buffered saline (PBS) or Eagle's Minimum Essential Medium (EMEM) and then subjected to virus capture using NMAPs. The NMAPs and the captured viruses were clarified on a magnetic stand, reconstituted in PBS or EMEM, and analyzed separately by VI and virus-specific qPCR/RT-qPCR. The PCR results showed up to a 100-fold increase in the sensitivity of detection of the viruses following virus capture compared to the untreated viruses from the same dilutions. Experimental and clinical samples were subjected to virus capture using NMAPs and analyzed by PCR to determine diagnostic sensitivity (DSe) that was comparable (100%) to that determined using untreated (-NMAPs) samples. NMAPs were also used to capture spiked viruses from EDTA whole blood (EWB). Virus capture from EWB was partially blocked, most likely by hemoglobin (HMB), which also binds NMAPs and outcompetes the viruses. The effect of HMB could be removed by either dilution (in PBS) or using HemogloBind™ (Biotech Support Group; Monmouth Junction, NJ, USA), which specifically binds and precipitates HMB. Enhanced recovery and detection of viruses using NMAPs can be applicable to other highly pathogenic animal viruses of agricultural importance.

Molecular-Sieving Label-Free Surface-Enhanced Raman Spectroscopy for Sensitive Detection of Trace Small-Molecule Biomarkers in Clinical Samples

Small-molecule biomarkers are ubiquitous in biological fluids with pathological implications, but major challenges persist in their quantitative analysis directly in complex clinical samples. Herein, a molecular-sieving label-free surface-enhanced Raman spectroscopy (SERS) biosensor is reported for selective quantitative analysis of trace small-molecule trimetazidine (TMZ) in clinical samples. Our biosensor is fabricated by decorating a superhydrophobic monolayer of microporous metal-organic frameworks (MOF) shell-coated Au nanostar nanoparticles on a silicon substrate. The design strategy principally combines the hydrophobic surface-enabled physical confinement and preconcentration, MOF-assisted molecular enrichment and sieving of small molecules, and sensitive SERS detection. Our biosensor utilizes such a "molecular confinement-and-sieving" strategy to achieve a five orders-of-magnitude dynamic detection range and a limit of detection of ≈0.5 nM for TMZ detection in either urine or whole blood. We further demonstrate the applicability of our biosensing platform for longitudinal label-free SERS detection of the TMZ level directly in clinical samples in a mouse model.

Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater

Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.

Combination of Fe(OH)3 modified diatomaceous earth and qPCR for the enrichment and detection of African swine fever virus in water

Water is one of the primary vectors for African swine fever virus (ASFV) transmission among swine herds. However, the low concentrations of ASFV in water represent a challenge for the detection of the virus by conventional PCR methods, and enrichment of the virus would increase the test sensitivity. In this study, aiming to enrich ASFV in water quickly and efficiently, a rapid and efficient water-borne virus enrichment system (MDEF, modified diatomaceous earth by ferric hydroxide colloid) was used to enrich ASFV in water. After enrichment by MDEF, conventional real-time PCR (qPCR) was used for ASFV detection. ASFV were inactivated and diluted in 10 L of water, of which 4 mL were collected after 60 min treatment using the MDEF system. Two thousand five hundred times reduction of the sample volume was achieved after enrichment. A high adsorption rate of about 99.99 (±0.01)% and a high recovery rate of 64.01 (±10.20)% to 179.65 (±25.53)% was achieved by using 1g modified diatomaceous earth for 10 L ASFV contaminated water. The limit of qPCR detection of ASFV decreased to 1 × 10^-1.11 GU ml^-1 (genomic units per milliliter) from 1 × 10^2.71 GU ml^-1 after concentrating the spiked water from 10 L to 4 ml. Preliminary application of MDEF allowed successful detection of African swine fever virus (ASFV), porcine circovirus type 2 (PCV2), and pseudorabies virus (PRV) in sewage. Thus, the combination of modified diatomaceous earth and real-time PCR is a promising strategy for the detection of viruses in water.

Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19

Much of what is known and theorized concerning passive sampling techniques has been developed considering chemical analytes. Yet, historically, biological analytes, such as Salmonella typhi, have been collected from wastewater via passive sampling with Moore swabs. In response to the COVID-19 pandemic, passive sampling is re-emerging as a promising technique to monitor SARS-CoV-2 RNA in wastewater. Method comparisons and disease surveillance using composite, grab, and passive sampling for SARS-CoV-2 RNA detection have found passive sampling with a variety of materials routinely produced qualitative results superior to grab samples and useful for sub-sewershed surveillance of COVID-19. Among individual studies, SARS-CoV-2 RNA concentrations derived from passive samplers demonstrated heterogeneous correlation with concentrations from paired composite samples ranging from weak (R2 = 0.27, 0.31) to moderate (R2 = 0.59) to strong (R2 = 0.76). Among passive sampler materials, electronegative membranes have shown great promise with linear uptake of SARS-CoV-2 RNA observed for exposure durations of 24 to 48 h and in several cases RNA positivity on par with composite samples. Continuing development of passive sampling methods for the surveillance of infectious diseases via diverse forms of fecal waste should focus on optimizing sampler materials for the efficient uptake and recovery of biological analytes, kit-free extraction, and resource-efficient testing methods capable of rapidly producing qualitative or quantitative data. With such refinements passive sampling could prove to be a fundamental tool for scaling wastewater surveillance of infectious disease, especially among the 1.8 billion persons living in low-resource settings served by non-traditional wastewater collection infrastructure.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Centrifugal Microfluidic Method for Enrichment and Enzymatic Extraction of Severe Acute Respiratory Syndrome Coronavirus 2 RNA

The diversification of analytical tools for diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is imperative for effective virus surveillance and transmission control worldwide. Development of robust methods for rapid, simple isolation of viral RNA permits more expedient pathogen detection by downstream real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR) to minimize stalled containment and enhance treatment efforts. Here, we describe an automatable rotationally driven microfluidic platform for enrichment and enzymatic extraction of SARS-CoV-2 RNA from multiple sample types. The multiplexed, enclosed microfluidic centrifugal device (μCD) is capable of preparing amplification-ready RNA from up to six samples in under 15 min, minimizing user intervention and limiting analyst exposure to pathogens. Sample enrichment leverages Nanotrap Magnetic Virus Particles to isolate intact SARS-CoV-2 virions from nasopharyngeal and/or saliva samples, enabling the removal of complex matrices that inhibit downstream RNA amplification and detection. Subsequently, viral capsids are lysed using an enzymatic lysis cocktail for release of pathogenic nucleic acids into a PCR-compatible buffer, obviating the need for downstream purification. Early in-tube assay characterization demonstrated comparable performance between our technique and a "gold-standard" commercial RNA extraction and purification kit. RNA obtained using the fully integrated μCDs permitted reliable SARS-CoV-2 detection by real-time RT-PCR. Notably, we successfully analyzed full-process controls, positive clinical nasopharyngeal swabs suspended in viral transport media, and spiked saliva samples, showcasing the method's broad applicability with multiple sample matrices commonly encountered in clinical diagnostics.