Highly sensitive extraction-free saliva-based molecular assay for rapid diagnosis of SARS-CoV-2

The COVID-19 pandemic highlighted the necessity of fast, sensitive, and efficient methods to test large populations for respiratory viruses. The "gold standard" molecular assays for detecting respiratory viruses, such as quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR), rely on invasive swab samples and require time-consuming and labor-intensive extraction processes. Moreover, the turnaround time for RT-qPCR-based assays is too lengthy for rapid screening. Extraction-free saliva-based methods provide a non-invasive sampling process with a fast turnaround time and are suitable for high-throughput applications. However, when used with a standard RT-qPCR system, the absence of extraction significantly reduces the assays' sensitivity. Here, using a novel optical modulation biosensing (OMB) platform, we developed a rapid and highly sensitive extraction-free saliva-based molecular assay. We blindly tested 364 paired nasopharyngeal swabs and saliva samples from suspected SARS-CoV-2 cases in Israel. Compared with the gold standard swab-based RT-qPCR assay, the sensitivity of the extraction-free saliva-based OMB assay is 90.7%, much higher than the sensitivity of extraction-free saliva-based RT-qPCR assay (77.8%) with similar specificity (95.3% and 97.6%, respectively). Moreover, out of 12 samples identified by the OMB-based assay as positive, 8 samples were collected from hospitalized patients in a COVID-19 ward and were verified to be SARS-CoV-2-positive upon admission, indicating that the actual clinical sensitivity and specificity of the OMB assay are higher. Considering its user-friendly saliva-based protocol, short and cost-effective extraction-free process, and high clinical accuracy, the OMB-based molecular assay is very suitable for high-throughput testing of large populations for respiratory viruses.

IMPORTANCE

Three years after the SARS-CoV-2 outbreak, there are no molecular tests that combine low-cost and straightforward sample preparation, effective sample handling, minimal reagent and disposable requirements, high sensitivity, and high throughput required for mass screening. Existing rapid molecular techniques typically sacrifice certain requirements to meet others. Yet, localized outbreaks of novel viral diseases happen daily in different parts of the world. In this context, respiratory diseases are of specific importance, as they are frequently airborne and highly contagious, with the potential for a rapid global spread. The widely accepted opinion is that another pandemic is just a question of time. To ensure that the containment efforts for the upcoming "disease X" are successful, introducing rapid, high-throughput, and highly sensitive diagnostic methods for detecting and identifying pathogens is critical. A few months into the pandemic, saliva was suggested as a diagnostic matrix for SARS-CoV-2 detection. The collection of saliva does not require swabs and is minimally invasive. In particular, extraction-free saliva-based assays require fewer reagents and disposables, and therefore are faster and cheaper, offering an appealing alternative for low-income countries. Unfortunately, current extraction-free saliva-based detection methods, such as direct RT-qPCR or isothermal amplification, have either low sensitivity or low throughput. Therefore, we believe that the presented highly sensitive ht-OMBi platform and the extraction-free saliva-based molecular assay can become an essential tool in the infectious disease monitoring toolbox.

Recent Advances in Rapid and Highly Sensitive Detection of Proteins and Specific DNA Sequences Using a Magnetic Modulation Biosensing System

In early disease stages, biomolecules of interest exist in very low concentrations, presenting a significant challenge for analytical devices and methods. Here, we provide a comprehensive overview of an innovative optical biosensing technology, termed magnetic modulation biosensing (MMB), its biomedical applications, and its ongoing development. In MMB, magnetic beads are attached to fluorescently labeled target molecules. A controlled magnetic force aggregates the magnetic beads and transports them in and out of an excitation laser beam, generating a periodic fluorescent signal that is detected and demodulated. MMB applications include rapid and highly sensitive detection of specific nucleic acid sequences, antibodies, proteins, and protein interactions. Compared with other established analytical methodologies, MMB provides improved sensitivity, shorter processing time, and simpler protocols.

High throughput optical modulation biosensing for highly sensitive and rapid detection of biomarkers

Rapid, highly sensitive, and high-throughput detection of biomarkers at low concentrations is invaluable for early diagnosis of various diseases. In many highly sensitive immunoassays, magnetic beads are used to capture fluorescently labeled target molecules. The target molecules are then quantified by detecting the fluorescent signal from individual beads, which is time consuming and requires a complicated and expensive detection system. Here, we demonstrate a high-throughput optical modulation biosensing (ht-OMB) system, which uses a small permanent magnet to aggregate the beads into a small detection volume and eliminates background noise by steering a laser beam in and out of the cluster of beads. Shortening the aggregation, acquisition, and well-to-well scanning transition times enables reading a 96-well plate within 10 min. Using the ht-OMB system to detect human Interleukin-8, we demonstrated a limit of detection of 0.14 ng/L and a 4-log dynamic range. Testing 94 RNA extracts from 36 confirmed RT-qPCR SARS-CoV-2-positive patients (C_t≤40) and 58 confirmed RT-qPCR SARS-CoV-2-negative individuals resulted in 100% sensitivity and 100% specificity.

A Magnetic Modulation Biosensing-Based Molecular Assay for Rapid and Highly Sensitive Clinical Diagnosis of Coronavirus Disease 2019 (COVID-19)

Rapid and sensitive detection of human pathogens, such as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is an urgent and challenging task for clinical laboratories. Currently, the gold standard for SARS-CoV-2-specific RNA is based on quantitative RT-PCR (RT-qPCR), which relies on target amplification by Taq polymerase and uses a fluorescent resonance energy transfer-based hydrolysis probe. Although this method is accurate and specific, it is also time consuming. Here, a new molecular assay is described that combines a highly sensitive magnetic modulation biosensing (MMB) system, rapid thermal cycling, and a modified double-quenched hydrolysis probe. In vitro transcribed SARS-CoV-2 RNA targets spiked in PCR-grade water, were used to show that the calculated limit of detection of the MMB-based molecular assay was 1.6 copies per reaction. Testing 309 RNA extracts from 170 confirmed RT-qPCR SARS-CoV-2-negative individuals (30 of whom were positive for other respiratory viruses) and 139 RT-qPCR SARS-CoV-2-positive patients (C_T ≤ 42) resulted in 97.8% sensitivity, 100% specificity, and 0% cross-reactivity. The total turnaround time of the MMB-based assay is 30 minutes, which is three to four times faster than a standard RT-qPCR. By adjusting the primers and the probe set, the platform can be easily adapted to detect most of the pathogens that are currently being diagnosed by RT-qPCR.

Optical modulation biosensing system for rapid detection of biological targets at low concentrations

In many sensitive assays, target molecules are tagged using fluorescently labeled probes and captured using magnetic beads. Here, we introduce an optical modulation biosensing (OMB) system, which aggregates the beads into a small detection area and separates the signal from the background noise by manipulating the laser beam in and out of the cluster of beads. Using the OMB system to detect human interleukin-8, we demonstrated a limit of detection of 0.02 ng/L and a 4-log dynamic range. Using Zika-positive and healthy individuals' serum samples, we show that the OMB-based Zika IgG serological assay has 96% sensitivity and 100% specificity.

Discovery of MK-8153, a Potent and Selective ROMK Inhibitor and Novel Diuretic/Natriuretic

A renal outer medullary potassium channel (ROMK, Kir1.1) is a putative drug target for a novel class of diuretics with potential for treating hypertension and heart failure. Our first disclosed clinical ROMK compound, 2 (MK-7145), demonstrated robust diuresis, natriuresis, and blood pressure lowering in preclinical models, with reduced urinary potassium excretion compared to the standard of care diuretics. However, 2 projected to a short human half-life (∼5 h) that could necessitate more frequent than once a day dosing. In addition, a short half-life would confer a high peak-to-trough ratio which could evoke an excessive peak diuretic effect, a common liability associated with loop diuretics such as furosemide. This report describes the discovery of a new ROMK inhibitor 22e (MK-8153), with a longer projected human half-life (∼14 h), which should lead to a reduced peak-to-trough ratio, potentially extrapolating to more extended and better tolerated diuretic effects.

A novel approach for simultaneous tibiofibular synostosis takedown and peroneus longus ligamentoplasty for posttraumatic tibiofibular synostosis: a case report and review of the literature

Introduction

A singular procedure involving both a distal tibiofibular synostosis resection with syndesmosis repair by peroneus longus ligamentoplasty has not been reported in the English literature. We report a case of simultaneous distal tibiofibular synostosis resection and syndesmosis stabilization by peroneus longus ligamentoplasty for the treatment of symptomatic distal tibiofibular synostosis formation, following neglected syndesmosis injury.

Case presentation

A 42-year-old Caucasian man presented with ankle pain and painful range of motion 20 months following ankle trauma. Distal tibiofibular synostosis was identified, and our patient was successfully treated by simultaneous synostosis takedown and peroneus longus ligamentoplasty for distal tibiofibular syndesmosis repair.

Conclusions

Our experience illustrates that in cases of painful posttraumatic distal tibiofibular synostosis, simultaneous synostosis resection with peroneus longus ligamentoplasty may show good clinical results.

Level of evidence

5

Detecting nucleic acid fragments in serum using a magnetically modulated sandwich assay

We present a novel assay for rapid and highly sensitive detection of specific nucleic acid fragments in human serum. In a magnetic modulation biosensing (MMB) system, magnetic beads and fluorescently labeled probes are attached to the target analyte and form a "sandwich" complex. An alternating external magnetic field gradient condenses the magnetic beads (and hence the target molecules with the fluorescently labeled probes) to the detection volume and sets them in a periodic motion, in and out of a laser beam. A synchronous detection enables the removal of background signal from the oscillating target signal without complicated sample preparation. The high sensitivity of the MMB system, combined with the specificity of a sandwich hybridization assay, enables detection of DNA fragments without enzymatic signal amplification. Here, we demonstrate the sensitivity of the assay by directly detecting the EML4-ALK oncogenic translocation sequence spiked in human serum. The calculated limit of detection is 1.4 pM, which is approximately 150 times better than a conventional plate reader. In general, the MMB-assisted SHA can be implemented in many other applications for which enzymatic amplification, such as PCR, is not applicable and where rapid detection of specific nucleic acid targets is required.

Rapid and Sensitive Detection of Repetitive Nucleic Acid Sequences Using Magnetically Modulated Biosensors

Repetitive DNA sequences are abundant in the genome of most biological species. These sequences are naturally "preamplified", which makes them a preferential target for a variety of biological assays. Current methods to detect specific DNA sequences are based on the quantitative polymerase chain reaction (PCR), which relies on target amplification by Taq polymerase and uses a fluorescent resonance energy transfer (FRET)-based probe. Here, to rapidly detect a repetitive DNA sequence, we combine a highly sensitive magnetic modulation biosensing (MMB) system and a modified double-quenched FRET-based probe. The high numbers of copies of the female-specific XhoI sequence of the domestic chicken (Gallus gallus), combined with the low background fluorescence levels of the modified double-quenched probe and the high sensitivity of the MMB system, allow us to determine the chick sex in ovo within 13 min, with 100% sensitivity and specificity. Compared to quantitative PCR, the presented assay is 4-9 times faster. More broadly, by specifically tailoring the primers and probe, the proposed assay can detect any target DNA sequence, either repetitive or nonrepetitive.

Bilateral Common Peroneal Nerve Entrapment After Excessive Weight Loss: Case Report and Review of the Literature

We report a case of excessive weight loss causing bilateral common peroneal nerve entrapment in a 60-year-old patient. The bilateral peroneal involvement suggested a systemic cause. Excessive weight loss during a relatively short period can cause changes in the tissues surrounding the common peroneal nerve and lead to its entrapment in the peroneal tunnel. Our patient underwent successful surgical decompression with significant improvement.

Discovery of a Potent and Selective ROMK Inhibitor with Pharmacokinetic Properties Suitable for Preclinical Evaluation

A new subseries of ROMK inhibitors exemplified by 28 has been developed from the initial screening hit 1. The excellent selectivity for ROMK inhibition over related ion channels and pharmacokinetic properties across preclinical species support further preclinical evaluation of 28 as a new mechanism diuretic. Robust pharmacodynamic effects in both SD rats and dogs have been demonstrated.

Bicyclo[3.1.0]hexyl urea melanin concentrating hormone (MCH) receptor-1 antagonists: Impacting hERG liability via aryl modifications

Herein, we report the discovery of an effective strategy to modulate liabilities related to affinity of previously disclosed bicyclohexane MCHR-1 antagonists for the hERG channel. This paper describes one of several strategies incorporated to limit hERG binding via modifications of a terminal aryl group in an otherwise promising bicyclohexyl urea series.

Characterization of a hERG Screen Using the IonWorks HT: Comparison to a hERG Rubidium Efflux Screen

The introduction of parallel patch clamp instruments offers the promise of moderate-throughput, high-fidelity voltage clamp for drug screening assays. One such device, the IonWorks HT (Molecular Devices, Sunnyvale, CA), was evaluated and compared to conventional human ethera- go-go-related gene (hERG) patch clamp data and an alternative functional screen based on rubidium flux. Data generated by the IonWorks HT and rubidium assays were compared to determine if either offered superior predictive value compared to conventional patch clamp. Concentration-effect curves for a panel of known hERG blockers were shifted to higher concentrations on the IonWorks HT compared to conventional voltage clamp determinations. The magnitude of the potency shifts was compound-specific and ranged from no shift (e.g., quinidine) to over 200-fold (astemizole). When the extreme value for astemizole was disregarded, the potency shift for 13 other known reference standards was 12-fold or less, with an average shift of fivefold. The same subset of compounds in the rubidium efflux assay exhibited an average potency shift of 12-fold. To provide a simulation of how the IonWorks HT assay might perform in a single concentration screening mode, a panel of test compounds was evaluated. The IonWorks HT screen did not outperform the rubidium efflux screen in predicting conventional voltage clamp measurements. The most likely explanation appears to rest with variable and compound-specific potency shifts in the IonWorks HT assay. The variable potency shifts make it difficult to select a screening concentration that meets the criterion of a high positive predictive value while avoiding false-positives.

Functional synapses are formed between human NTera2 (NT2N, hNT) neurons grown on astrocytes

The formation of functional synapses is a late milestone of neuronal differentiation. The establishment of functional synapses can be used to assess neuronal characteristics of different cell lines. In the present study, we examined the in vitro conditions that influence the ability of human neurons derived from the NT2 cell line (NT2N neurons) to establish synapses. The morphologic, immunologic, and electrophysiologic characteristics of these synapses was examined. In the absence of astrocytes, NT2N neurons rarely formed synapses and their action potentials were weak and uncommon. In contrast, when plated on primary astrocytes, NT2N neurons were able to form both glutamatergic excitatory (71%) and GABAergic inhibitory (29%) functional synapses whose properties (kinetics, ion selectivity, pharmacology, and ultrastructure) were similar to those of synapses of neurons in primary cultures. In addition, coculture of NT2N neurons with astrocytes modified the morphology of the neurons and extended their in vitro viability to more than 1 year. Because astrocyte-conditioned medium did not produce these effects, we infer that direct contact between NT2N neurons and astrocytes is required. These results suggest that NT2N neurons are similar to primary neurons in their synaptogenesis and their requirement for glial support for optimal survival and maturation. This system provides a model for further investigations into the neurobiology of synapses formed by human neurons.

Temporal integration can readily switch between sublinear and supralinear summation

Temporal summation at dendrites of cultured rat hippocampal neurons was examined as a function of the interval separating two dendritic inputs. A novel method that relies on single-mode optical fibers to achieve rapid photorelease of glutamate was developed. Dendritic excitation achieved with this approach resembles that associated with miniature excitatory postsynaptic currents (mEPSCs), but the strengths, sites, and timing of the inputs can be precisely controlled. Dendritic summation deviated markedly from behavior predicted by passive cable theory. Subthreshold temporal summation varied as a triphasic function of the interpulse interval. As the interpulse interval decreased, local dendritic Na+ conductances were recruited to generate a marked transition from sublinear to supralinear summation. These results suggest that active dendritic conductances acting in concert with passive cable properties may serve to boost coincident synaptic inputs and attenuate noncoincident inputs.

N-Nmoc-L-glutamate, a new caged glutamate with high chemical stability and low pre-photolysis activity

We report the synthesis, the physicochemical characterization, and biological evaluation of a new caged glutamate, N-(o-nitromandelyl)oxycarbonyl-L-glutamic acid (Nmoc-Glu), that liberates free glutamate on photolysis. The low affinity of certain glutamate receptors and their rapid entry into desensitization have effectively prevented the creation of an ideal caged glutamate. In the absence of an ideal compound, Nmoc-Glu was designed to resist spontaneous hydrolysis while maintaining reasonable photorelease yield and kinetics. Chemical and physiological analyses reveal that Nmoc-Glu, indeed, has exceptionally low residual activity and high chemical stability. The quantum yield of Nmoc-Glu is 0.11. Photolytic uncaging and release of free glutamate occur in two steps, consisting of an initial light-induced cleavage that proceeds on the sub-millisecond time scale, and a subsequent light-independent, pH-dependent decarboxylation step that proceeds on the millisecond time scale. The low residual activity and high chemical stability of Nmoc-Glu are important advantages in applications where pre-photolysis Glu receptor activation and desensitization must be minimized.

Saturation of postsynaptic glutamate receptors after quantal release of transmitter

Miniature excitatory postsynaptic currents (mEPSCs) were elicited from small numbers of release sites after brief microperfusion of Ba2+ and K+ onto proximal dendritic processes of hippocampal neurons in culture. Temporal summation of closely timed mEPSCs deviated significantly from linearity. The number of instances of closely timed mEPSCs that were also closely matched in terms of peak amplitudes was significantly greater than that expected by chance. Amplitude pairing became statistically more significant after prolongation of mEPSC duration and inhibition of glutamate receptor desensitization with cyclothiazide. These results are best explained by postsynaptic receptors that approach saturation after quantal release of transmitter.