Highly Sensitive and Specific Zika Virus Serological Assays Using a Magnetic Modulation Biosensing System

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.

Using Temporally and Spatially Resolved Measurements to Improve the Sensitivity of Fluorescence-Based Immunoassays

Detecting low concentrations of biomarkers is essential in clinical laboratories. To improve analytical sensitivity, especially in identifying fluorescently labeled molecules, typical optical detection systems, consisting of a photodetector or camera, utilize time-resolved measurements. Taking a different approach, magnetic modulation biosensing (MMB) is a novel technology that combines fluorescently labeled probes and magnetic particles to create a sandwich assay with the target molecules. By concentrating the target molecules and then using time-resolved measurements, MMB provides the rapid and highly sensitive detection of various biomarkers. Here, we propose a novel signal-processing algorithm that enhances the detection and estimation of target molecules at low concentrations. By incorporating both temporally and spatially resolved measurements using human interleukin-8 as a target molecule, we show that the new algorithm provides a 2-4-fold improvement in the limit of detection and an ~25% gain in quantitative resolution.

A novel approach for rapid and sensitive detection of Zika virus utilizing silver nanoislands as SERS platform

To control the spread of the disease, the Zika virus (ZIKV), a flavivirus infection spread by mosquitoes and common in across the world, needs to be accurately and promptly diagnosed. This endeavour gets challenging when early-stage illnesses have low viral loads. As a result, we have created a biosensor based on surface-enhanced Raman scattering (SERS) for the quick, accurate, and timely diagnosis of the Zika virus. In this study, a glass coverslip was coated with silver nanoislands, which were then utilized as the surface for creating the sensing platform. Silver nanoislands exhibit strong plasmonic activity and good conductive characteristics. It enhances the Raman signals as a result and gives the SERS platform an appropriate surface. The created platform has been applied to Zika virus detection. With a limit of detection (LOD) of 0.11 ng/mL, the constructed sensor exhibits a linear range from 5 ng/mL to 1000 ng/mL. Hence, even at the nanogram scale, this technique may be a major improvement over clinical diagnosis approaches for making proper, precise, and accurate Zika virus detection.

Optomagnetic biosensors: Volumetric sensing based on magnetic actuation-induced optical modulations

In comparison to alternative nanomaterials, magnetic micron/nano-sized particles show unique advantages, e.g., easy manipulation, stable signal, and high contrast. By applying magnetic actuation, magnetic particles exert forces on target objects for highly selective operation even in non-purified samples. We herein describe a subgroup of magnetic biosensors, namely optomagnetic biosensors, which employ alternating magnetic fields to generate periodic movements of magnetic labels. The optical modulation induced by the dynamics of magnetic labels is then analyzed by photodetectors, providing information of, e.g., hydrodynamic size changes of the magnetic labels. Optomagnetic sensing mechanisms can suppress the noise (by performing lock-in detection), accelerate the reaction (by magnetic force-enhanced molecular collision), and facilitate homogeneous/volumetric detection. Moreover, optomagnetic sensing can be performed using a low magnetic field (<10 mT) without sophisticated light sources or pickup coils, further enhancing its applicability for point-of-care tests. This review concentrates on optomagnetic biosensing techniques of different concepts classified by the magnetic actuation strategy, i.e., magnetic field-enhanced agglutination, rotating magnetic field-based particle rotation, and oscillating magnetic field-induced Brownian relaxation. Optomagnetic sensing principles applied with different actuation strategies are introduced as well. For each representative optomagnetic biosensor, a simple immunoassay strategy-based application is introduced (if possible) for methodological comparison. Thereafter, challenges and perspectives are discussed, including minimization of nonspecific binding, on-chip integration, and multiplex detection, all of which are key requirements in point-of-care diagnostics.

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.

Rapid Biosensing Method for Detecting Protein-DNA Interactions

Identifying and investigating protein-DNA interactions, which play significant roles in many biological processes, is essential for basic and clinical research. Current techniques for identification of protein-DNA interactions are laborious, time-consuming, and suffer from nonspecific binding and limited sensitivity. To overcome these challenges and assess protein-DNA interactions, we use a magnetic modulation biosensing (MMB) system. In MMB, one of the interacting elements (protein or DNA) is immobilized to magnetic beads, and the other is coupled to a fluorescent molecule. Thus, the link between the magnetic bead and the fluorescent molecule is established only when binding occurs, enabling detection of the protein-DNA interaction. Using magnetic forces, the beads are concentrated and manipulated in a periodic motion in and out of a laser beam, producing a detectable oscillating signal. Using MMB, we detected protein-DNA interactions between short GC-rich DNA sequences and both a purified specificity protein 1 (Sp1) and an overexpressed Buttonhead (BTD) protein in a cell lysate. The specificity of the interactions was assessed using mutated DNA sequences and competition experiments. The assays were experimentally compared with commonly used electrophoretic mobility shift assay, which takes approximately 4-72 h. In comparison, the MMB-based assay's turnaround time is ∼2 h, and it provides unambiguous results and quantitative measures of performance. The MMB system uses simple and cheap components, making it an attractive alternative method over current costly and time-consuming techniques for analyzing protein-DNA interactions. Therefore, we anticipate that the MMB-based technique will significantly advance the detection of protein-DNA interactions in biomedical research.

Highly Sensitive and Specific SARS-CoV-2 Serological Assay Using a Magnetic Modulation Biosensing System

Sensitive serological assays are needed to provide valuable information about acute and past viral infections. For example, detection of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG antibodies could serve as the basis for an "immunity passport" that would enable individuals to travel internationally. Here, utilizing a novel Magnetic Modulation Biosensing (MMB) system and the receptor-binding domain of the SARS-CoV-2 spike protein, we demonstrate a highly sensitive and specific anti-SARS-CoV-2 IgG serological assay. Using anti-SARS-CoV-2 IgG antibodies, RT-qPCR SARS-CoV-2-positive and healthy patients' samples, and vaccinees' samples, we compare the MMB-based SARS-CoV-2 IgG assay's analytical and clinical sensitivities to those of the enzyme-linked immunosorbent assay (ELISA). Compared with ELISA, the MMB-based assay has an ~6-fold lower limit of detection (129 ng/L vs. 817 ng/L), and it detects an increase in the IgG concentration much earlier after vaccination. Using 85 RT-qPCR SARS-CoV-2-positive samples and 79 -negative samples, the MMB-based assay demonstrated similar clinical specificity (98% vs. 99%) and sensitivity (93% vs. 92%) to the ELISA test, but with a much faster turnaround time (45 min vs. 245 min). The high analytical and clinical sensitivity, short turnaround time, and simplicity of the MMB-based assay makes it a preferred method for antibody detection.

A Systematic Evaluation of IgM and IgG Antibody Assay Accuracy in Diagnosing Acute Zika Virus Infection in Brazil: Lessons Relevant to Emerging Infections

Accurate diagnostics underpin effective public health responses to emerging viruses. For viruses, such as Zika virus (ZIKV), where the viremia clears quickly, antibody-based (IgM or IgG) diagnostics are recommended for patients who present 7 days after symptom onset. However, cross-reactive antibody responses can complicate test interpretation among populations where closely related viruses circulate. We examined the accuracy (proportion of samples correctly categorized as Zika positive or negative) for antibody-based diagnostics among Brazilian residents (Rio de Janeiro) during the ZIKV outbreak. Four ZIKV enzyme-linked immunosorbent assays (ELISAs; IgM and IgG Euroimmun, IgM Novagnost, and CDC MAC), two dengue ELISAs (IgM and IgG Panbio), and the ZIKV plaque reduction neutralization test (PRNT) were evaluated. Positive samples were ZIKV PCR confirmed clinical cases collected in 2015-2016 (n = 169); negative samples (n = 236) were collected before ZIKV was present in Brazil (≤2013). Among serum samples collected ≥7 days from symptom onset, PRNT exhibited the highest accuracy (93.7%), followed by the Euroimmun IgG ELISA (77.9%). All IgM assays exhibited lower accuracy (<75%). IgG was detected more consistently than IgM among ZIKV cases using Euroimmun ELISAs (68% versus 22%). Anti-dengue virus IgM ELISA was positive in 41.1% of confirmed ZIKV samples tested. The Euroimmun IgG assay, although misdiagnosing 22% of samples, provided the most accurate ELISA. Anti-ZIKV IgG was detected more reliably than IgM among ZIKV patients, suggesting a secondary antibody response to assay antigens following ZIKV infection. Antibody ELISAs need careful evaluation in their target population to optimize use and minimize misdiagnosis, prior to widespread deployment, particularly where related viruses cocirculate.

Multiplex Biosensing for Simultaneous Detection of Mutations in SARS-CoV-2

COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has become the world's largest public health emergency of the past few decades. Thousands of mutations were identified in the SARS-CoV-2 genome. Some mutants are more infectious and may replace the original strains. Recently, B.1.1.7(Alpha), B1.351(Beta), and B.1.617.2(Delta) strains, which appear to have increased transmissibility, were detected. These strains accounting for the high proportion of newly diagnosed cases spread rapidly over the world. Particularly, the Delta variant has been reported to account for a vast majority of the infections in several countries over the last few weeks. The application of biosensors in the detection of SARS-CoV-2 is important for the control of the COVID-19 pandemic. Due to high demand for SARS-CoV-2 genotyping, it is urgent to develop reliable and efficient systems based on integrated multiple biosensor technology for rapid detection of multiple SARS-CoV-2 mutations simultaneously. This is important not only for the detection and analysis of the current but also for future mutations. Novel biosensors combined with other technologies can be used for the reliable and effective detection of SARS-CoV-2 mutants.

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.

Rapid and Sensitive Inhibitor Screening Using Magnetically Modulated Biosensors

Inhibitor screening is an important tool for drug development, especially during the COVID-19 pandemic. The most used in vitro inhibitor screening tool is an enzyme-linked immunosorbent assay (ELISA). However, ELISA-based inhibitor screening is time consuming and has a limited dynamic range. Using fluorescently and magnetically modulated biosensors (MMB), we developed a rapid and sensitive inhibitor screening tool. This study demonstrates its performance by screening small molecules and neutralizing antibodies as potential inhibitors of the interaction between the spike protein 1 (S1) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the angiotensin-converting enzyme 2 (ACE2) receptor. The MMB-based assay is highly sensitive, has minimal non-specific binding, and is much faster than the commonly used ELISA (2 h vs. 7–24 h). We anticipate that our method will lead to a remarkable advance in screening for new drug candidates.

Serial real-time RT-PCR and serology measurements substantially improve Zika and Dengue virus infection classification in a co-circulation area

BACKGROUND

Real-time RT-PCR (Reverse Transcriptase Polymerase Chain Reaction) is considered the gold standard for Zika virus (ZIKV) infection diagnosis, despite its low sensitivity. Diagnosis using recommended serologic cutoffs in co-circulating Flaviviruses areas maybe inadequate due to in-vitro cross-reactivities of Flaviviruses-specific antibodies. We evaluated Zika diagnosis in symptomatic patients using serial RT-PCR and develop a classification model using serial Dengue virus (DENV) and ZIKV serologies.

METHODS

A prospective longitudinal multicentric study in Southern Mexico (NCT02831699) enrolled symptomatic and non-symptomatic participants. In the classification model, true positives were symptomatic (using a modified World Health Organization/Pan American Health Organization definition) with RT-PCR positive for ZIKV or DENV. True negatives were non-symptomatic with negative RT-PCR. Serial serology measurements were used to predict disease status.

RESULTS

Analyzing ZIKV and DENV RT-PCR at 3 timepoints between days 3 and 13 of symptom onset detected 25% more cases than a single RT-PCR analysis between day 0 and 6. When considering sensitivity and specificity together, the serial serology model predicted all categories of disease and negatives better than manufactures cutoffs. Their cutoffs optimized sensitivity or specificity but not both.

CONCLUSIONS

We demonstrated the importance of serial RT-PCR and antibody measurements to diagnose arbovirus infection in symptomatic patients living in regions with co-circulating flaviviruses.

Configuration and Design of Electromagnets for Rapid and Precise Manipulation of Magnetic Beads in Biosensing Applications

Rapid and precise manipulation of magnetic beads on the nano and micro scales is essential in many biosensing applications, such as separating target molecules from background molecules and detecting specific proteins and DNA sequences in plasma. Accurately moving magnetic beads back and forth requires at least two adjustable magnetic field gradients. Unlike permanent magnets, electromagnets are easy to design and can produce strong and adjustable magnetic field gradients without mechanical motion, making them desirable for use in robust and safe medical devices. However, using multiple magnetic field sources to manipulate magnetic beads presents several challenges, including overlapping magnetic fields, added bulk, increased cost, and reduced durability. Here, we provide a thorough analysis, including analytical calculations, numerical simulations, and experimental measurements, of using two electromagnets to manipulate magnetic beads inside a miniature glass cell. We analyze and experimentally demonstrate different aspects of the electromagnets’ design, such as their mutual influence, the advantages and disadvantages of different pole tip geometries, and the correlation between the electromagnets’ positions and the beads’ aggregation during movement. Finally, we have devised a protocol to maximize the magnetic forces acting on magnetic beads in a two-electromagnet setup while minimizing the electromagnets’ size. We used two such electromagnets in a small footprint magnetic modulation biosensing system and detected as little as 13 ng/L of recombinant Zika virus antibodies, which enables detection of Zika IgM antibodies as early as 5 days and as late as 180 days post symptoms onset, significantly extending the number of days that the antibodies are detectable.