PCR-Free Innovative Strategies for SARS-CoV-2 Detection

The pandemic outbreak caused by SARS-CoV-2 coronavirus brought a crucial issue in public health causing up to now more than 600 million infected people and 6.5 million deaths. Conventional diagnostic methods are based on quantitative reverse transcription polymerase chain reaction (RT-qPCR assay) and immuno-detection (ELISA assay). However, despite these techniques have the advantages of being standardized and consolidated, they keep some main limitations in terms of accuracy (immunoassays), time/cost consumption of analysis, the need for qualified personnel, and lab constrain (molecular assays). There is crucial the need to develop new diagnostic approaches for accurate, fast and portable viral detection and quantification. Among these, PCR-free biosensors represent the most appealing solution since they can allow molecular detection without the complexity of the PCR. This will enable the possibility to be integrated in portable and low-cost systems for massive and decentralized screening of SARS-CoV-2 in a point-of-care (PoC) format, pointing to achieve a performant identification and control of infection. In this review, the most recent approaches for the SARS-CoV-2 PCR-free detection are reported, describing both the instrumental and methodological features, and highlighting their suitability for a PoC application.

SARS-CoV-2 and omicron variant detection with a high selectivity, sensitivity, and low-cost silicon bio-nanosensor

The recent SARS-CoV-2 pandemic has highlighted the urgent need for novel point-of-care devices to be promptly used for a rapid and reliable large screening analysis of several biomarkers like genetic sequences and antibodies. Currently, one of the main limitations of rapid tests is the high percentage of false negatives in the presence of variants and, in particular for the Omicron one. We demonstrate in this work the detection of SARS-CoV-2 and the Omicron variant with a cost-effective silicon nanosensor enabling high sensitivity, selectivity, and fast response. We have shown that a silicon (Si) nanowires (NW) platform detects both Sars-CoV-2 and its Omicron variant with a limit of detection (LoD) of four effective copies (cps), without any amplification of the genome, and with high selectivity. This ultrasensitive detection of 4 cps allows to obtain an extremely early diagnosis paving the way for efficient and widespread tracking. The sensor is made with industrially compatible techniques, which in perspective may allow easy and cost-effective industrialization.

A Miniaturized Silicon Lab-on-Chip for Integrated PCR and Hybridization Microarray for High Multiplexing Nucleic Acids Analysis

A silicon lab-on-chip, for the detection of nucleic acids through the integrated PCR and hybridization microarray, was developed. The silicon lab-on-chip manufactured through bio-MEMS technology is composed of two PCR microreactors (each volume 11.2 µL) and a microarray-hybridization microchamber (volume 30 µL), fluidically connected by buried bypass. It contains heaters and temperature sensors for the management and control of the temperature cycles during the PCR amplification and hybridization processes. A post-silicon process based on (i) plasmo-O2 cleaning/activation, (ii) vapor phase epoxy silanization, (iii) microarray fabrication and (iv) a protein-based passivation step was developed and fully characterized. The ssDNA microarray (4 rows × 10 columns) composed of 400 spots (spot size—70 ± 12 µm; spot-to-spot distance—130 ± 13 µm) was manufactured by piezo-dispense technology. A DNA microarray probe density in the range of 1310 to 2070 probe µm⁻² was observed, together with a limit of detection of about 19 target µm⁻². The performances of the silicon lab-on-chip were validated by the detection of the beta-globin gene directly from human blood. Remarkable sensitivity, multiplexing analysis and specificity were demonstrated for the detection of beta-globin and mycobacterium tuberculosis sequences.

Comparison between various biosensor methods for human T-lymphotropic virus-1 (HTLV-1) detection

Due to the drawback of traditional and current diagnostic methods including serological and molecular assays, the development of the rapid and free-PCR techniques can be an alternative technique for the human T-cell lymphotropic virus (HTLV-1) DNA detection sequences. On the other hand, early detection of HTLV-1 prevents two dangerous diseases including Adult T-cell leukemia/lymphoma and HTLV-1 Associated Myelopathy/Tropical Spastic Paraparesis. The biosensor-based methods are sensitive techniques that can provide new opportunities to detect infectious diseases, particularly in the early stage. This study provides a comparative view among recently designed biosensors for the detection of HTLV-1.

Nucleic Acids Analytical Methods for Viral Infection Diagnosis: State-of-the-Art and Future Perspectives

The analysis of viral nucleic acids (NA), DNA or RNA, is a crucial issue in the diagnosis of infections and the treatment and prevention of related human diseases. Conventional nucleic acid tests (NATs) require multistep approaches starting from the purification of the pathogen genetic material in biological samples to the end of its detection, basically performed by the consolidated polymerase chain reaction (PCR), by the use of specialized instruments and dedicated laboratories. However, since the current NATs are too constraining and time and cost consuming, the research is evolving towards more integrated, decentralized, user-friendly, and low-cost methods. These will allow the implementation of massive diagnoses addressing the growing demand of fast and accurate viral analysis facing such global alerts as the pandemic of coronavirus disease of the recent period. Silicon-based technology and microfluidics, in this sense, brought an important step up, leading to the introduction of the genetic point-of-care (PoC) systems. This review goes through the evolution of the analytical methods for the viral NA diagnosis of infection diseases, highlighting both advantages and drawbacks of the innovative emerging technologies versus the conventional approaches.

Electronic and electrochemical viral detection for point-of-care use: A systematic review

Detecting viruses, which have significant impact on health and the economy, is essential for controlling and combating viral infections. In recent years there has been a focus towards simpler and faster detection methods, specifically through the use of electronic-based detection at the point-of-care. Point-of-care sensors play a particularly important role in the detection of viruses. Tests can be performed in the field or in resource limited regions in a simple manner and short time frame, allowing for rapid treatment. Electronic based detection allows for speed and quantitative detection not otherwise possible at the point-of-care. Such approaches are largely based upon voltammetry, electrochemical impedance spectroscopy, field effect transistors, and similar electrical techniques. Here, we systematically review electronic and electrochemical point-of-care sensors for the detection of human viral pathogens. Using the reported limits of detection and assay times we compare approaches both by detection method and by the target analyte of interest. Compared to recent scoping and narrative reviews, this systematic review which follows established best practice for evidence synthesis adds substantial new evidence on 1) performance and 2) limitations, needed for sensor uptake in the clinical arena. 104 relevant studies were identified by conducting a search of current literature using 7 databases, only including original research articles detecting human viruses and reporting a limit of detection. Detection units were converted to nanomolars where possible in order to compare performance across devices. This approach allows us to identify field effect transistors as having the fastest median response time, and as being the most sensitive, some achieving single-molecule detection. In general, we found that antigens are the quickest targets to detect. We also observe however, that reports are highly variable in their chosen metrics of interest. We suggest that this lack of systematisation across studies may be a major bottleneck in sensor development and translation. Where appropriate, we use the findings of the systematic review to give recommendations for best reporting practice.

Environmental Management of Legionella in Domestic Water Systems: Consolidated and Innovative Approaches for Disinfection Methods and Risk Assessment

Legionella is able to remain in water as free-living planktonic bacteria or to grow within biofilms that adhere to the pipes. It is also able to enter amoebas or to switch into a viable but not culturable (VBNC) state, which contributes to its resistance to harsh conditions and hinders its detection in water. Factors regulating Legionella growth, such as environmental conditions, type and concentration of available organic and inorganic nutrients, presence of protozoa, spatial location of microorganisms, metal plumbing components, and associated corrosion products are important for Legionella survival and growth. Finally, water treatment and distribution conditions may affect each of these factors. A deeper comprehension of Legionella interactions in water distribution systems with the environmental conditions is needed for better control of the colonization. To this purpose, the implementation of water management plans is the main prevention measure against Legionella. A water management program requires coordination among building managers, health care providers, and Public Health professionals. The review reports a comprehensive view of the state of the art and the promising perspectives of both monitoring and disinfection methods against Legionella in water, focusing on the main current challenges concerning the Public Health sector.

Miniaturized electrochemical biosensor based on whole-cell for heavy metal ions detection in water

The heavy metals pollution represents one of the important issues in the environmental field since it is involved in many pathologies from cancer, neurodegenerative, and metabolic diseases. We propose an innovative portable biosensor for the determination of traces of trivalent arsenic (As(III)) and bivalent mercury (Hg(II)) in water. The system implements a strategy combining two advanced sensing modules consisting in (a) a whole cell based on engineered Escherichia coli as selective sensing element towards the metals and (b) an electrochemical miniaturised silicon device with three microelectrodes and a portable reading system. The sensing mechanism relies on the selective recognition from the bacterium of given metals producing the 4-aminophenol redox active mediator detected through a cyclic voltammetry analysis. The miniaturized biosensor is able to operate a portable, robust, and high-sensitivity detection of As(III) with a sensitivity of 0.122 µA ppb^-1 , LoD of 1.5 ppb, and a LoQ of 5 ppb. The LoD value is one order of magnitude below of the value indicated to WHO to be dangerous (10 μg/L). The system was proved to be fully versatile being effective in the detection of Hg(II) as well. A first study on Hg(II) showed sensitivity value of 2.11 µA/ppb a LOD value of 0.1 ppb and LoQ value of 0.34 ppb. Also in this case, the detected LOD was 10 times lower than that indicated by WHO (1 ppb). These results pave the way for advanced sensing strategies suitable for the environmental monitoring and the public safety.

Machine learning improves our knowledge about miRNA functions towards plant abiotic stresses

During the last two decades, human has increased his knowledge about the role of miRNAs and their target genes in plant stress response. Biotic and abiotic stresses result in simultaneous tissue-specific up/down-regulation of several miRNAs. In this study, for the first time, feature selection algorithms have been used to investigate the contribution of individual plant miRNAs in Arabidopsis thaliana response towards different levels of several abiotic stresses including drought, salinity, cold, and heat. Results of information theory-based feature selection revealed that miRNA-169, miRNA-159, miRNA-396, and miRNA-393 had the highest contributions to plant response towards drought, salinity, cold, and heat, respectively. Furthermore, regression models, i.e., decision tree (DT), support vector machines (SVMs), and Naïve Bayes (NB) were used to predict the plant stress by having the plant miRNAs' concentration. SVM with Gaussian kernel was capable of predicting plant stress (R2 = 0.96) considering miRNA concentrations as input features. Findings of this study prove the performance of machine learning as a promising tool to investigate some aspects of miRNAs' contribution to plant stress responses that have been undiscovered until today.

An integrated biosensor platform for extraction and detection of nucleic acids

The development of portable systems for analysis of nucleic acids (NAs) is crucial for the evolution of biosensing in the context of future healthcare technologies. The integration of NA extraction, purification, and detection modules, properly actuated by microfluidics technologies, is a key point for the development of portable diagnostic systems. In this paper, we describe an integrated biosensor platform based on a silicon-plastic hybrid lab-on-disk technology capable of managing NA extraction, purification, and detection processes in an integrated format. The sample preparation process is performed by solid-phase extraction technology using magnetic beads on a plastic disk, while detection is done through quantitative real-time polymerase chain reaction (qRT-PCR) on a miniaturized silicon device. The movement of sample and reagents is actuated by a centrifugal force induced by a disk actuator instrument. The assessment of the NA extraction and detection performance has been carried out by using hepatitis B virus (HBV) DNA genome as a biological target. The quantification of the qRT-PCR chip in the hybrid disk showed an improvement in sensitivity with respect to the qRT-PCR commercial platforms, which means an optimization of time and cost. Limit of detection and limit of quantification values of about 8 cps/reaction and 26 cps/reaction, respectively, were found by using analytical samples (synthetic clone), while the results with real samples (serum with spiked HBV genome) indicate that the system performs as well as the standard methods.

Designing expanded bipyridinium as redox and optical probes for DNA

We report on the light-switch behaviour of two head-to-tail expanded bipyridinium species as a function of their interaction with calf thymus DNA and polynucleotides. In particular, both DNA and polynucleotides containing exclusively adenine or guanine moieties quench the luminescence of the fused expanded bipyridinium species. This behaviour has been rationalized demonstrating that a reductive photoinduced electron transfer process takes place involving both adenine or guanine moieties. The charge separated state so produced recombines in the tens of picoseconds. These results could help in designing new organic substrates for application in DNA probing technology and lab on chip-based sensing systems.

Gold nanoparticles-based biosensor can detect drought stress in tomato by ultrasensitive and specific determination of miRNAs

Drought stress can significantly affect the yield and quality of tomato production. However, the development of a sensitive and specific method for the determination of drought stress is somehow challenging since plant common morpho-physiological and biochemical characteristic are not generally specific to biotic and abiotic stresses. As a solution, the concentration of miRNAs in plant tissues can be a selective and specific indicator of plant stress. In this study, an optical biosensor based on gold nanoparticles is introduced to determine miRNA-1886 in tomato plant roots. Results showed that irrigation levels from 100% to 60% of field capacity increased the concentration of miRNA-1886 in a range from ca. 100 to 6800 fM (fM) causing a linear change in the biosensor response (R² = 0.97). Results also revealed that in contrast with plant conventional morpho-physiological and biochemical characteristic, miRNA-1886 concentration was not significantly affected (P < 0.01) by other stresses, i.e., salinity and temperature during the growth period. The biosensor introduced in this study is a reliable method to study stress-related functions of miRNAs in plants and their application in specific plant stress determination.

The cooperative interaction of triplex forming oligonucleotides on DNA-triplex formation at electrode surface: Molecular dynamics studies and experimental evidences

An extensive study on cooperative interaction of Triplex Forming Oligonucleotides (TFOs) with a double strand DNA, to form a triplex-DNA structure at electrode surface, is here reported. The cooperative effect on triplex structure formation was assumed by the higher binding enthalpy value, calculated for the interaction between the duplex DNA structure and the TFO1 and TFO2 probes (-67.3 KJ/mol), respect the sum of the single duplex-TFO1 and duplex-TFO2 interactions (-47.0 kJ/mol). The formation of triplex-DNA structure was proven by kinetic modelling study performed using the Luzar and Chandler model. The results indicate that after 500 ns from interaction, H-bonds between the base pairs in the double strand DNA are weaken while new H-bonds between the TFOs and duplex DNA are formed. Molecular dynamic (MD) simulations indicate that the TFOs sequence distance (138 bps) and the amount of TA*T triplet units are the keystones for the effectiveness of the cooperative effect, reaching for the selected target a minimum of energy value of -19452.6 kJ/mol. The MD data were experimentally corroborated by electrochemical measurements, detecting a HBV-clone genome at TFOs modified electrode surface. The interaction was electrochemical transduced by an intercalative Osmium based compound. The Langmuir isotherm model reports for the forming triplex DNA an association constant value of about 2.9 × 10¹⁶M^-1, this high value could be attributed to the synergic contribution of the TFOs cooperative effect and to the rigid circular duplex structure. Finally, AFM and SEM investigations suggest the formation of a triplex-DNA structure at electrode surface, consisting in circles of about 1.5 um in diameter with asymmetric stranded thickness. This finding data paving the way to future development of advanced miniaturized DNA computing and biosensors.

An innovative silicon-chip for sensitive real time PCR improvement in pathogen detection

An innovative miniaturized silicon-chip was developed for highly sensitive detection of pathogen genomes of both viruses and bacteria through real time PCR (qRT-PCR). The device was properly designed to enhance the optical signal and perform accurate thermal control. Results show an improvement of PCR amplification by one order of magnitude in sensitivity compared to the standard RT-PCR method. In particular for hepatitis B virus a decrease of the mean value of Ct of about 2.9 ± 0.9 compared to the standard system was observed. Similarly, for the bacteria Pseudomonas aeruginosa, Staphylococcus aureus and Acinetobacter baumannii, a decrease of the mean values of Ct of 1.8 ± 0.5, 3.1 ± 0.5 and 3.9 ± 0.9, respectively, was observed.

Novel Surface-Enhanced Raman Spectroscopy Techniques for DNA, Protein and Drug Detection

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique in which the Raman scattering signal strength of molecules, absorbed by rough metals or the surface of nanoparticles, experiences an exponential growth (10³-10⁶ times and even 10¹⁴-10¹⁵ times) because of electromagnetic or chemical enhancements. Nowadays, SERS has attracted tremendous attention in the field of analytical chemistry due to its specific advantages, including high selectivity, rich informative spectral properties, nondestructive testing, and the prominent multiplexing capabilities of Raman spectroscopy. In this review, we present the applications of state-of-the-art SERS for the detection of DNA, proteins and drugs. Moreover, we focus on highlighting the merits and mechanisms of achieving enhanced SERS signals for food safety and clinical treatment. The machine learning techniques, combined with SERS detection, are also indicated herein. This review concludes with recommendations for future studies on the development of SERS.

Functionalization of Bulk SiO2 Surface with Biomolecules for Sensing Applications: Structural and Functional Characterizations

Biomolecule immobilization on bulk silicon dioxide (SiO2) is an important aspect in the field of Si-based interfaces for biosensing. The approach used for surface preparation should guarantee not only the stable anchoring of biomolecules but also their structural integrity and biological functioning. In this paper, we review our findings on the SiO2 functionalization process to immobilize a variety of biomolecules, including glucose oxidase, horseradish peroxide, metallothionein, and DNA molecules. Morphological and chemical characterization of SiO2 surfaces after biomolecule immobilization using techniques already employed in the microelectronic industry are presented and discussed. Optical and spectrophotometric analysis revealed the preservation of biomolecules’ activity once they are anchored on the biointerface.

Carbohydrates and Charges on Oligo(phenylenethynylenes): Towards the Design of Cancer Bullets

Two new tetralkylammonium-OPEs, bearing one or two positively charged groups directly linked to the aromatic residues and two β-d-glucopyranose terminations, were synthesized. Their peculiar structural features, joining the biologically relevant sugar moieties, flat aromatic cores and positive charges, make these luminescent dyes soluble in aqueous media and able to strongly interact with DNA. As a result of UV/Vis spectral variations, DNA melting temperature measures, viscometric titrations and induced CD, we propose a partial insertion of the OPEs aromatic core into the helix, stabilized by glucose H-bonding with the groups accessible from the grooves. This interaction leads to the quenching of the OPE luminescence due to guanine reduction. The biocompatibility of the monocationic OPE with healthy and cancer cells, and the reduction of proliferation in HEp-2 cancer cells induced by the dicationic one, make this class of compounds promising for future biological applications.

Ultrasensitive Label- and PCR-Free Genome Detection Based on Cooperative Hybridization of Silicon Nanowires Optical Biosensors

The realization of an innovative label- and PCR-free silicon nanowires (NWs) optical biosensor for direct genome detection is demonstrated. The system is based on the cooperative hybridization to selectively capture DNA and on the optical emission of quantum confined carriers in Si NWs whose quenching is used as detection mechanism. The Si NWs platform was tested with Hepatitis B virus (HBV) complete genome and it was able to reach a Limit of Detection (LoD) of 2 copies/reaction for the synthetic genome and 20 copies/reaction for the genome extracted from human blood. These results are even better than those obtained with the gold standard real-time PCR method in the genome analysis. The Si NWs sensor showed high sensitivity and specificity, easy detection method, and low manufacturing cost fully compatible with standard silicon process technology. All these points are key factors for the future development of a new class of genetic point-of-care devices that are reliable, fast, low cost, and easy to use for self-testing including in the developing countries.

An Advanced, Silicon-Based Substrate for Sensitive Nucleic Acids Detection

Surface substrate and chemical functionalization are crucial aspects for the fabrication of the sensitive biosensor based on microarray technology. In this paper, an advanced, silicon-based substrate (A-MA) allowing enhancement of optical signal for microarray application is described. The substrate consists in a multilayer of Si/Al/SiO₂ layers. The optical signal enhancement is reached by a combination of the mirror effect of Al film and the SiO₂ thickness around 830 nm, which is able to reach the maximum of interference for the emission wavelength of the Cy5 fluorescent label. Moreover, SiO₂ layer is suitable for the immobilization of single-strand DNA through standard silane chemistry, and probe densities of about 2000 F/µm² are reached. The microarray is investigated in the detection of HBV (Hepatitis B Virus) pathogen with analytical samples, resulting in a dynamic linear range of 0.05–0.5 nM, a sensitivity of about 18000 a.u. nM⁻¹, and a Limit of Detection in the range of 0.031–0.043 Nm as a function of the capture probe sequence.

PCR Technologies for Point of Care Testing: Progress and Perspectives

Since the Human Genome Project completed in 2000, the sequencing of the first genome, massive progress has been made by medical science in the early diagnosis and personalized therapies based on nucleic acids (NA) analysis. To allow the extensive use of these molecular methods in medical practice, scientific research is nowadays strongly focusing on the development of new miniaturized and easy-to-use technologies and devices allowing fast and low cost NA analysis in decentralized environments. It is now the era of so-called genetic "Point-of-Care" (PoC). These systems must integrate and automate all steps necessary for molecular analysis such as sample preparation (extraction and purification of NA) and detection based on PCR (Polymerase Chain Reaction) technology in order to perform, by unskilled personnel, in vitro genetic analysis near the patient (in hospital, in the physician office, clinic, or home), with rapid answers and low cost. In this review, the recent advances in genetic PoC technologies are discussed, including the extraction and PCR amplification chemistry suitable for PoC use and the new frontiers of research in this field.

A facile method for urinary phenylalanine measurement on paper-based lab-on-chip for PKU therapy monitoring

A miniaturized paper-based lab-on-chip (LoC) was developed for the facile measurement of urinary Phe (phenylalanine) level on PKU (Phenylketonuria) treated patient.