Diagnosis of Tamiflu-Resistant Influenza Virus in Human Nasal Fluid and Saliva Using Surface-Enhanced Raman Scattering

Air sampling and simultaneous detection of airborne influenza virus via gold nanorod-based plasmonic PCR

Reliable and sensitive virus detection is essential to prevent airborne virus transmission. The polymerase chain reaction (PCR) is one of the most compelling and effective diagnostic techniques for detecting airborne pathogens. However, most PCR diagnostics rely on thermocycling, which involves a time-consuming Peltier block heating methodology. Plasmonic PCR is based on light-driven photothermal heating of plasmonic nanostructures to address the key drawbacks of traditional PCR. This study introduces a methodology for plasmonic PCR detection of air-sampled influenza virus (H1N1). An electrostatic air sampler was used to collect the aerosolized virus in a carrier liquid for 10 min. Simultaneously, the viruses collected in the liquid were transferred to a tube containing gold (Au) nanorods (aspect ratio = 3.6). H1N1 viruses were detected in 12 min, which is the total time required for reverse transcription, fast thermocycling via plasmonic heating through gold nanorods, and in situ fluorescence detection. This methodology showed a limit of detection of three RNA copies/μL liquid for H1N1 influenza virus, which is comparable to that of commercially available PCR devices. This methodology can be used for the rapid and precise identification of pathogens on-site, while significantly reducing the time required for monitoring airborne viruses.

Spectral effects and enhancement quantification in healthy human saliva with surface-enhanced Raman spectroscopy using silver nanopillar substrates

OBJECTIVES

Raman spectroscopy as a diagnostic tool for biofluid applications is limited by low inelastic scattering contributions compared to the fluorescence background from biomolecules. Surface-enhanced Raman spectroscopy (SERS) can increase Raman scattering signals, thereby offering the potential to reduce imaging times. We aimed to evaluate the enhancement related to the plasmonic effect and quantify the improvements in terms of spectral quality associated with SERS measurements in human saliva.

METHODS

Dried human saliva was characterized using spontaneous Raman spectroscopy and SERS. A fabrication protocol was implemented leading to the production of silver (Ag) nanopillar substrates by glancing angle deposition. Two different imaging systems were used to interrogate saliva from 161 healthy donors: a custom single-point macroscopic system and a Raman micro-spectroscopy instrument. Quantitative metrics were established to compare spontaneous RS and SERS measurements: the Raman spectroscopy quality factor (QF), the photonic count rate (PR), the signal-to-background ratio (SBR).

RESULTS

SERS measurements acquired with an excitation energy four times smaller than with spontaneous RS resulted in improved QF, PR values an order of magnitude larger and a SBR twice as large. The SERS enhancement reached 100×, depending on which Raman bands were considered.

CONCLUSIONS

Single-point measurement of dried saliva with silver nanopillars substrates led to reproducible SERS measurements, paving the way to real-time tools of diagnosis in human biofluids.

Recent Trends in SERS-Based Plasmonic Sensors for Disease Diagnostics, Biomolecules Detection, and Machine Learning Techniques

Surface-enhanced Raman spectroscopy/scattering (SERS) has evolved into a popular tool for applications in biology and medicine owing to its ease-of-use, non-destructive, and label-free approach. Advances in plasmonics and instrumentation have enabled the realization of SERS's full potential for the trace detection of biomolecules, disease diagnostics, and monitoring. We provide a brief review on the recent developments in the SERS technique for biosensing applications, with a particular focus on machine learning techniques used for the same. Initially, the article discusses the need for plasmonic sensors in biology and the advantage of SERS over existing techniques. In the later sections, the applications are organized as SERS-based biosensing for disease diagnosis focusing on cancer identification and respiratory diseases, including the recent SARS-CoV-2 detection. We then discuss progress in sensing microorganisms, such as bacteria, with a particular focus on plasmonic sensors for detecting biohazardous materials in view of homeland security. At the end of the article, we focus on machine learning techniques for the (a) identification, (b) classification, and (c) quantification in SERS for biology applications. The review covers the work from 2010 onwards, and the language is simplified to suit the needs of the interdisciplinary audience.

Hybrid CRISPR/Cas protein for one-pot detection of DNA and RNA

Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have emerged as next-generation molecular diagnostics. In CRISPR-based diagnostics, Cas12 and Cas13 proteins have been widely employed to detect DNA and RNA, respectively. Herein, we developed a novel hybrid Cas protein capable of detecting universal nucleic acids (DNA and RNA). The CRISPR/hybrid Cas system simultaneously recognizes both DNA and RNA, enabling the dual detection of pathogenic viruses in a single tube. Using wild-type (WT) and N501Y mutant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as detection models, we successfully detected both virus strains with a detection limit of 10 viral copies per reaction without cross-reactivity. Furthermore, it is demonstrated the detection of WT SARS-CoV-2 and N501Y mutant variants in clinical samples by using the CRISPR/hybrid Cas system. The hybrid Cas protein is expected to be utilized in a molecular diagnostic method for infectious diseases, tissue and liquid biopsies, and other nucleic acid biomarkers.

Label-free laser spectroscopy for respiratory virus detection: A review

Infectious diseases are among the most severe threats to modern society. Current methods of virus infection detection based on genome tests need reagents and specialized laboratories. The desired characteristics of new virus detection methods are noninvasiveness, simplicity of implementation, real-time, low cost and label-free detection. There are two groups of methods for molecular biomarkers' detection and analysis: (i) a sample physical separation into individual molecular components and their identification, and (ii) sample content analysis by laser spectroscopy. Variations in the spectral data are typically minor. It requires the use of sophisticated analytical methods like machine learning. This review examines the current technological level of laser spectroscopy and machine learning methods in applications for virus infection detection.

Nanomaterials for virus sensing and tracking

The effect of the on-going COVID-19 pandemic on global healthcare systems has underlined the importance of timely and cost-effective point-of-care diagnosis of viruses. The need for ultrasensitive easy-to-use platforms has culminated in an increased interest for rapid response equipment-free alternatives to conventional diagnostic methods such as polymerase chain reaction, western-blot assay, etc. Furthermore, the poor stability and the bleaching behavior of several contemporary fluorescent reporters is a major obstacle in understanding the mechanism of viral infection thus retarding drug screening and development. Owing to their extraordinary surface-to-volume ratio as well as their quantum confinement and charge transfer properties, nanomaterials are desirable additives to sensing and imaging systems to amplify their signal response as well as temporal resolution. Their large surface area promotes biomolecular integration as well as efficacious signal transduction. Due to their hole mobility, photostability, resistance to photobleaching, and intense brightness, nanomaterials have a considerable edge over organic dyes for single virus tracking. This paper reviews the state-of-the-art of combining carbon-allotrope, inorganic and organic-based nanomaterials with virus sensing and tracking methods, starting with the impact of human pathogenic viruses on the society. We address how different nanomaterials can be used in various virus sensing platforms (e.g. lab-on-a-chip, paper, and smartphone-based point-of-care systems) as well as in virus tracking applications. We discuss the enormous potential for the use of nanomaterials as simple, versatile, and affordable tools for detecting and tracing viruses infectious to humans, animals, plants as well as bacteria. We present latest examples in this direction by emphasizing major advantages and limitations.

Rapid detection of viruses: Based on silver nanoparticles modified with bromine ions and acetonitrile

Nearly 200 million people have been diagnosed with COVID-19 since the outbreak in 2019, and this disease has claimed more than 5 million lives worldwide. Currently, researchers are focusing on vaccine development and the search for an effective strategy to control the infection source. This work designed a detection platform based on Surface-Enhanced Raman Spectroscopy (SERS) by introducing acetonitrile and calcium ions into the silver nanoparticle reinforced substrate system to realize the rapid detection of novel coronavirus. Acetonitrile may amplify the calcium-induced hot spots of silver nanoparticles and significantly enhanced the stability of silver nanoparticles. It also elicited highly sensitive SERS signals of the virus. This approach allowed us to capture the characteristic SERS signals of SARS-CoV-2, Human Adenovirus 3, and H1N1 influenza virus molecules at a concentration of 100 copies/test (PFU/test) with upstanding reproduction and signal-to-noise ratio. Machine learning recognition technology was employed to qualitatively distinguish the three virus molecules with 1000 groups of spectra of each virus. Acetonitrile is a potent internal marker in regulating the signal intensity of virus molecules in saliva and serum. Thus, we used the SERS peak intensity to quantify the virus content in saliva and serum. The results demonstrated a satisfactory linear relationship between peak intensity and protein concentration. Collectively, this rapid detection method has a broad application prospect in clinical diagnosis of viruses, management of emergent viral infectious diseases, and exploration of the interaction between viruses and host cells.

A novel enhanced substrate for label-free detection of SARS-CoV-2 based on surface-enhanced Raman scattering

Accurate and sensitive detection of SARS-CoV-2 is an effective strategy for preventing the COVID-19 pandemic in the current absence of specific drug therapy. This study presents a novel enhanced substrate for label-free detection of respiratory viruses using surface-enhanced Raman Scattering. Sodium borohydride reduces silver ions to clustered silver nanoparticles to eliminate the disorganized peak signal of the traditional citrate reducing agent. Meanwhile, the study obtained the fingerprints and concentration-dependent curves of many respiratory viruses, including SARS-CoV-2, human adenovirus type 7, and H1N1 virus, with good linear relationships. The three viruses were also identified in serum and saliva within two minutes, combined with linear discriminant diagnostic analysis. Therefore, establishing this enhanced substrate is greatly valuable for the global response to the COVID-19 pandemic.

Surface-enhanced Raman scattering-based immunoassay for severe acute respiratory syndrome coronavirus 2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected humans worldwide for over a year now. Although various tests have been developed for the detection of SARS-CoV-2, advanced sensing methods are required for the diagnosis, screening, and surveillance of coronavirus disease 2019 (COVID-19). Here, we report a surface-enhanced Raman scattering (SERS)-based immunoassay involving an antibody pair, SERS-active hollow Au nanoparticles (NPs), and magnetic beads for the detection of SARS-CoV-2. The selected antibody pair against the SARS-CoV-2 antigen, along with the magnetic beads, facilitates the accurate direct detection of the virus. The hollow Au NPs exhibit strong, reproducible SERS signals, allowing sensitive quantitative detection of SARS-CoV-2. This assay had detection limits of 2.56 fg/mL for the SARS-CoV-2 antigen and 3.4 plaque-forming units/mL for the SARS-CoV-2 lysates. Furthermore, it facilitated the identification of SARS-CoV-2 in human nasopharyngeal aspirates and diagnosis of COVID-19 within 30 min using a portable Raman device. Thus, this assay can be potentially used for the diagnosis and prevention of COVID-19.

Raman, Infrared and Brillouin Spectroscopies of Biofluids for Medical Diagnostics and for Detection of Biomarkers

This review surveys Infrared, Raman/SERS and Brillouin spectroscopies for medical diagnostics and detection of biomarkers in biofluids, that include urine, blood, saliva and other biofluids. These optical sensing techniques are non-contact, noninvasive and relatively rapid, accurate, label-free and affordable. However, those techniques still have to overcome some challenges to be widely adopted in routine clinical diagnostics. This review summarizes and provides insights on recent advancements in research within the field of vibrational spectroscopy for medical diagnostics and its use in detection of many health conditions such as kidney injury, cancers, cardiovascular and infectious diseases. The six comprehensive tables in the review and four tables in supplementary information summarize a few dozen experimental papers in terms of such analytical parameters as limit of detection, range, diagnostic sensitivity and specificity, and other figures of merits. Critical comparison between SERS and FTIR methods of analysis reveals that on average the reported sensitivity for biomarkers in biofluids for SERS vs FTIR is about 103 to 105 times higher, since LOD SERS are lower than LOD FTIR by about this factor. High sensitivity gives SERS an edge in detection of many biomarkers present in biofluids at low concentration (nM and sub nM), which can be particularly advantageous for example in early diagnostics of cancer or viral infections.HighlightsRaman, Infrared spectroscopies use low volume of biofluidic samples, little sample preparation, fast time of analysis and relatively inexpensive instrumentation.Applications of SERS may be a bit more complicated than applications of FTIR (e.g., limited shelf life for nanoparticles and substrates, etc.), but this can be generously compensated by much higher (by several order of magnitude) sensitivity in comparison to FTIR.High sensitivity makes SERS a noninvasive analytical method of choice for detection, quantification and diagnostics of many health conditions, metabolites, and drugs, particularly in diagnostics of cancer, including diagnostics of its early stages.FTIR, particularly ATR-FTIR can be a method of choice for efficient sensing of many biomarkers, present in urine, blood and other biofluids at sufficiently high concentrations (mM and even a few µM)Brillouin scattering spectroscopy detecting visco-elastic properties of probed liquid medium, may also find application in clinical analysis of some biofluids, such as cerebrospinal fluid and urine.

Identifying infectiousness of SARS-CoV-2 by ultra-sensitive SnS2 SERS biosensors with capillary effect

The current COVID-19 pandemic urges us to develop ultra-sensitive surface-enhanced Raman scattering (SERS) substrates to identify the infectiousness of SARS-CoV-2 virions in actual environments. Here, a micrometer-sized spherical SnS₂ structure with the hierarchical nanostructure of "nano-canyon" morphology was developed as semiconductor-based SERS substrate, and it exhibited an extremely low limit of detection of 10^-13 M for methylene blue, which is one of the highest sensitivities among the reported pure semiconductor-based SERS substrates. Such ultra-high SERS sensitivity originated from the synergistic enhancements of the molecular enrichment caused by capillary effect and the charge transfer chemical enhancement boosted by the lattice strain and sulfur vacancies. The novel two-step SERS diagnostic route based on the ultra-sensitive SnS₂ substrate was presented to diagnose the infectiousness of SARS-CoV-2 through the identification standard of SERS signals for SARS-CoV-2 S protein and RNA, which could accurately identify non-infectious lysed SARS-CoV-2 virions in actual environments, whereas the current PCR methods cannot.

Development of antibody against drug-resistant respiratory syncytial virus: Rapid detection of mutant virus using split superfolder green fluorescent protein-antibody system

Respiratory syncytial virus (RSV) infections are associated with severe bronchiolitis or pneumonia. Although palivizumab is used to prevent RSV infections, the occurrence of palivizumab-resistant RSV strains is increasing, and these strains pose a threat to public health. Herein, we report an antibody with affinity to the S275F RSV antigen, enabling the specific detection of palivizumab-resistant RSV strains. Experimental and simulation results confirmed the affinity of the antibody to the S275F RSV antigen. Furthermore, we developed a rapid S275F RSV antigen detection method using a split superfolder green fluorescent protein (ssGFP) that can interact with the antibody. In the presence of the mutant virus antigen, ssGFP emitted fluorescence within 1 min, allowing the rapid identification of S275F RSV. We anticipate that the developed antibody would be useful for the precise diagnosis of antiviral drug-resistant RSV strains and help treat patients with RSV infections.

Human ACE2-Functionalized Gold "Virus-Trap" Nanostructures for Accurate Capture of SARS-CoV-2 and Single-Virus SERS Detection

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold "virus traps" nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 10⁶-fold virus enrichment originating from high-affinity of ACE2 with S protein as well as "virus-traps" composed of oblique gold nanoneedles, and 10⁹-fold enhancement of Raman signals originating from multi-component SERS effects. Furthermore, the identification standard of virus signals is established by machine-learning and identification techniques, resulting in an especially low detection limit of 80 copies mL^-1 for the simulated contaminated water by SARS-CoV-2 virus with complex circumstance as short as 5 min, which is of great significance for achieving real-time monitoring and early warning of coronavirus. Moreover, here-developed method can be used to establish the identification standard for future unknown coronavirus, and immediately enable extremely sensitive and rapid detection of novel virus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40820-021-00620-8.

Behaviours of antiviral Oseltamivir in different media: DFT and SQMFF calculations

The synthetic cyclohexenecarboxylate ester antiviral Oseltamivir (O) have been theoretically studied by B3LYP/6–311 +  + G** calculations to estimate its reactivity and behaviour in gas and aqueous media. The most stable structure obtained in above media is consistent with that reported experimental for Oseltamivir phosphate. The solvation energy value of (O) in aqueous media is between the predicted for antiviral Idoxuridine and Ribavirin. Besides, (O) containing a NH₂ group and NH group reveals lower solvation energy compared with other antiviral agents with an NH₂ group, such as Ribavirin, Cidofovir, and Brincidofovir. Atomic charges on N and O atoms in acceptors and donor groups reveal different behaviours in both media, while the natural bond orbital (NBO) studies show a raised stability of (O) in aqueous solution. This latter resulted is in concordance with the lower reactivity evidenced in water. Frontier orbital studies have revealed that (O) in gas phase has a very similar gap value to antiviral Cidofovir used against the ebola disease, while Chloroquine in the two media are more reactive than (O). This study will allow to identify (O) by using vibrational spectroscopy because the 144 vibration modes expected have been assigned using the harmonic force fields calculated from the scaled mechanical force field methodology (SQMFF). Scaled force constants for (O) in the mentioned media are also reported for first time. Due to hydration of the C = O and NH₂ groups by solvent molecules, the calculations in solution produce variations not only in the IR wavenumbers bands, but also in their intensities.

Spectroscopic molecular-fingerprint profiling of saliva

Saliva analysis has been gaining interest as a potential non-invasive source of disease indicative biomarkers due to being a complex biofluid correlating with blood-based constituents on a molecular level. For saliva to cement its usage for analytical applications, it is paramount to gain underpinning molecular knowledge and establish a 'baseline' of the salivary composition in healthy individuals as well as characterize how these factors are impacting its performance as potential analytical biofluid. Here, we have systematically studied the molecular spectral fingerprint of saliva, including the changes associated with gender, age, and time. Via hybrid artificial neural network algorithms and Raman spectroscopy, we have developed a non-destructive molecular profiling approach enabling the assessment of salivary spectral changes yielding the determination of gender and age of the biofluid source. Our classification algorithm successfully identified the gender and age from saliva with high classification accuracy. Discernible spectral molecular 'barcodes' were subsequently constructed for each class and found to primarily stem from amino acid, protein, and lipid changes in saliva. This unique combination of Raman spectroscopy and advanced machine learning techniques lays the platform for a variety of applications in forensics and biosensing.

Advanced Nanomaterials for Preparedness Against (Re-)Emerging Viral Diseases

While the coronavirus disease (COVID-19) accounts for the current global pandemic, the emergence of other unknown pathogens, named "Disease X," remains a serious concern in the future. Emerging or re-emerging pathogens continue to pose significant challenges to global public health. In response, the scientific community has been urged to create advanced platform technologies to meet the ever-increasing needs presented by these devastating diseases with pandemic potential. This review aims to bring new insights to allow for the application of advanced nanomaterials in future diagnostics, vaccines, and antiviral therapies, thereby addressing the challenges associated with the current preparedness strategies in clinical settings against viruses. The application of nanomaterials has advanced medicine and provided cutting-edge solutions for unmet needs. Herein, an overview of the currently available nanotechnologies is presented, highlighting the significant features that enable them to control infectious diseases, and identifying the challenges that remain to be addressed for the commercial production of nano-based products is presented. Finally, to conclude, the development of a nanomaterial-based system using a "One Health" approach is suggested. This strategy would require a transdisciplinary collaboration and communication between all stakeholders throughout the entire process spanning across research and development, as well as the preclinical, clinical, and manufacturing phases.

Unveiling the interaction of protein fibrils with gold nanoparticles by plasmon enhanced nano-spectroscopy

The development of various degenerative diseases is suggested to be triggered by the uncontrolled organisation and aggregation of proteins into amyloid fibrils. For this reason, there are ongoing efforts to develop novel agents and approaches, including metal nanoparticle-based colloids, that dissolve amyloid structures and prevent pathogenic protein aggregation. In this contribution, the role of gold nanoparticles (AuNPs) in degrading amyloid fibrils of the model protein lysozyme is investigated. The amino acid composition of fibril surfaces before and after the incubation with AuNPs is determined at the single fibril level by exploiting the high spatial resolution and sensitivity provided by tip-enhanced and surface-enhanced Raman spectroscopies. This combined spectroscopic approach allows to reveal the molecular mechanisms driving the interaction between fibrils and AuNPs. Our results provide an important input for the understanding of amyloid fibrils and could have a potential translational impact on the development of strategies for the prevention and treatment of amyloid-related diseases.

Plasmon Nanocomposite-Enhanced Optical and Electrochemical Signals for Sensitive Virus Detection

The social impact of virus spread is immeasurable. Vaccine prophylaxes take considerable time to develop because clinical trials are required. The best initial response to an emerging virus is establishing a virus detection technology adapted by simply preparing virus-specific antibodies. A virus detection system that detects two signals from one analyte has been developed to detect the target virus more sensitively and reliably. Plasmon regions on the surface of nanoparticles are effective in enhancing optical and electrochemical signals. Thus, CdSeTeS quantum dots (QDs) have been used as optical and electrochemical signal-generating materials. In contrast, gold nanoparticle-magnetic nanoparticle-carbon nanotube (AuNP-MNP-CNT) nanocomposites are used for the magnetic separation of the virus from interferences and for signal enhancement. In the presence of the target virus, the QDs optically show a virus concentration-dependent fluorescence enhancement effect due to the localized surface plasmon resonance (LSPR) of AuNPs. Regarding the electrochemical signal, Cd ions eluted by acid degradation of the QDs in solution show a virus concentration-dependent increase in the current peak on an electrode whose electrochemical properties are improved by the deposition of these nanocomposites. Both nanomaterials are conjugated with antibodies specific to influenza virus A (IFV/A), binding this target in a sandwich structure. We are successfully detecting the virus from these two signals during actual virus detection, even when the virus particles are in a human serum matrix. The limit of detection is 2.16 fg/mL for optical detection and 13.66 fg/mL for electrochemical detection.

SP, N. M, Barik AK, Pai KM, Unnikrishnan VK, George SD, Kartha VB, Chidangil S. Photonics of human saliva: potential optical methods for the screening of abnormal health conditions and infections

Human saliva can be treated as a pool of biological markers able to reflect on the state of personal health. Recent years have witnessed an increase in the use of optical devices for the analysis of body fluids. Several groups have carried out studies investigating the potential of saliva as a non-invasive and reliable clinical specimen for use in medical diagnostics. This brief review aims to highlight the optical technologies, mainly surface plasmon resonance (SPR), Raman, and Fourier transform infrared (FTIR) spectroscopy, which are being used for the probing of saliva for diverse biomedical applications. Advances in bio photonics offer the promise of unambiguous, objective and fast detection of abnormal health conditions and viral infections (such as COVID-19) from the analysis of saliva.

Development of 6E3 antibody-mediated SERS immunoassay for drug-resistant influenza virus

Influenza viruses are responsible for several pandemics and seasonal epidemics and pose a major public health threat. Even after a major outbreak, the emergence of drug-resistant influenza viruses can pose disease control problems. Here we report a novel 6E3 monoclonal antibody capable of recognizing and binding to the H275Y neuraminidase (NA) mutation, which has been associated with reduced susceptibility of influenza viruses to NA inhibitors. The 6E3 antibody had a K_D of 72.74 μM for wild-type NA and 32.76 pM for H275Y NA, suggesting that it can identify drug-resistant pandemic H1N1 (pH1N1) influenza virus. Molecular modeling studies also suggest the high-affinity binding of this antibody to pH1N1 H275Y NA. This antibody was also subject to dot-blot, enzyme-linked immunosorbent assay, bare-eye detection, and lateral flow assay to demonstrate its specificity to drug-resistant pH1N1. Furthermore, it was immobilized on Au nanoplate and nanoparticles, enabling surface-enhanced Raman scattering (SERS)-based detection of the H275Y mutant pH1N1. Using 6E3 antibody-mediated SERS immunoassay, the drug-resistant influenza virus can be detected at a low concentration of 10² plaque-forming units/mL. We also detected pH1N1 in human nasopharyngeal aspirate samples, suggesting that the 6E3-mediated SERS assay has the potential for diagnostic application. We anticipate that this newly developed antibody and SERS-based immunoassay will contribute to the diagnosis of drug-resistant influenza viruses and improve treatment strategies for influenza patients.

Small-volume detection: platform developments for clinically-relevant applications

Biochemical analysis of human body fluids is a frequent and fruitful strategy for disease diagnosis. Point-of-care (POC) diagnostics offers the tantalizing possibility of providing rapid diagnostic results in non-laboratory settings. Successful diagnostic testing using body fluids has been reported on in the literature; however, small-volume detection devices, which offer remarkable advantages such as portability, inexpensiveness, capacity for mass production, and tiny sample volume requirements have not been thoroughly discussed. Here, we review progress in this research field, with a focus on developments since 2015. In this review article, we provide a summary of articles that have detailed the development of small-volume detection strategies using clinical samples over the course of the last 5 years. Topics covered include small-volume detection strategies in ophthalmology, dermatology or plastic surgery, otolaryngology, and cerebrospinal fluid analysis. In ophthalmology, advances in technology could be applied to examine tear or anterior chamber (AC) fluid for glucose, lactoferrin, interferon, or VEGF. These approaches could impact detection and care for diseases including diabetic mellitus, dry-eye disease, and age-related maculopathy. Early detection and easy monitoring are critical approaches for improving overall care and outcome. In dermatology or plastic surgery, small-volume detection strategies have been applied for passive or interactive wound dressing, wound healing monitoring, and blister fluid analysis for autoimmune disease diagnosis. In otolaryngology, the analysis of nasal secretions and mucosa could be used to differentiate between allergic responses and infectious diseases. Cerebrospinal fluid analysis could be applied in neurodegenerative diseases, central neural system infection and tumor diagnosis. Other small-volume fluids that have been analyzed for diagnostic and monitoring purposes include semen and cervico-vaginal fluids. We include more details regarding each of these fluids, associated collection and detection devices, and approaches in our review.

Applicability of Raman spectroscopy on porcine parvovirus and porcine circovirus type 2 detection

Porcine parvovirus (PPV) is one of the major infectious causes of reproductive failure of swine. This disease is characterized by embryonic and fetal infection and death, responsible for important economic losses. PPV is also implicated as a trigger in the development of post-weaning multisystemic wasting syndrome (PMWS) caused by Porcine circovirus type 2 (PCV2). Their detection is PCR-based, which is quite sensitive and specific, but laborious, costly and time-demanding. Therefore, this study aimed to assess Raman spectroscopy (RS) as a diagnostic tool for PPV and PCV2 due to its label-free properties and unique ability to search and identify molecular fingerprints. Briefly, swine testis (ST) cells were inoculated with PPV or PCV2 and in vitro cultured (37 °C, 5% CO₂) for four days. Fixed cells were then submitted to RS investigation using a 633 nm laser. A total of 225 spectra centered at 1300 cm^-1 was obtained for each sample (5 spectra/cell; 15 cells/replicate; 3 replicates) of PPV-, PCV2-infected and uninfected (control) ST cells. Clear statistical discrimination between samples from both virus-infected cells was achieved with a Principal Component - Linear Discriminant Analysis (PCA-LDA) model, reaching sensitivity rates from 95.55% to 97.77%, respectively to PCV2- and PPV-infected cells. These results were then submitted to a Leave-One-Out (LOO) validation algorithm resulting in 99.97% of accuracy. Extensive band assignment was analyzed and compiled for better understanding of PPV and PCV2 virus-cell interaction, demonstrating that specific protein, lipids and DNA/RNA bands are the most important assignments related to discrimination of virus-infected from uninfected cells. In conclusion, these results represent promising bases for RS application on PCV2 and PPV detection for future diagnostic applications.

Toward rapid infectious disease diagnosis with advances in surface-enhanced Raman spectroscopy

In a pandemic era, rapid infectious disease diagnosis is essential. Surface-enhanced Raman spectroscopy (SERS) promises sensitive and specific diagnosis including rapid point-of-care detection and drug susceptibility testing. SERS utilizes inelastic light scattering arising from the interaction of incident photons with molecular vibrations, enhanced by orders of magnitude with resonant metallic or dielectric nanostructures. While SERS provides a spectral fingerprint of the sample, clinical translation is lagged due to challenges in consistency of spectral enhancement, complexity in spectral interpretation, insufficient specificity and sensitivity, and inefficient workflow from patient sample collection to spectral acquisition. Here, we highlight the recent, complementary advances that address these shortcomings, including (1) design of label-free SERS substrates and data processing algorithms that improve spectral signal and interpretability, essential for broad pathogen screening assays; (2) development of new capture and affinity agents, such as aptamers and polymers, critical for determining the presence or absence of particular pathogens; and (3) microfluidic and bioprinting platforms for efficient clinical sample processing. We also describe the development of low-cost, point-of-care, optical SERS hardware. Our paper focuses on SERS for viral and bacterial detection, in hopes of accelerating infectious disease diagnosis, monitoring, and vaccine development. With advances in SERS substrates, machine learning, and microfluidics and bioprinting, the specificity, sensitivity, and speed of SERS can be readily translated from laboratory bench to patient bedside, accelerating point-of-care diagnosis, personalized medicine, and precision health.

Optical technologies for the detection of viruses like COVID-19: Progress and prospects

The outbreak of life-threatening pandemic like COVID-19 necessitated the development of novel, rapid and cost-effective techniques that facilitate detection of viruses like SARS-CoV-2. The presently popular approach of a collection of samples using the nasopharyngeal swab method and subsequent detection of RNA using the real-time polymerase chain reaction suffers from false-positive results and a longer diagnostic time scale. Alternatively, various optical techniques namely optical sensing, spectroscopy, and imaging shows a great promise in virus detection. Herein, a comprehensive review of the various photonics technologies employed for virus detection, particularly the SARS-CoV family, is discussed. The state-of-art research activities in utilizing the photonics tools such as near-infrared spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, fluorescence-based techniques, super-resolution microscopy, surface plasmon resonance-based detection, for virus detection accounted extensively with an emphasis on coronavirus detection. Further, an account of emerging photonics technologies of SARS-CoV-2 detection and future possibilities is also explained. The progress in the field of optical techniques for virus detection unambiguously show a great promise in the development of rapid photonics-based devices for COVID-19 detection.

Recent advances in visual detection for cancer biomarkers and infectious pathogens

It is an urgency to detect infectious pathogens or cancer biomarkers using rapid, simple, convenient and cost-effective methods in complex biological samples. Many existing approaches (traditional virus culture, ELISA or PCR) for the pathogen and biomarker assays face several challenges in the clinical applications that require lengthy time, sophisticated sample pre-treatment and expensive instruments. Due to the simple and rapid detection manner as well as no requirement of expensive equipment, many visual detection methods have been considered to resolve the aforementioned problems. Meanwhile, various new materials and colorimetric/fluorescent methods have been tried to construct new biosensors for infectious pathogens and biomarkers. However, the recent progress of these aspects is rarely reviewed, especially in terms of integration of new materials, microdevice and detection mechanism into the visual detection systems. Herein, we provide a broad field of view to discuss the recent progress in the visual detection of infectious pathogens and cancer biomarkers along with the detection mechanism, new materials, novel detection methods, special targets as well as multi-functional microdevices and systems. The novel visual approaches for the infectious pathogens and biomarkers, such as bioluminescence resonance energy transfer (BRET), metal-induced metallization and clustered regularly interspaced short palindromic repeats (CRISPR)-based biosensors, are discussed. Additionally, recent advancements in visual assays utilizing various new materials for proteins, nucleic acids, viruses, exosomes and small molecules are comprehensively reviewed. Future perspectives on the visual sensing systems for infectious pathogens and cancers are also proposed.

Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9

Viruses have been a continuous threat to human beings. The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a pandemic that is still ongoing worldwide. Previous pandemic influenza A virus (pH1N1) might be re-emerging through a drug-resistant mutation. We report a colorimetric viral detection method based on the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 endonuclease dead (dCas9) system. In this method, RNA in the viral lysate was directly recognized by the CRISPR/dCas9 system with biotin-protospacer adjacent motif (PAM)-presenting oligonucleotide (PAMmer). Streptavidin-horseradish peroxidase then bound to biotin-PAMmer, inducing a color change through the oxidation of 3,3',5,5'-tetramethylbenzidine. Using the developed method, we successfully identified SARS-CoV-2, pH1N1, and pH1N1/H275Y viruses by the naked eye. Moreover, the detection of viruses in human nasopharyngeal aspirates and sputum was demonstrated. Finally, clinical samples from COVID-19 patients led to a successful diagnosis. We anticipate that the current method can be employed for simple and accurate diagnosis of viruses.

Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9

Viruses have been a continuous threat to human beings. The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a pandemic that is still ongoing worldwide. Previous pandemic influenza A virus (pH1N1) might be re-emerging through a drug-resistant mutation. We report a colorimetric viral detection method based on the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 endonuclease dead (dCas9) system. In this method, RNA in the viral lysate was directly recognized by the CRISPR/dCas9 system with biotin-protospacer adjacent motif (PAM)-presenting oligonucleotide (PAMmer). Streptavidin-horseradish peroxidase then bound to biotin-PAMmer, inducing a color change through the oxidation of 3,3',5,5'-tetramethylbenzidine. Using the developed method, we successfully identified SARS-CoV-2, pH1N1, and pH1N1/H275Y viruses by the naked eye. Moreover, the detection of viruses in human nasopharyngeal aspirates and sputum was demonstrated. Finally, clinical samples from COVID-19 patients led to a successful diagnosis. We anticipate that the current method can be employed for simple and accurate diagnosis of viruses.

Vibrational Spectroscopy Saliva Profiling as Biometric Tool for Disease Diagnostics: A Systematic Literature

Saliva is a biofluid that can be considered as a “mirror” reflecting our body’s health status. Vibrational spectroscopy, Raman and infrared, can provide a detailed salivary fingerprint that can be used for disease biomarker discovery. We propose a systematic literature review based on the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to evaluate the potential of vibrational spectroscopy to diagnose oral and general diseases using saliva as a biological specimen. Literature searches were recently conducted in May 2020 through MEDLINE-PubMed and Scopus databases, without date limitation. Finally, over a period of 10 years, 18 publications were included reporting on 10 diseases (three oral and seven general diseases), with very high diagnostic performance rates in terms of sensitivity, specificity, and accuracy. Thirteen articles were related to six different cancers of the following anatomical sites: mouth, nasopharynx, lung, esophagus, stomach, and breast. The other diseases investigated and included in this review were periodontitis, Sjögren’s syndrome, diabetes, and myocardial infarction. Moreover, most articles focused on Raman spectroscopy (n = 16/18) and more specifically surface-enhanced Raman spectroscopy (n = 12/18). Interestingly, vibrational spectroscopy appears promising as a rapid, label-free, and non-invasive diagnostic salivary biometric tool. Furthermore, it could be adapted to investigate subclinical diseases—even if developmental studies are required.