Detection and monitoring of virus infections by real-time PCR

Focused ion beam-fabricated nanorod substrate for label-free surface-enhanced Raman spectroscopy and enabling dual virus detection

The COVID-19 pandemic presents global challenges, notably with co-infections in respiratory tract involving SARS-CoV-2 variants and influenza strains. Detecting multiple viruses simultaneously is crucial for accurate diagnosis, effective tracking infectious sources, and containment of the epidemic. This study uses a label-free surface-enhanced Raman spectroscopy (SERS) method using Au NPs/pZrO2 (250) and FIB-made Au NRs (100) to detect dual viruses, including SARS-CoV-2 Delta variant (D) and influenza A (A) or B (B) virus. Results demonstrate distinct peaks facilitating virus differentiation, especially between D and A or B, with clear disparities between substrates; specific peaks at 950 and 1337 cm-1 are pivotal for discerning viruses using Au NPs/pZrO2 (250), while those at 1050, 1394, and 1450 cm-1 and 1033, 1165, 1337, and 1378 cm-1 are key for validation using Au NRs (100). Differences in substrate surface morphology and spatial disposition of accommodating viruses significantly influence hotspot formation and Raman signal amplification efficiency, thereby affecting the ability to distinguish various viruses. Furthermore, both substrates offer insights, even in the presence of oxymetazoline hydrochloride (an interfering substance), with practical implications in viral diagnosis. The customized design and reproducibility underscore efficient Raman signal amplification, even in challenging environments, highlighting potential for widespread virus detection.

Single-tube, single-strip lateral flow assays utilizing loop-mediated isothermal amplification for simultaneous hepatitis B and C viral detection

Globally, hepatitis B virus (HBV) affects over 250 million people, whereas hepatitis C virus (HCV) affects approximately 70 million people, posing major public health challenges. Despite the availability of vaccines and treatments, a lack of comprehensive diagnostic coverage has left many cases undiagnosed and untreated. To address the need for sensitive, specific, and accessible diagnostics, this study introduced a multiplex loop-mediated isothermal amplification assay with lateral flow detection for simultaneous HBV and HCV testing. This assay achieved exceptional sensitivity and was capable of detecting HBV and HCV concurrently in a single tube and on a single strip within 25 min, achieving the required clinical sensitivity (10 and 103 genomic copies/reaction for HBV and HCV, respectively). The method was validated in clinical samples of various viral genotypes, achieving an equivalent limit of detection. Additionally, a custom portable heating device was developed for field use. The assay developed here, capable of direct viral detection on the strip, shows promise in supplanting current methods that solely identify antibodies and necessitate additional qPCR for viral activity assessment. This economical and rapid assay aligns with point-of-care testing needs, offering significant advancements in enhancing viral hepatitis diagnostics in settings with limited resources.

Rapid and specific detection of single nanoparticles and viruses in microfluidic laminar flow via confocal fluorescence microscopy

Mainstream virus detection relies on the specific amplification of nucleic acids via polymerase chain reaction, a process that is slow and requires extensive laboratory expertise and equipment. Other modalities, such as antigen-based tests, allow much faster virus detection but have reduced sensitivity. In this study, we report the development of a flow virometer for the specific and rapid detection of single nanoparticles based on confocal microscopy. The combination of laminar flow and multiple dyes enable the detection of correlated fluorescence signals, providing information on nanoparticle volumes and specific chemical composition properties, such as viral envelope proteins. We evaluated and validated the assay using fluorescent beads and viruses, including SARS-CoV-2. Additionally, we demonstrate how hydrodynamic focusing enhances the assay sensitivity for detecting clinically-relevant virus loads. Based on our results, we envision the use of this technology for clinically relevant bio-nanoparticles, supported by the implementation of the assay in a portable and user-friendly setup.

Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting

A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.

Development of a Real-Time Quantitative PCR Based on a TaqMan-MGB Probe for the Rapid Detection of Theileria haneyi

Equine piroplasmosis (EP) is a parasitic disease caused by Theileria equi (T. equi), Babesia caballi (B. caballi) and Theileria haneyi (T. haneyi). This disease is considered to be reportable by the World Organization for Animal Health (WOAH). Real-time quantitative PCR (qPCR) is regarded as a straightforward, rapid and sensitive diagnostic method to detect pathogens. However, qPCR has not been employed in the various epidemiological investigations of T. haneyi. In this study, we developed a new qPCR method to detect T. haneyi based on the chr1sco (chromosome 1 single-copy open reading frame (ORF)) gene, which has no detectable orthologs in T. equi or B. caballi. A TaqMan MGB probe was used in the development of the qPCR assay. A plasmid containing the chr1sco gene was constructed and used to establish the standard curves. The novel qPCR technique demonstrated great specificity for detecting additional frequent equine infectious pathogens and sensitivity for detecting diluted standard plasmids. This qPCR was further validated by comparison with an optimized nested PCR (nPCR) assay in the analysis of 96 clinical samples. The agreement between the nPCR assay and the established qPCR assay was 85.42%. The newly established method could contribute to the accurate diagnosis of T. haneyi infections in horses.

Cont-ID: detection of sample cross-contamination in viral metagenomic data

BACKGROUND

High-throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important detection technique for virus diagnostics. They have the potential to replace or complement the current PCR-based methods thanks to their improved inclusivity and analytical sensitivity, as well as their overall good repeatability and reproducibility. Cross-contamination is a well-known phenomenon in molecular diagnostics and corresponds to the exchange of genetic material between samples. Cross-contamination management was a key drawback during the development of PCR-based detection and is now adequately monitored in routine diagnostics. HTS technologies are facing similar difficulties due to their very high analytical sensitivity. As a single viral read could be detected in millions of sequencing reads, it is mandatory to fix a detection threshold that will be informed by estimated cross-contamination. Cross-contamination monitoring should therefore be a priority when detecting viruses by HTS technologies.

RESULTS

We present Cont-ID, a bioinformatic tool designed to check for cross-contamination by analysing the relative abundance of virus sequencing reads identified in sequence metagenomic datasets and their duplication between samples. It can be applied when the samples in a sequencing batch have been processed in parallel in the laboratory and with at least one specific external control called Alien control. Using 273 real datasets, including 68 virus species from different hosts (fruit tree, plant, human) and several library preparation protocols (Ribodepleted total RNA, small RNA and double-stranded RNA), we demonstrated that Cont-ID classifies with high accuracy (91%) viral species detection into (true) infection or (cross) contamination. This classification raises confidence in the detection and facilitates the downstream interpretation and confirmation of the results by prioritising the virus detections that should be confirmed.

CONCLUSIONS

Cross-contamination between samples when detecting viruses using HTS (Illumina technology) can be monitored and highlighted by Cont-ID (provided an alien control is present). Cont-ID is based on a flexible methodology relying on the output of bioinformatics analyses of the sequencing reads and considering the contamination pattern specific to each batch of samples. The Cont-ID method is adaptable so that each laboratory can optimise it before its validation and routine use.

Development of a Real-Time PCR Assay for the Detection of the Phlebovirus Fermo Virus

Fermo virus is a Phlebovirus that is increasingly reported in sand flies from northern Italy. The natural cycle is not fully understood, but the virus has been detected by direct methods only in sand flies. Although there is serological evidence that it can infect vertebrates, the virus has not been directly detected in animals or humans. Here, we have developed and reported a specific real-time PCR for Fermo virus. The availability of the described method will be useful to characterize the epidemiology of the FERV, ensuring, compared to previously available protocols, a more sensitive detection in insects and the possible detection in vertebrates to evaluate the presence of reservoirs and the pathogenic potential of the virus in humans or animals.

CRISPR-Cas13a-based detection method for avian influenza virus

Avian influenza virus (AIV) causes huge losses to the global poultry industry and poses a threat to humans and other mammals. Fast, sensitive, and portable diagnostic methods are essential for efficient avian influenza control. Here, a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a based platform was developed to detect AIV. This novel method was developed to specifically detect H1-H16 subtypes of AIV with fluorescence and lateral flow-based readouts and exhibited no cross-reactivity with Newcastle disease virus, avian infectious bronchitis virus, or infectious bursal disease virus. The limit of detection was determined to be 69 and 690 copies/μL using fluorescence and lateral flow as readouts, respectively. The developed assay exhibited 100% consistency with quantitative real-time polymerase chain reaction in detecting clinical samples. The heating of unextracted diagnostic samples to obliterate nuclease treatment was introduced to detect viral RNA without nucleic acid extraction. Single-step optimization was used to perform reverse transcription, recombinase polymerase amplification, and CRISPR-Cas13a detection in a tube. These advances resulted in an optimized assay that could specifically detect AIV with simplified procedures and reduced contamination risk, highlighting the potential to be used in point-of-care testing.

Immunization and Host Responses to MB-1, a Live Hatchery Vaccine against Infectious Bursal Disease

MB-1 is an attenuated infectious bursal disease virus vaccine. Previously, we observed a temporal delay of vaccine virus replication in the bursae of chicks due to maternally derived antibodies (MDAs). The mechanism that allowed its survival despite MDA neutralization remained unclear. We hypothesized that after vaccination at 1 day of age (DOA), the MB-1 virus penetrates and resides in local macrophages that are then distributed to lymphoid organs. Furthermore, MB-1's ability to survive within macrophages ensures its survival during effective MDA protection. PCR analysis of lymphoid organs from chicks with MDA, vaccinated on 1 DOA, demonstrated that the MB-1 virus was identified at low levels solely in the spleen pre-14 days of age. Fourteen days after vaccination, the virus was identified using PCR in the bursa, with viral levels increasing with time. The possible delay in viral colonization of the bursa was attributed to the presence of anti-IBDV capsid VP2 maternal IgA and IgY in the bursa interstitium. These indicate that during the period of high MDA levels, a small but viable MB-1 viral reservoir was maintained in the spleen, which might have served to colonize the bursa after MDA levels declined. Thereafter, individual immunization of chicks against Gumboro disease was achieved.

Epidemiology of COVID-19 and the Utility of Cycle Threshold (Ct) Values in Predicting the Severity of Disease

OBJECTIVES

Advanced molecular diagnostic methods like real-time polymerase chain reaction (PCR) play a vital role in the early recognition of viral infections, including the coronavirus disease 2019 (COVID-19). Therefore, in the context of the recent COVID-19 pandemic, this study aimed to determine the correlation of cycle threshold (Ct) values with symptoms in COVID-19-positive patients.

MATERIALS AND METHODS

A retrospective study was conducted in a virus research diagnostic laboratory (VRDL) at a COVID-19-dedicated tertiary care hospital in South India. A total of 5563 COVID-19-positive patients were analyzed for symptom spectrum and duration of illness with Ct values of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

RESULTS

Around 80% (n= 4401) of the patients were symptomatic and the rest were asymptomatic. Among the symptomatic patients, fever (66%) was the most common symptom. About 44% of symptomatic patients had a low Ct value (Ct ≤ 24). There was a significant difference in symptoms among patients with low, medium, and high Ct values. In the subpopulation of symptomatic patients analyzed for the association of Ct value and duration of illness, the mean duration of illness was three days and almost 88% of the patients were tested within five days of onset of symptoms. It has been observed that a shorter duration of illness lowers the Ct values. A significant association was seen between the mean Ct value and days since symptom onset (p-value = 0.016).

CONCLUSION

Most of the symptomatic patients had lower Ct values in comparison to the asymptomatic patients. A significant association between low Ct values and the duration of symptoms observed in our study explains the viral dynamics, i.e., higher viral shedding at the onset of symptoms and declines thereafter.

Medical viruses: diagnostic techniques

The recent epidemics and pandemics caused by different viruses such as SARS-CoV-2, monkey pox, H1N1, ebola virus etc. have been a cause of mass destruction in the human race, the biggest decline slope in the global economy and mental trauma. A number of viruses have been discovered that may cause serious problems and to overcome this problem, early diagnosis of the viruses and understanding their infection pattern is a must. Early detection of viruses inside the host provides timely management in a strategic manner. Scientists have developed some effective and efficient methods to detect the viruses. In this review, we have explained a few types of diagnostic techniques: Biosensor based, immunological-based, and molecular-based diagnostic techniques that are prominent methodologies to identify and detect the course of infection related to the medical viruses. In biosensor-based diagnostic technique, an analytical device consisting of biological elements and physicochemical component gives a signal upon detection of viral antigen. In immunological-based diagnostic techniques, enzyme-linked antibodies are utilized to find the particular antiviral antibody or viral antigen in human specimens, and nucleic acid-based diagnostic techniques are based on the principle of amplification of the viral genome.

CRISPR-Based Biosensing Strategies: Technical Development and Application Prospects

Biosensing based on CRISPR-Cas systems is a young but rapidly evolving technology. The unprecedented properties of the CRISPR-Cas system provide an innovative tool for developing new-generation biosensing strategies. To date, a series of nucleic acid and non-nucleic acid detection methods have been developed based on the CRISPR platform. In this review, we first introduce the core biochemical properties underpinning the development of CRISPR bioassays, such as diverse reaction temperatures, programmability in design, high reaction efficiency, and recognition specificity, and highlight recent efforts to improve these parameters. We then introduce the technical developments, including how to improve sensitivity and quantification capabilities, develop multiplex assays, achieve convenient one-pot assays, create advanced sensors, and extend the applications of detection. Finally, we analyze obstacles to the commercial application of CRISPR detection technology and explore development opportunities and directions.

Label-free detection and discrimination of respiratory pathogens based on electrochemical synthesis of biomaterials-mediated plasmonic composites and machine learning analysis

Seasonal outbreaks of respiratory viral infections remain a global concern, with increasing morbidity and mortality rates recorded annually. Timely and false responses contribute to the widespread of respiratory pathogenic diseases owing to similar symptoms at an early stage and subclinical infection. The prevention of emerging novel viruses and variants is also a big challenge. Reliable point-of-care diagnostic assays for early infection diagnosis play a critical role in the response to threats of epidemics or pandemics. We developed a facile method for specifically identifying different viruses based on surface-enhanced Raman spectroscopy (SERS) with pathogen-mediated composite materials on Au nanodimple electrodes and machine learning (ML) analyses. Virus particles were trapped in three-dimensional plasmonic concave spaces of the electrode via electrokinetic preconcentration, and Au films were simultaneously electrodeposited, leading to the acquisition of intense and in-situ SERS signals from the Au-virus composites for ultrasensitive SERS detection. The method was useful for rapid detection analysis (<15 min), and the ML analysis for specific identification of eight virus species, including human influenza A viruses (i.e., H1N1 and H3N2 strains), human rhinovirus, and human coronavirus, was conducted. The highly accurate classification was achieved using the principal component analysis-support vector machine (98.9%) and convolutional neural network (93.5%) models. This ML-associated SERS technique demonstrated high feasibility for direct multiplex detection of different virus species for on-site applications.

MAVS-Based Reporter Systems for Real-Time Imaging of EV71 Infection and Antiviral Testing

Enterovirus consists of a variety of viruses that could cause a wide range of illness in human. The pathogenesis of these viruses remains incompletely understood and no specific treatment is available. Better methods to study enterovirus infection in live cells will help us better understand the pathogenesis of these viruses and might contribute to antiviral development. Here in this study, we developed fluorescent cell-based reporter systems that allow sensitive distinction of individual cells infected with enterovirus 71 (EV71). More importantly, these systems could be easily used for live-cell imaging by monitoring viral-induced fluorescence translocation after EV71 infection. We further demonstrated that these reporter systems could be used to study other enterovirus-mediated MAVS cleavage and they are sensitive for antiviral activity testing. Therefore, integration of these reporters with modern image-based analysis has the potential to generate new insights into enterovirus infection and facilitate antiviral development.

Fluorescent detection of emerging virus based on nanoparticles: From synthesis to application

The spread of COVID-19 has caused huge economic losses and irreversible social impact. Therefore, to successfully prevent the spread of the virus and solve public health problems, it is urgent to develop detection methods with high sensitivity and accuracy. However, existing detection methods are time-consuming, rely on instruments, and require skilled operators, making rapid detection challenging to implement. Biosensors based on fluorescent nanoparticles have attracted interest in the field of detection because of their advantages, such as high sensitivity, low detection limit, and simple result readout. In this review, we systematically describe the synthesis, intrinsic advantages, and applications of organic dye-doped fluorescent nanoparticles, metal nanoclusters, up-conversion particles, quantum dots, carbon dots, and others for virus detection. Furthermore, future research initiatives are highlighted, including green production of fluorescent nanoparticles with high quantum yield, speedy signal reading by integrating with intelligent information, and error reduction by coupling with numerous fluorescent nanoparticles.

Harnessing the LdCsm RNA Detection Platform for Efficient microRNA Detection

In cancer diagnosis, diverse microRNAs (miRNAs) are used as biomarkers for carcinogenesis of distinctive human cancers. Thus, the detection of these miRNAs and their quantification are very important in prevention of cancer diseases in human beings. However, efficient RNA detection often requires RT-PCR, which is very complex for miRNAs. Recently, the development of CRISPR-based nucleic acid detection tools has brought new promises to efficient miRNA detection. Three CRISPR systems can be explored for miRNA detection, including type III, V, and VI, among which type III (CRISPR-Cas10) systems have a unique property as they recognize RNA directly and cleave DNA collaterally. In particular, a unique type III-A Csm system encoded by Lactobacillus delbrueckii subsp. bulgaricus (LdCsm) exhibits robust target RNA-activated DNase activity, which makes it a promising candidate for developing efficient miRNA diagnostic tools. Herein, LdCsm was tested for RNA detection using fluorescence-quenched DNA reporters. We found that the system is capable of specific detection of miR-155, a microRNA implicated in the carcinogenesis of human breast cancer. The RNA detection system was then improved by various approaches including assay conditions and modification of the 5'-repeat tag of LdCsm crRNAs. Due to its robustness, the resulting LdCsm detection platform has the potential to be further developed as a better point-of-care miRNA diagnostics relative to other CRISPR-based RNA detection tools.

VPrimer: A Method of Designing and Updating Primer and Probe With High Variant Coverage for RNA Virus Detection

Fatal infectious diseases caused by RNA viruses, such as COVID-19, have emerged around the world. RT-PCR is widely employed for virus detection, and its accuracy depends on the primers and probes since RT-PCR can detect a virus only when the primers and probes bind to the target gene of the virus. Most of primer design methods are for a single host and so require a great deal of effort to design for RNA virus detection, including homology tests among the host and all the viruses for the host using BLAST-like tools. Furthermore, they do not consider variant sequences, which are very common in viruses. In this study, we describe VPrimer, a method of designing high-quality primer-probe sets for RNA viruses. VPrimer can find primer-probe sets that cover more than 95% of the variants of a target virus but do not cover any sequences of other viruses or the host. With VPrimer, we found 381,698,582 primer-probe sets for 3,104 RNA viruses. Multiplex PCR assays using the top 2 primer-probe sets suggested by VPrimer usually cover 100% of variants. To address the rapid changes in viral genomes, VPrimer finds the best and up-to-date primer-probe sets incrementally against the most recently reported variants.

Intestinal Shedding of SARS-CoV-2 in Children: No Evidence for Infectious Potential

The clinical courses of COVID-19 in children are often mild and may remain undiagnosed, but prolonged intestinal virus shedding has been documented, thus potentially enabling fecal-oral transmission. However, the infectious potential of SARS-CoV-2 viruses excreted with feces has remained unclear. Here, we investigated 247 stool specimens from 213 pediatric patients to assess the prevalence of intestinal SARS-CoV-2 shedding in hospitalized children without or with COVID-19 and determined the infectious capacity of stool-borne viruses. Upon RT-qPCR screening, the infectivity of virus-positive samples was tested in cell culture using the Vero-E6 permissive cell line. SARS-CoV-2 RNA was detected by RT-qPCR in 32 (13%) stool specimens, but the analysis of virus-positive samples in cell culture revealed no cytopathic effects attributable to SARS-CoV-2-related cell damage. Our findings do not support the notion of potential fecal-oral SARS-CoV-2 spreading, thus questioning the role of hygienic measures designed to prevent this mode of viral transmission.

Recent Development in Plasmonic Nanobiosensors for Viral DNA/RNA Biomarkers

Recently, due to the coronavirus pandemic, the need for early diagnosis of infectious diseases, including viruses, is emerging. Though early diagnosis is essential to prevent infection and progression to severe illness, there are few technologies that accurately measure low concentrations of biomarkers. Plasmonic nanomaterials are attracting materials that can effectively amplify various signals, including fluorescence, Raman, and other optical and electromagnetic output. In this review, we introduce recently developed plasmonic nanobiosensors for measuring viral DNA/RNA as potential biomarkers of viral diseases. In addition, we discuss the future perspective of plasmonic nanobiosensors for DNA/RNA detection. This review is expected to help the early diagnosis and pathological interpretation of viruses and other diseases.

Ultrafast PCR Detection of COVID-19 by Using a Microfluidic Chip-Based System

With the evolution of the pandemic caused by the Coronavirus disease of 2019 (COVID-19), reverse transcriptase-polymerase chain reactions (RT-PCR) have invariably been a golden standard in clinical diagnosis. Nevertheless, the traditional polymerase chain reaction (PCR) is not feasible for field application due to its drawbacks, such as time-consuming and laboratory-based dependence. To overcome these challenges, a microchip-based ultrafast PCR system called SWM-02 was proposed to make PCR assay in a rapid, portable, and low-cost strategy. This novel platform can perform 6-sample detection per run using multiple fluorescent channels and complete an ultrafast COVID-19 RT-PCR test within 40 min. Here, we evaluated the performance of the microdevice using the gradient-diluted COVID-19 reference samples and commercial PCR kit and determined its limit-of-detection (LoD) as 500 copies/mL, whose variation coefficients for the nucleocapsid (N) gene and open reading frame 1 ab region (ORF1ab) gene are 1.427% and 0.7872%, respectively. The system also revealed an excellent linear correlation between cycle threshold (Ct) values and dilution factors (R2 > 0.99). Additionally, we successfully detected the target RNAs and internal gene in the clinical samples by fast PCR, which shows strong consistency with conventional PCR protocol. Hence, with compact dimension, user-friendly design, and fast processing time, SWM-02 has the capability of offering timely and sensitive on-site molecular diagnosis for prevention and control of pathogen transmission.

CRISPR-Cas systems for diagnosing infectious diseases

Infectious diseases are a global health problem affecting billions of people. Developing rapid and sensitive diagnostic tools is key for successful patient management and curbing disease spread. Currently available diagnostics are very specific and sensitive but time-consuming and require expensive laboratory settings and well-trained personnel; thus, they are not available in resource-limited areas, for the purposes of large-scale screenings and in case of outbreaks and epidemics. Developing new, rapid, and affordable point-of-care diagnostic assays is urgently needed. This review focuses on CRISPR-based technologies and their perspectives to become platforms for point-of-care nucleic acid detection methods and as deployable diagnostic platforms that could help to identify and curb outbreaks and emerging epidemics. We describe the mechanisms and function of different classes and types of CRISPR-Cas systems, including pros and cons for developing molecular diagnostic tests and applications of each type to detect a wide range of infectious agents. Many Cas proteins (Cas3, Cas9, Cas12, Cas13, Cas14 etc.) have been leveraged to create highly accurate and sensitive diagnostic tools combined with technologies of signal amplification and fluorescent, potentiometric, colorimetric, lateral flow assay detection and other. In particular, the most advanced platforms -- SHERLOCK/v2, DETECTR, CARMEN or CRISPR-Chip -- enable detection of attomolar amounts of pathogenic nucleic acids with specificity comparable to that of PCR but with minimal technical settings. Further developing CRISPR-based diagnostic tools promises to dramatically transform molecular diagnostics, making them easily affordable and accessible virtually anywhere in the world. The burden of socially significant diseases, frequent outbreaks, recent epidemics (MERS, SARS and the ongoing COVID-19) and outbreaks of zoonotic viruses (African Swine Fever Virus etc.) urgently need the developing and distribution of express-diagnostic tools. Recently devised CRISPR-technologies represent the unprecedented opportunity to reshape epidemiological surveillance and molecular diagnostics.

Application of Next-Generation Sequencing in Infections After Allogeneic Haematopoietic Stem Cell Transplantation: A Retrospective Study

This retrospective study aimed to determine the characteristics of infection and diagnostic efficacy of next-generation sequencing (NGS) in patients with fever after allogeneic hematopoietic stem cell transplantation (allo-HSCT). A total of 71 patients with fever after HSCT were enrolled in this study. Compared with conventional microbiological test (CMT), we found that the sensitivity of NGS versus CMT in peripheral blood samples was 91.2% vs. 41.2%, and that NGS required significantly less time to identify the pathogens in both monomicrobial infections (P=0.0185) and polymicrobial infections (P= 0.0027). The diagnostic performance of NGS was not affected by immunosuppressant use. Viruses are the most common pathogens associated with infections. These results indicated that the sensitivity, timeliness, and clinical significance of NGS are superior for the detection of infections. Although NGS has the advantage of identifying a wide range of potential pathogens, the positive rate is related closely to the sample type. Therefore, we recommend that, in the clinical application of NGS to detect pathogens in patients after allo-HSCT, an appropriate sample type and time should be selected and submitted to improve the positive rate and accuracy of NGS. NGS holds promise as a powerful technology for the diagnosis of fever after HSCT.

Efficiency, sensitivity and specificity of a quantitative real-time PCR assay for Tilapia Lake virus (TiLV)

Tilapia lake virus (TiLV) is an emerging viral pathogen of tilapiines worldwide in wild and farmed tilapia. TiLV is an orthomyxo-like, negative sense segmented RNA virus, belonging to genus Tilapinevirus, family Amnoonviridae. Here we developed a quantitative real-time PCR (qRT-PCR) assay testing primer sets targeting the 10 segments of TiLV. Sensitivity, specificity, efficiency and reproducibility of these assays were examined. Detection sensitivity was equivalent to 2 TCID₅₀/ml when tested on supernatants from cell culture-grown TiLV. Specificity tests showed that all primer sets amplified their respective TiLV segments, and standard curves showed linear correlation of R² > 0.998 and amplification efficiencies between 93 % and 98 %. Intra- and inter-assay coefficients of variation (CV %) were in the range of 0.0 %- 2.6 % and 0.0 %- 5.9 %, respectively. Sensitivity tests showed that primer sets targeting segments 1, 2, 3 and 4 had the highest detection sensitivities (10^0.301 TCID₅₀/ml). The qRT-PCR used for detection of viral genome in TiLV infected organs gave virus titers equivalent to 3.80 log₁₀, 3.94 log₁₀ and 3.52 log₁₀ TCID₅₀/ml for brain, kidney and liver tissues, respectively as calculated on the basis of Ct values. These findings suggest that primer optimization for qPCR should not only focus on attaining high amplification efficiency but also sensitivity comparison of primer sets targeting different viral segments in order to develop a method with the highest sensitivity.

Recent Advances in Signal Amplification to Improve Electrochemical Biosensing for Infectious Diseases

The field of infectious disease diagnostics is burdened by inequality in access to healthcare resources. In particular, “point-of-care” (POC) diagnostics that can be utilized in non-laboratory, sub-optimal environments are appealing for disease control with limited resources. Electrochemical biosensors, which combine biorecognition elements with electrochemical readout to enable sensitive and specific sensing using inexpensive, simple equipment, are a major area of research for the development of POC diagnostics. To improve the limit of detection (LOD) and selectivity, signal amplification strategies have been applied towards these sensors. In this perspective, we review recent advances in electrochemical biosensor signal amplification strategies for infectious disease diagnostics, specifically biosensors for nucleic acids and pathogenic microbes. We classify these strategies into target-based amplification and signal-based amplification. Target-based amplification strategies improve the LOD by increasing the number of detectable analytes, while signal-based amplification strategies increase the detectable signal by modifying the transducer system and keep the number of targets static. Finally, we argue that signal amplification strategies should be designed with application location and disease target in mind, and that the resources required to produce and operate the sensor should reflect its proposed application, especially when the platform is designed to be utilized in low-resource settings. We anticipate that, based on current technologies to diagnose infectious diseases, incorporating signal-based amplification strategies will enable electrochemical POC devices to be deployed for illnesses in a wide variety of settings.

Electrochemical Impedimetric Real-Time Polymerase Chain Reactions Using Anomalous Charge Transfer Enhancement

We developed a new electrochemical impedimetric method for the real-time detection of polymerase chain reactions (PCR) based on our recent discovery that the DNA intercalator, [Ru(bpy)₂DPPZ]²⁺, anomalously enhances charge transfer between redox mediators, K₄[Fe(CN)₆]/K₃[Fe(CN)₆], and a carbon electrode. Three mM [Fe(CN)₆]^3-/4- and 5 μM [Ru(bpy)₂DPPZ]²⁺ were added to the PCR solution, and electrochemical impedance spectroscopy (EIS) measurements were performed at each elongation heat cycle. The charge transfer resistance (Rct) was initially low due to the presence of [Ru(bpy)₂DPPZ]²⁺ in the solution. As PCR progressed, amplicon dsDNA was produced exponentially, and intercalated [Ru(bpy)₂DPPZ]²⁺ ions, which could be detected as a steep Rct, increased at specific heat cycles depending on the amount of template DNA. The Rct increase per heat cycle, ΔRct, showed a peak at the same heat cycle as optical detection, proving that PCR can be accurately monitored in real time by impedance measurement. This simple method will enable a cost-effective and portable PCR device.

Diagnostic power of one-step and two-step RT-qPCR methods to SARS‑CoV‑2 detection

BACKGROUND

Coronavirus-2019 (COVID-2019) is a novel coronavirus known as Acute Respiratory Syndrome (SARS-CoV-2). The premier standard test for SARS-CoV-2 diagnosis is a one-step RT-qPCR method, which requires specific probes and reagents. Therefore, detection on a large scale is expensive and cannot be very accurate.

METHODS

A cost-effective technique based on SYBR green was evaluated in the current study. The specific primers for S and N genes were designed, then performed the cross-reactivity test with other coronavirus and respiratory viruses positive samples. Moreover, the analytical sensitivity test was carried out with 8 dilutions (1:10). Lastly, the SARS-CoV-2 clinical samples (n = 210) were tested by these two methods, and receiver operating characteristic (ROC) analysis was performed to investigate the incremental diagnostic value of each gene in the study methods.

RESULTS

The two-step method detected up to 6th dilutions of the SARS-CoV-2 samples and did not show any amplification of the positive samples of other respiratory viruses. ROC analysis revealed a diagnostic ability of the two-step method for SARS-CoV-2 with an area under the ROC curve of ≥ 0.7 (P ˂ 0.05) and relatively high sensitivity and specificity. The combination of N and S genes increased the sensitivity up to 88%, specificity up to 86%, and area under the ROC curve up to 0.85 (95% confidence interval (95% CI) 0.72 to 0.93, P = 0.0461).

CONCLUSION

Our findings indicated that the two-step method has comparable sensitivity and specificity to the one-step method. Therefore, this method can be considered a potential diagnostic method for diagnosing and monitoring COVID-19 patients. It suggests that when the one-step RT-qPCR method is not available, the two-step RT-qPCR can be used to identify SARS-CoV-2.

Combining recombinase polymerase amplification and DNA-templated reaction for SARS-CoV-2 sensing with dual fluorescence and lateral flow assay output

The early phase of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic was exacerbated by a diagnostic challenge of unprecedented magnitude. In the absence of effective therapeutics or vaccines, breaking the chain of transmission through early disease detection and patient isolation was the only means to control the growing pandemic. While polymerase chain reaction (PCR)‐based methods and rapid‐antigen tests rose to the occasion, the analytical challenge of rapid and sequence‐specific nucleic acid‐sensing at a point‐of‐care or home setting stimulated intense developments. Herein we report a method that combines recombinase polymerase amplification and a DNA‐templated reaction to achieve a dual readout with either fluorescence (microtiter plate) or naked eye (lateral flow assay: LFA) detection. The nucleic acid templated reaction is based on an S_NAr that simultaneously transfers biotin from one Peptide Nucleic Acid (PNA) strand to another PNA strand, enabling LFA detection while uncaging a coumarin for fluorescence readout. This methodology has been applied to the detection of a DNA or RNA sequence uniquely attributed to the SARS‐CoV‐2.

Exploring nano-enabled CRISPR-Cas-powered strategies for efficient diagnostics and treatment of infectious diseases

Biomedical researchers have subsequently been inspired the development of new approaches for precisely changing an organism's genomic DNA in order to investigate customized diagnostics and therapeutics utilizing genetic engineering techniques. Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR) is one such technique that has emerged as a safe, targeted, and effective pharmaceutical treatment against a wide range of disease-causing organisms, including bacteria, fungi, parasites, and viruses, as well as genetic abnormalities. The recent discovery of very flexible engineered nucleic acid binding proteins has changed the scientific area of genome editing in a revolutionary way. Since current genetic engineering technique relies on viral vectors, issues about immunogenicity, insertional oncogenesis, retention, and targeted delivery remain unanswered. The use of nanotechnology has the potential to improve the safety and efficacy of CRISPR/Cas9 component distribution by employing tailored polymeric nanoparticles. The combination of two (CRISPR/Cas9 and nanotechnology) offers the potential to open new therapeutic paths. Considering the benefits, demand, and constraints, the goal of this research is to acquire more about the biology of CRISPR technology, as well as aspects of selective and effective diagnostics and therapies for infectious illnesses and other metabolic disorders. This review advocated combining nanomedicine (nanomedicine) with a CRISPR/Cas enabled sensing system to perform early-stage diagnostics and selective therapy of specific infectious disorders. Such a Nano-CRISPR-powered nanomedicine and sensing system would allow for successful infectious illness control, even on a personal level. This comprehensive study also discusses the current obstacles and potential of the predicted technology.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40097-022-00472-7.

Development of a multiplex qRT-PCR assay for detection of African swine fever virus, classical swine fever virus and porcine reproductive and respiratory syndrome virus

BACKGROUND

African swine fever virus (ASFV), classical swine fever virus (CSFV), and porcine reproductive and respiratory syndrome virus (PRRSV) are still prevalent in many regions of China. Co-infections make it difficult to distinguish their clinical symptoms and pathological changes. Therefore, a rapid and specific method is needed for the differential detection of these pathogens.

OBJECTIVES

The aim of this study was to develop a multiplex real-time quantitative reverse transcription polymerase chain reaction (multiplex qRT-PCR) for the simultaneous differential detection of ASFV, CSFV, and PRRSV.

METHODS

Three pairs of primers and TaqMan probes targeting the ASFV p72 gene, CSFV 5' untranslated region, and PRRSV ORF7 gene were designed. After optimizing the reaction conditions, including the annealing temperature, primer concentration, and probe concentration, multiplex qRT-PCR for simultaneous and differential detection of ASFV, CSFV, and PRRSV was developed. Subsequently, 1,143 clinical samples were detected to verify the practicality of the assay.

RESULTS

The multiplex qRT-PCR assay could specifically and simultaneously detect the ASFV, CSFV, and PRRSV with a detection limit of 1.78 × 10⁰ copies for the ASFV, CSFV, and PRRSV, but could not amplify the other major porcine viruses, such as pseudorabies virus, porcine circovirus type 1 (PCV1), PCV2, PCV3, foot-and-mouth disease virus, porcine parvovirus, atypical porcine pestivirus, and Senecavirus A. The assay had good repeatability with coefficients of variation of intra- and inter-assay of less than 1.2%. Finally, the assay was used to detect 1,143 clinical samples to evaluate its practicality in the field. The positive rates of ASFV, CSFV, and PRRSV were 25.63%, 9.36%, and 17.50%, respectively. The co-infection rates of ASFV+CSFV, ASFV+PRRSV, CSFV+PRRSV, and ASFV+CSFV+PRRSV were 2.45%, 2.36%, 1.57%, and 0.17%, respectively.

CONCLUSIONS

The multiplex qRT-PCR developed in this study could provide a rapid, sensitive, specific diagnostic tool for the simultaneous and differential detection of ASFV, CSFV, and PRRSV.

Lateral flow assays (LFA) as an alternative medical diagnosis method for detection of virus species: The intertwine of nanotechnology with sensing strategies

Viruses are responsible for multiple infections in humans that impose huge health burdens on individuals and populations worldwide. Therefore, numerous diagnostic methods and strategies have been developed for prevention, management, and decreasing the burden of viral diseases, each having its advantages and limitations. Viral infections are commonly detected using serological and nucleic acid-based methods. However, these conventional and clinical approaches have some limitations that can be resolved by implementing other detector devices. Therefore, the search for sensitive, selective, portable, and costless approaches as efficient alternative clinical methods for point of care testing (POCT) analysis has gained much attention in recent years. POCT is one of the ultimate goals in virus detection, and thus, the tests need to be rapid, specific, sensitive, accessible, and user-friendly. In this review, after a brief overview of viruses and their characteristics, the conventional viral detection methods, the clinical approaches, and their advantages and shortcomings are firstly explained. Then, LFA systems working principles, benefits, classification are discussed. Furthermore, the studies regarding designing and employing LFAs in diagnosing different types of viruses, especially SARS-CoV-2 as a main concern worldwide and innovations in the LFAs' approaches and designs, are comprehensively discussed here. Furthermore, several strategies addressed in some studies for overcoming LFA limitations like low sensitivity are reviewed. Numerous techniques are adopted to increase sensitivity and perform quantitative detection. Employing several visualization methods, using different labeling reporters, integrating LFAs with other detection methods to benefit from both LFA and the integrated detection device advantages, and designing unique membranes to increase reagent reactivity, are some of the approaches that are highlighted.

Nanowire-based sensor electronics for chemical and biological applications

Detection and recognition of chemical and biological species via sensor electronics are important not only for various sensing applications but also for fundamental scientific understanding. In the past two decades, sensor devices using one-dimensional (1D) nanowires have emerged as promising and powerful platforms for electrical detection of chemical species and biologically relevant molecules due to their superior sensing performance, long-term stability, and ultra-low power consumption. This paper presents a comprehensive overview of the recent progress and achievements in 1D nanowire synthesis, working principles of nanowire-based sensors, and the applications of nanowire-based sensor electronics in chemical and biological analytes detection and recognition. In addition, some critical issues that hinder the practical applications of 1D nanowire-based sensor electronics, including device reproducibility and selectivity, stability, and power consumption, will be highlighted. Finally, challenges, perspectives, and opportunities for developing advanced and innovative nanowire-based sensor electronics in chemical and biological applications are featured.

Micro and Nanoscale Technologies for Diagnosis of Viral Infections

Viral infection is one of the leading causes of mortality worldwide. The growth of globalization significantly increases the risk of virus spreading, making it a global threat to future public health. In particular, the ongoing coronavirus disease 2019 (COVID-19) pandemic outbreak emphasizes the importance of devices and methods for rapid, sensitive, and cost-effective diagnosis of viral infections in the early stages by which their quick and global spread can be controlled. Micro and nanoscale technologies have attracted tremendous attention in recent years for a variety of medical and biological applications, especially in developing diagnostic platforms for rapid and accurate detection of viral diseases. This review addresses advances of microneedles, microchip-based integrated platforms, and nano- and microparticles for sampling, sample processing, enrichment, amplification, and detection of viral particles and antigens related to the diagnosis of viral diseases. Additionally, methods for the fabrication of microchip-based devices and commercially used devices are described. Finally, challenges and prospects on the development of micro and nanotechnologies for the early diagnosis of viral diseases are highlighted.

A Closer Look into FDA-EUA Approved Diagnostic Techniques of Covid-19

The 2019 coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 virus, caused a worldwide pandemic in 2020 and is the most urgent health issue worldwide. In this review, we highlight the details of Food and Drug Administration-Emergency Use Authorizations approved diagnostics kits, focusing on the similarities and differences. It is essential to understand the currently available options and the advantages and disadvantages each provides to select the appropriate products that maximize the testing efficiency. We believe this work will provide a holistic evaluation of the current COVID-19 diagnostic resources, including variations across the countries, and guide developing novel diagnostic techniques to improve and optimize the current testing options.

In-house reverse transcriptase polymerase chain reaction for detection of SARS-CoV-2 with increased sensitivity

As the COVID-19 infection continues to ravage the world, the advent of an efficient as well as the economization of the existing RT-PCR based detection assay essentially can become a blessing in these testing times and significantly help in the management of the pandemic. This study demonstrated an innovative and rapid corroboration of COVID-19 test based on innovative multiplex PCR. An assessment of optimal PCR conditions to simultaneously amplify the SARS-CoV-2 genes E, S and RdRp has been made by fast-conventional and HRM coupled multiplex real-time PCR using the same sets of primers. All variables of practical value were studied by amplifying known target-sequences from ten-fold dilutions of archived positive samples of COVID-19 disease. The multiplexing with newly designed E, S and RdRp primers have shown an efficient amplification of the target region of SARS-CoV-2. A distinct amplification was observed in 37 min using thermal cycler while it took 96 min in HRM coupled real time detection using SYBR green over a wide range of template concentrations. Our findings revealed decent concordance with other commercially available detection kits. This fast HRM coupled multiplex real-time PCR with SYBR green approach offers rapid and sensitive detection of SARS-CoV-2 in a cost-effective manner apart from the added advantage of primer compatibility for use in conventional multiplex PCR. The highly reproducible novel approach can propel extended applicability for developing sustainable commercial product besides providing relief to a resource limited setting.

Surface Plasmon Resonance (SPR)- and Localized SPR (LSPR)-Based Virus Sensing Systems: Optical Vibration of Nano- and Micro-Metallic Materials for the Development of Next-Generation Virus Detection Technology

The global damage that a widespread viral infection can cause is evident from the ongoing COVID-19 pandemic. The importance of virus detection to prevent the spread of viruses has been reaffirmed by the pandemic and the associated social and economic damage. Surface plasmon resonance (SPR) in microscale and localized SPR (LSPR) in nanoscale virus sensing systems are thought to be useful as next-generation detection methods. Many studies have been conducted on ultra-sensitive technologies, especially those based on signal amplification. In some cases, it has been reported that even a low viral load can be measured, indicating that the virus can be detected in patients even in the early stages of the viral infection. These findings corroborate that SPR and LSPR are effective in minimizing false-positives and false-negatives that are prevalent in the existing virus detection techniques. In this review, the methods and signal responses of SPR and LSPR-based virus detection technologies are summarized. Furthermore, this review surveys some of the recent developments reported and discusses the limitations of SPR and LSPR-based virus detection as the next-generation detection technologies.

Nanotechnology-based Colorimetric Approaches for Pathogenic Virus Sensing: A review

Fast and inexpensive virus identification protocols are paramount to hinder the further extent of pandemic diseases, minimize economic and social damages, and expedite proper clinical rehabilitation. Until now, various biosensors have been fabricated for the identification of pathogenic particles. But, they offer many difficulties. Nanotechnology resolves these difficulties and offers direct identification of pathogenic species in real-time. Among them, nanomaterial based-colorimetric sensing approach of pathogenic viruses by the naked eye has attracted much awareness because of their simplicity, speed, and low cost. In this review, the latest tendencies and advancements are overviewed in detecting pathogenic viruses using colorimetric concepts. We focus on and reconsider the use of distinctive nanomaterials such as metal nanoparticles, carbon nanotubes, graphene oxide, and conducting polymer to form colorimetric pathogenic virus sensors.

CRISPR-based diagnostics

The accurate and timely diagnosis of disease is a prerequisite for efficient therapeutic intervention and epidemiological surveillance. Diagnostics based on the detection of nucleic acids are among the most sensitive and specific, yet most such assays require costly equipment and trained personnel. Recent developments in diagnostic technologies, in particular those leveraging clustered regularly interspaced short palindromic repeats (CRISPR), aim to enable accurate testing at home, at the point of care and in the field. In this Review, we provide a rundown of the rapidly expanding toolbox for CRISPR-based diagnostics, in particular the various assays, preamplification strategies and readouts, and highlight their main applications in the sensing of a wide range of molecular targets relevant to human health.

Presence of viremia during febrile neutropenic episodes in patients undergoing chemotherapy for malignant neoplasms

The importance of viral infections as a leading cause of morbidity and mortality is well documented in severely immunosuppressed patients undergoing allogeneic stem cell transplantation. By contrast, viral infections generally receive less attention in patients with malignant disorders undergoing chemotherapy, where the onset of neutropenic fever is mostly associated with bacterial or fungal infections, and screening for viral infections is not routinely performed. To address the occurrence of invasive viral infections in a clinical setting commonly associated with less pronounced immunosuppression, we have prospectively screened 237 febrile neutropenic episodes in pediatric (n = 77) and adult (n = 69) patients undergoing intensive chemotherapy, primarily for treatment of acute leukemia. Serial peripheral blood specimens were tested by RQ-PCR assays for the presence and quantity of the clinically relevant viruses CMV, EBV, HHV6 and HAdV, commonly reactivated in highly immunocompromised patients. Viremia was documented in 36 (15%) episodes investigated, including the detection of HHV6 (n = 14), EBV (n = 15), CMV (n = 6), or HAdV (n = 1). While low or intermediate levels of viremia (<10⁴ virus copies/mL) were commonly associated with bacterial or fungal co-infection, viremia at higher levels (>10⁴ copies/mL) was documented in patients without evidence for other infections, raising the possibility that at least in some instances the onset of fever may have been attributable to the virus detected. The observations suggest that viral infections, potentially resulting from reactivation, might also play a clinically relevant role in patients receiving chemotherapy for treatment of malignant neoplasms, and routine screening for viremia in this clinical setting might be warranted.

Wastewater-Based Epidemiology as an Early Warning System for the Spreading of SARS-CoV-2 and Its Mutations in the Population

New methodologies based on the principle of "sewage epidemiology" have been successfully applied before in the detection of illegal drugs. The study describes the idea of early detection of a virus, e.g., SARS-CoV-2, in wastewater in order to focus on the area of virus occurrence and supplement the results obtained from clinical examination. By monitoring temporal variation in viral loads in wastewater in combination with other analysis, a virus outbreak can be detected and its spread can be suppressed early. The use of biosensors for virus detection also seems to be an interesting application. Biosensors are highly sensitive, selective, and portable and offer a way for fast analysis. This manuscript provides an overview of the current situation in the area of wastewater analysis, including genetic sequencing regarding viral detection and the technological solution of an early warning system for wastewater monitoring based on biosensors.

Biosensing strategies for the electrochemical detection of viruses and viral diseases - A review

Viruses are the causing agents for many relevant diseases, including influenza, Ebola, HIV/AIDS, and COVID-19. Its rapid replication and high transmissibility can lead to serious consequences not only to the individual but also to collective health, causing deep economic impacts. In this scenario, diagnosis tools are of significant importance, allowing the rapid, precise, and low-cost testing of a substantial number of individuals. Currently, PCR-based techniques are the gold standard for the diagnosis of viral diseases. Although these allow the diagnosis of different illnesses with high precision, they still present significant drawbacks. Their main disadvantages include long periods for obtaining results and the need for specialized professionals and equipment, requiring the tests to be performed in research centers. In this scenario, biosensors have been presented as promising alternatives for the rapid, precise, low-cost, and on-site diagnosis of viral diseases. This critical review article describes the advancements achieved in the last five years regarding electrochemical biosensors for the diagnosis of viral infections. First, genosensors and aptasensors for the detection of virus and the diagnosis of viral diseases are presented in detail regarding probe immobilization approaches, detection methods (label-free and sandwich), and amplification strategies. Following, immunosensors are highlighted, including many different construction strategies such as label-free, sandwich, competitive, and lateral-flow assays. Then, biosensors for the detection of viral-diseases-related biomarkers are presented and discussed, as well as point of care systems and their advantages when compared to traditional techniques. Last, the difficulties of commercializing electrochemical devices are critically discussed in conjunction with future trends such as lab-on-a-chip and flexible sensors.

A Novel Imaging Approach for Single-Cell Real-Time Analysis of Oncolytic Virus Replication and Efficacy in Cancer Cells

Oncolytic viruses (OVs) are novel cancer gene therapies that are moving toward the forefront of modern medicines. However, their full therapeutic potential is hindered by the lack of convenient and reliable strategies to visualize and quantify OV growth kinetics and therapeutic efficacy in live cells. In this study, we present an innovative imaging approach for single-cell real-time analysis of OV replication and efficacy in cancer cells. We selected SG33 as a prototypic new OV that derives from wild-type Myxoma virus (MYXV). Lausanne Toulouse 1 (T1) was used as control. We equipped SG33 and T1 genomes with the ANCHOR system and infected a panel of cell lines. The ANCHOR system is composed of a fusion protein (OR-GFP) that specifically binds to a short nonrepetitive DNA target sequence (ANCH) and spreads onto neighboring sequences by protein oligomerization. Its accumulation on the tagged viral DNA results in the creation of fluorescent foci. We found that (1) SG33 and T1-ANCHOR DNA can be readily detected and quantified by live imaging, (2) both OVs generate perinuclear replication foci after infection clustering into horse-shoe shape replication centers, and (3) SG33 replicates to higher levels as compared with T1. Lastly, as a translational proof of concept, we benchmarked SG33 replication and oncolytic efficacy in primary cancer cells derived from pancreatic adenocarcinoma (PDAC) both at the population and at the single-cell levels. In vivo, SG33 significantly replicates in experimental tumors to inhibit tumor growth. Collectively, we provide herein for the first time a novel strategy to quantify each step of OV infection in live cells and in real time by tracking viral DNA and provide first evidence of theranostic strategies for PDAC patients. Thus, this approach has the potential to rationalize the use of OVs for the benefit of patients with incurable diseases.

Pathogenic Virus Detection by Optical Nanobiosensors

The novel coronavirus pandemic is sweeping the world and causing global crises. The lack of effective methods of early diagnosis and accurate detection may result in severe infection as well as mortality. Therefore, it is urgently required that rapid, selective, and accurate techniques for detecting pathogenic viruses are developed. Nanotechnology-based biosensors are finding many applications in biological detection, which may address these issues and realize direct detection of molecular targets in real time. Among various nanoplatforms, optical nanobiosensors have aroused much interest due to their inherent advantages of high sensitivity and direct readout. In this review, a summary of recent progress on the optical biosensors based on nanotechnology for pathogenic virus detection is provided, with focus on quantum dots (QDs), upconversion nanoparticles (UCNPs), noble metal nanoparticles, and organic fluorescent molecules-based nanoprobes and chemiluminescence assays. These representative studies demonstrate appealing performance as biosensors and hold great promise for clinical diagnosis.

Advances in biosensing: The CRISPR/Cas system as a new powerful tool for the detection of nucleic acids

A main challenge in the development of biosensing devices for the identification and quantification of nucleic acids is to avoid the amplification of the genetic material from the sample by polymerase chain reaction (PCR), which is at present necessary to enhance sensitivity and selectivity of assays. PCR has undoubtedly revolutionized genetic analyses, but it requires careful purification procedures that are not easily implemented in point of care (POC) devices. In recent years, a new strategy for nucleic acid detection based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated protein systems (Cas) seems to offer unprecedented possibilities. The coupling of the CRISPR/Cas system with recent isothermal amplification methods is fostering the development of innovative optical and electrochemical POC devices. In this review, the mechanisms of action of several new CRISRP/Cas systems are reported together with their use in biosensing of nucleic acids.

Human Herpes Virus 7-related encephalopathy in children

BACKGROUND

Primary HHV7 infection is almost ubiquitous, and it can present as exanthema subitem. Little is known on the clinical relevance of HHV7 neuroinvasion in immunocompetent children.

METHODS

We describe 12 patients (median age 9.45 years, 50% males) with acute encephalopathy and active HHV7 infection. In all patients, HHV7-DNA was detected on cerebrospinal fluid (CSF) by RT-PCR.

RESULTS

7/12 patients had meningoencephalitis (two with ADEM and one with MOG antibody-associated CIS); 5/12 showed acute neuropsychiatric symptoms. EEG showed anomalies exclusively in patients with meningoencephalitis. Six patients had RMN anomalies. CSF HHV7 copies ranged between 20 and 3,500 copies/mL (median 66 copies/mL) and mean HHV7 CSF/blood ratio was 0.75. Outcome was favorable in all children, although 3/12 had minor neurobehavioral sequelae. Mean follow-up period of 5.2 months.

CONCLUSIONS

HHV7 can determine neuroinvasion in immunocompetent children, leading to acute encephalopathy. Blood-brain barrier damage and high CSF/blood viral copies ratio correlated with a more severe presentation. We speculate on the importance of immune-mediated mechanisms in provoking clinical features.

Evaluation of SYBR Green real time PCR for detecting SARS-CoV-2 from clinical samples

The pandemic caused by SARS-CoV-2 has triggered an extraordinary collapse of healthcare systems and hundred thousand of deaths worldwide. Following the declaration of the outbreak as a Public Health Emergency of International Concern by the World Health Organization (WHO) on January 30th, 2020, it has become imperative to develop diagnostic tools to reliably detect the virus in infected patients. Several methods based on real time reverse transcription polymerase chain reaction (RT-qPCR) for the detection of SARS-CoV-2 genomic RNA have been developed. In addition, these methods have been recommended by the WHO for laboratory diagnosis. Since most of these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low- and middle-income countries. In order to develop an inexpensive SARS-CoV-2 detection protocol using available resources we evaluated the SYBR Green based detection of SARS-CoV-2 to establish a suitable assay. To do so, we adapted one of the WHO recommended TaqMan-based one-step real time PCR protocols (from the University of Hong Kong) to SYBR Green. Our results indicate that SYBR-Green detection of ORF1b-nsp14 target represents a reliable cost-effective alternative to increase the testing capacity.

Viruses in wastewater: occurrence, abundance and detection methods

This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.

Microfluidic devices for detection of RNA viruses

There is a long way to go before the coronavirus disease 2019 (Covid‐19) outbreak comes under control. qRT‐PCR is currently used for the detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the causative agent of Covid‐19, but it is expensive, time‐consuming, and not as sensitive as it should be. Finding a rapid, easy‐to‐use, and cheap diagnostic method is necessary to help control the current outbreak. Microfluidic systems provide a platform for many diagnostic tests, including RT‐PCR, RT‐LAMP, nested‐PCR, nucleic acid hybridization, ELISA, fluorescence‐Based Assays, rolling circle amplification, aptamers, sample preparation multiplexer (SPM), Porous Silicon Nanowire Forest, silica sol‐gel coating/bonding, and CRISPR. They promise faster, cheaper, and easy‐to‐use methods with higher sensitivity, so microfluidic devices have a high potential to be an alternative method for the detection of viral RNA. These devices have previously been used to detect RNA viruses such as H1N1, Zika, HAV, HIV, and norovirus, with acceptable results. This paper provides an overview of microfluidic systems as diagnostic methods for RNA viruses with a focus on SARS‐CoV‐2.

Magneto-Optical Nanostructures for Viral Sensing

The eradication of viral infections is an ongoing challenge in the medical field, as currently evidenced with the newly emerged Coronavirus disease 2019 (COVID-19) associated with severe respiratory distress. As treatments are often not available, early detection of an eventual infection and its level becomes of outmost importance. Nanomaterials and nanotechnological approaches are increasingly used in the field of viral sensing to address issues related to signal-to-noise ratio, limiting the sensitivity of the sensor. Superparamagnetic nanoparticles (MPs) present one of the most exciting prospects for magnetic bead-based viral aggregation assays and their integration into different biosensing strategies as they can be easily separated from a complex matrix containing the virus through the application of an external magnetic field. Despite the enormous potential of MPs as capture/pre-concentrating elements, they are not ideal with regard of being active elements in sensing applications as they are not the sensor element itself. Even though engineering of magneto-plasmonic nanostructures as promising hybrid materials directly applicable for sensing due to their plasmonic properties are often used in sensing, to our surprise, the literature of magneto-plasmonic nanostructures for viral sensing is limited to some examples. Considering the wide interest this topic is evoking at present, the different approaches will be discussed in more detail and put into wider perspectives for sensing of viral disease markers.