Diagnostics for SARS-CoV-2 infections

Liquid-metal-based microfluidic nanoplasmonic platform for point-of-care naked-eye antibody detection

Despite high sensitivity of nanoparticle-on-mirror cavities, a crucial branch of plasmonic nanomaterials, complex preparation and readout processes limit their extensive application in biosensing. Alternatively, liquid metals (LMs) combining fluidity and excellent plasmonic characteristics have become potential candidates for constructing plasmonic nanostructures. Herein, we propose a microfluidic-integration strategy to construct LM-based immunoassay platform, enabling LM-based nanoplasmonic sensors to be used for point-of-care (POC) clinical biomarker detection. Flowable LM is introduced onto protein-coated Au nanoparticle monolayer to form a "mirror-on-nanoparticle" nanostructure, simplifying the fabrication process in the conventional nanoparticle-on-mirror cavities. When antibodies were captured by antigens coated on the Au nanoparticle monolayer, devices respond both thickness and refractive index change of biomolecular layers, outputting naked-eye readable signals with high sensitivity (limit of detection: ∼ 604 fM) and a broad dynamic range (6 orders). This new assay, which generates quantitative results in 30 min, allows for high-throughput, smartphone-based detection of SARS-CoV-2 antibodies against multiple variants in clinical serum or blood samples. These results establish an advanced avenue for POC testing with LM materials, and demonstrate its potential to facilitate diagnostics, surveillance and prevalence studies for various infectious diseases.

A biosensor based on magnetoelastic waves for detection of antibodies in human plasma for COVID-19 serodiagnosis

This study proposes a new efficient wireless biosensor based on magnetoelastic waves for antibody detection in human plasma, aiming at the serological diagnosis of COVID-19. The biosensor underwent functionalization with the N antigen - nucleocapsid phosphoprotein of the SARS-CoV-2 virus. Validation analyses by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting (WB), atomic force microscopy (AFM), scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) microanalysis and micro-Raman spectroscopy confirmed the selectivity and effective surface functionalization of the biosensor. The research successfully obtained, expressed and purified the recombinant antigen, while plasma samples from COVID-19 positive and negative patients were applied to test the performance of the biosensor. A performance comparison with the enzyme-linked immunosorbent assays (ELISA) method revealed equivalent diagnostic capacity. These results indicate the robustness of the biosensor in reliably differentiating between positive and negative samples, highlighting its potential as an efficient and low-cost tool for the serological diagnosis of COVID-19. In addition to being fast to execute and having the potential for automation in large-scale diagnostic studies, the biosensor fills a significant gap in existing SARS-CoV-2 detection approaches.

Microglia Caspase11 non-canonical inflammasome drives fever

AIM

Animals exhibit physiological changes designed to eliminate the perceived danger, provoking similar symptoms of fever. However, a high-grade fever indicates poor clinical outcomes. Caspase11 (Casp11) is involved in many inflammatory diseases. Whether Casp11 leads to fever remains unclear. In this study, we investigate the role of the preoptic area of the hypothalamus (PO/AH) microglia Casp11 in fever.

METHODS

We perform experiments using a rat model of LPS-induced fever. We measure body temperature and explore the functions of peripheral macrophages and PO/AH microglia in fever signaling by ELISA, immunohistochemistry, immunofluorescence, flow cytometry, macrophage depletion, protein blotting, and RNA-seq. Then, the effects of macrophages on microglia in a hyperthermic environment are observed in vitro. Finally, adeno-associated viruses are used to knockdown or overexpress microglia Casp11 in PO/AH to determine the role of Casp11 in fever.

RESULTS

We find peripheral macrophages and PO/AH microglia play important roles in the process of fever, which is proved by macrophage and microglia depletion. By RNA-seq analysis, we find Casp11 expression in PO/AH is significantly increased during fever. Co-culture and conditioned-culture simulate the induction of microglia Casp11 activation by macrophages in a non-contact manner. Microglia Casp11 knockdown decreases body temperature, pyrogenic factors, and inflammasome, and vice versa.

CONCLUSION

We report that Casp11 drives fever. Mechanistically, peripheral macrophages transmit immune signals via cytokines to microglia in PO/AH, which activate the Casp11 non-canonical inflammasome. Our findings identify a novel player, the microglia Casp11, in the control of fever, providing an explanation for the transmission and amplification of fever immune signaling.

RNA extraction-free reduced graphene oxide-based RT-LAMP fluorescence assay for highly sensitive SARS-CoV-2 detection

Infectious diseases have always been a seriously endanger for human life and health. A rapid, accurate and ultra-sensitive virus nucleic acid detection is still a challenge to deal with infectious diseases. Here, a RNA extraction-free reduced graphene oxide-based reverse transcription-loop-mediated isothermal amplification (EF-G-RT-LAMP) fluorescence assay was developed to achieve high-throughput, rapid and ultra-sensitive SARS-CoV-2 RNA detection. The whole detection process only took ∼36 min. The EF-G-RT-LAMP assay achieves a detection limit of 0.6 copies μL-1 with a wide dynamic range of aM-pM. A large number (up to 384) of samples can be detected simultaneously. Simulated detection of the COVID-19 pseudovirus and clinical samples in nasopharyngeal swabs demonstrated a high-throughput, rapid and ultra-sensitive practical detection capability of the EF-G-RT-LAMP assay. The results proved that the assay would be used as a rapid, easy-to-implement approach for epidemiologic diagnosis and could be extended to other nucleic acid detections.

Bioinformatics analysis of potential common pathogenic mechanisms for COVID-19 and venous thromboembolism

BACKGROUND

A growing body of research has shown that patients with coronavirus disease 2019 (COVID-19) have significantly higher rates of venous thromboembolism (VTE) than healthy. However, the mechanism remains incompletely elucidated. This study aimed to further investigate the molecular mechanisms underlying the development of this complication.

METHODS

The gene expression profiles of COVID-19 and VTE were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) for COVID-19 and VTE, functional annotation, a protein-protein interactions (PPI) network, module construction, and hub gene identification were performed. Finally, we constructed a transcription factor (TF)-gene regulatory network and a TF-miRNA regulatory network for hub genes.

RESULTS

A total of 42 common DEGs were selected for subsequent analyses. Functional analyses showed that biological function and signaling pathways collectively participated in the development and progression of VTE and COVID-19. Finally, 8 significant hub genes were identified using the cytoHubba plugin, including RSL24D1, RPS17, RPS27, HINT1, COX7C, RPL35, RPL34, and NDUFA4, which had preferable values as diagnostic markers for COVID-19 and VTE.

CONCLUSIONS

Our study revealed the common pathogenesis of COVID-19 and VTE. These common pathways and pivotal genes may provide new ideas for further mechanistic studies.

Preamplification-free ultra-fast and ultra-sensitive point-of-care testing via LwaCas13a

CRISPR based nucleic acid detection technology provides a deployable approach to point of care testing. While, there remain challenges limiting its practical applications, such as the need for pre-amplification and the long turnaround time. Here, we present a self-cascade signal amplification method with LwaCas13a and an artificially designed "U" rich RNA of stem-loop structure (URH) for pre-amplification-free ultra-fast and ultra-sensitive point-of-care testing (PASSPORT). The PASSPORT system contains: URH, crRNA targeted the URH, crRNA targeted the interesting RNA, fluorescent RNA reporter and LwaCas13a. The assay realized the detection of 100 copies/mL, within 5 min. The PASSPORT platform was further adopted for the detection of marker gene from SASR-CoV-2 and Severe fever with thrombocytopenia syndrome virus (SFTSV), respectively, and 100% accuracy for the analysis of clinical specimens (100 SASR-CoV-2 specimens and 16 SFTSV specimens) was obtained. Integrated with a lateral flow assay device, this assay could provide an alternative platform for the development of point of care testing (POCT) biosensors. PASSPORT has the potential to enable sensitive, specific, user-friendly, rapid, affordable, equipment-free and point-of-care testing for the purpose of large-scale screening and in case of epidemic outbreak.

Simplified Electrochemical Approach for End-Point Yet Quantitative Detection of Nucleic Acids in Resource-Limited Settings

Nucleic acid detection plays a crucial role in various aspects of health care, necessitating accessible and reliable quantification methods, especially in resource-limited settings. This work presents a simplified electrochemical approach for end-point yet quantitative nucleic acid detection. By elevating the concentration of redox species and choosing potential as the signals, we achieved enhanced signal robustness, even in the presence of interfering substances. Leveraging this robustness, we accurately measured pH-induced redox potential changes in methylene blue solution for end-point nucleic acid detection after loop-mediated isothermal amplification (LAMP). Our method demonstrated quantitative detection of the SARS-CoV-2 N gene and human ATCB gene and successful discrimination of the human BRAF V600E mutation, comparable in sensitivity to commercial kits. The developed user-friendly electrochemical method offers a simplified and reliable approach for end-point yet quantitative detection of nucleic acids, potentially expanding the benefits of nucleic acid testing in resource-limited settings.

High-Throughput and Integrated CRISPR/Cas12a-Based Molecular Diagnosis Using a Deep Learning Enabled Microfluidic System

CRISPR/Cas-based molecular diagnosis demonstrates potent potential for sensitive and rapid pathogen detection, notably in SARS-CoV-2 diagnosis and mutation tracking. Yet, a major hurdle hindering widespread practical use is its restricted throughput, limited integration, and complex reagent preparation. Here, a system, microfluidic multiplate-based ultrahigh throughput analysis of SARS-CoV-2 variants of concern using CRISPR/Cas12a and nonextraction RT-LAMP (mutaSCAN), is proposed for rapid detection of SARS-CoV-2 and its variants with limited resource requirements. With the aid of the self-developed reagents and deep-learning enabled prototype device, our mutaSCAN system can detect SARS-CoV-2 in mock swab samples below 30 min as low as 250 copies/mL with the throughput up to 96 per round. Clinical specimens were tested with this system, the accuracy for routine and mutation testing (22 wildtype samples, 26 mutational samples) was 98% and 100%, respectively. No false-positive results were found for negative (n = 24) samples.

Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections

BACKGROUND

The emergence of the SARS-CoV-2 virus has highlighted the importance of genomic epidemiology in understanding the evolution of pathogens and guiding public health interventions. The Omicron variant in particular has underscored the role of epistasis in the evolution of lineages with both higher infectivity and immune escape, and therefore the necessity to update surveillance pipelines to detect them early on.

RESULTS

In this study, we apply a method based on mutual information between positions in a multiple sequence alignment, which is capable of scaling up to millions of samples. We show how it can reliably predict known experimentally validated epistatic interactions, even when using as little as 10,000 sequences, which opens the possibility of making it a near real-time prediction system. We test this possibility by modifying the method to account for the sample collection date and apply it retrospectively to multiple sequence alignments for each month between March 2020 and March 2023. We detected a cornerstone epistatic interaction in the Spike protein between codons 498 and 501 as soon as seven samples with a double mutation were present in the dataset, thus demonstrating the method's sensitivity. We test the ability of the method to make inferences about emerging interactions by testing candidates predicted after March 2023, which we validate experimentally.

CONCLUSIONS

We show how known epistatic interaction in SARS-CoV-2 can be detected with high sensitivity, and how emerging ones can be quickly prioritized for experimental validation, an approach that could be implemented downstream of pandemic genome sequencing efforts.

A compact microfluidic platform for rapid multiplex detection of respiratory viruses via centrifugal polar-absorbance spectroscopy

Nucleic acid detection technology has become a crucial tool in cutting-edge research within the life sciences and clinical diagnosis domains. Its significance is particularly highlighted during the respiratory virus pandemic, where nucleic acid testing plays a pivotal role in accurately detecting the virus. Isothermal amplification technologies have been developed and offer advantages such as rapidity, mild reaction conditions and excellent stability. Among these methods, recombinase polymerase amplification (RPA) has gained significant attention due to its simple primer design and resistance to multiple reaction inhibitors. However, the detection of RPA amplicons hinders the widespread adoption of this technology, leading to a research focus on cost-effective and convenient detection methods for RPA nucleic acid testing. In this study, we propose a novel computational absorption spectrum approach that utilizes the polar GelRed dye to efficiently detect RPA amplicons. By exploiting the asymmetry of GelRed molecules upon binding with DNA, polar electric dipoles are formed, leading to precipitate formation through centrifugal vibration and electrostatic interaction. The quantification of amplicon content is achieved by measuring the residual GelRed concentration in the supernatant. Our proposed portable and integrated microfluidic device successfully detected five respiratory virus genes simultaneously. The optimized linear detection was achieved and the sensitivity for all the targets reached 100 copies/μL. The total experiment could be finished in 27 min. The clinical experiments demonstrated the practicality and accuracy. This cost-effective and convenient detection scheme presents a promising biosensor for rapid virus detection, contributing to the advancement of RPA technology.

Wastewater Surveillance of SARS-CoV-2 in Zambia: An Early Warning Tool

Wastewater-based surveillance has emerged as an important method for monitoring the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study investigated the presence of SARS-CoV-2 in wastewater in Zambia. We conducted a longitudinal study in the Copperbelt and Eastern provinces of Zambia from October 2023 to December 2023 during which 155 wastewater samples were collected. The samples were subjected to three different concentration methods, namely bag-mediated filtration, skimmed milk flocculation, and polythene glycol-based concentration assays. Molecular detection of SARS-CoV-2 nucleic acid was conducted using real-time Polymerase Chain Reaction (PCR). Whole genome sequencing was conducted using Illumina COVIDSEQ assay. Of the 155 wastewater samples, 62 (40%) tested positive for SARS-CoV-2. Of these, 13 sequences of sufficient length to determine SARS-CoV-2 lineages were obtained and 2 sequences were phylogenetically analyzed. Various Omicron subvariants were detected in wastewater including BA.5, XBB.1.45, BA.2.86, and JN.1. Some of these subvariants have been detected in clinical cases in Zambia. Interestingly, phylogenetic analysis positioned a sequence from the Copperbelt Province in the B.1.1.529 clade, suggesting that earlier Omicron variants detected in late 2021 could still be circulating and may not have been wholly replaced by newer subvariants. This study stresses the need for integrating wastewater surveillance of SARS-CoV-2 into mainstream strategies for monitoring SARS-CoV-2 circulation in Zambia.

Virus and viral components transmitted through surgical smoke; a silent danger in operating room: a systematic review

BACKGROUND

During surgical procedures, heat-generating devices are widely used producing surgical smoke (SS). Since the SS can transmit infectious viruses, this systematic review was designed to investigate the potential viruses transmitted through SS.

METHODS

PubMed, Scopus, Web of Science, ProQuest, and Embase databases, along with Cochran Library, and Google Scholar search engine were searched systematically (by April 21, 2024). No language, place, and time restrictions were considered. All studies evaluating the SS and virus transmission, and whole investigations regarding the viral infections transmitted through SS were totally considered inclusion criteria. Besides, non-original, qualitative, case reports, case series, letters to the editor, editorial, and review studies were excluded from the analysis. This study was conducted in accordance with the PRISMA 2020 statement.

RESULTS

Twenty-six eligible studies were selected and reviewed for data extraction. The results showed that the SS contains virus and associated components. Six types of viruses or viral components were identified in SS including papillomavirus (HPV, BPV), Human Immunodeficiency Virus (HIV), varicella zoster, Hepatitis B (HBV), SARS-CoV-2, and Oral poliovirus (OPV), which are spread to surgical team through smoke-producing devices.

CONCLUSIONS

Since the studies confirm the presence of viruses, and viral components in SS, the potential risk to the healthcare workers, especially in operating room (OR), seems possible. Thus, the adoption of protective strategies against SS is critical. Despite the use of personal protective equipment (PPE), these viruses could affect OR personnel in surgical procedures.

Toward better pandemic governance and preparedness: South Korea's whole-of-nation approach to COVID-19

BACKGROUND

The profound impact of coronavirus disease (COVID-19) has led to an increased demand for sustainable pandemic governance practices. This study explored emerging hybrid governance practices that provide robust evidence on how to address the complex challenges of pandemics effectively. South Korea, which was severely affected by COVID-19, has implemented a novel governance approach using a whole-of-nation (WoN) model. This hybrid pandemic governance approach, which integrates both whole-of-government and whole-of-society approaches, has enabled synergistic and cohesive multi-sectoral coordination among all stakeholders (public authorities, private enterprises, and civil society) to address multifaceted challenges collectively and strengthen their resilience capacity. This study investigated South Korea's WoN practices and their embedded context and identified key governance enablers facilitating this approach.

METHODS

This study employed a case study design based on an extensive analysis of policy and program documents, drawing on South Korea's publicly available data from January 1, 2020 to March 30, 2023. It assessed six system-level collaborative pandemic governance practices and key enablers, all of which were intended to fortify the country's pandemic response.

RESULTS

The primary areas of the country's WoN governance practices for COVID-19 control were (i) whole-of-government policy-making and response, (ii) COVID-19 testing system, (iii) digital surveillance of COVID-19, (iv) COVID-19 triage and treatment system, (v) domestic vaccine production, and (vi) community engagement. Key governance enablers for implementing the WoN model were establishing a legal foundation, ensuring decisive and strong governance and leadership, increasing public investment, applying a whole-of-health approach with augmented investment in public health, enhancing crisis communication, and mobilizing local leaders and civil society organizations in the national public health response.

CONCLUSIONS

In exploring innovative approaches to pandemic governance for increased efficacy, responsiveness, and impact, the WoN approach emerged as highly relevant. This example of emerging practice allows policy-makers to re-evaluate their governance strategies and initiatives to improve multi-agency partnerships across the country in their pandemic-preparedness planning.

Unravelling the diagnostic methodologies for SARS-CoV-2; the Indispensable need for developing point-of-care testing

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic that continues to be a global menace and since its emergence in the late 2019, SARS-CoV-2 has been vigorously spreading throughout the globe putting the whole world into a multidimensional calamity. The suitable diagnosis strategies are on the front line of the battle against preventing the spread of infections. Since the clinical manifestation of COVID-19 is shared between various diseases, detection of the unique impacts of the pathogen on the host along with the diagnosis of the virus itself should be addressed. Employing the most suitable approaches to specifically, sensitively and effectively recognize the infected cases may be a real game changer in controlling the outbreak and the crisis management. In that matter, point-of-care assays (POC) appears to be the potential option, due to sensitivity, specificity, affordable, and availability. Here we brief the most recent findings about the virus, its variants, and the conventional methods that have been used for its detection, along with the POC strategies that have been applied to the virus diagnosis and the developing technologies which can accelerate the diagnosis procedure yet maintain its efficiency.

An end-point multiplex RT-PCR for SARS-CoV-2, Influenza A and B detection, including simultaneous RNAse P amplification: a timely tool for more accessible differential diagnosis

The multiplex molecular diagnostic assays described for severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), influenza A (IAV) and B (IBV) viruses have been mainly based on real-time reaction, which limits their access to many laboratories or diagnostic institutions. To contribute to available strategies and expand access to differential diagnosis, we describe an end-point multiplex RT-PCR targeting SARS-CoV-2, IAV and IBV with simultaneous endogenous control amplification. Initially, we looked for well-established primers sets for SARS-CoV-2, IAV, IBV and RNAse P whose amplicons could be distinguished on agarose gel. The multiplex assay was then standardized by optimizing the reaction mix and cycle conditions. The limit of detection (LoD) was determined using titrated viruses (for SARS-CoV-2 and IAV) and by dilution from a pool of IBV-positive samples. The diagnostic performance of the multiplex was evaluated by testing samples with different RNAse P and viral loads, previously identified as positive or negative for the target viruses. The amplicons of IAV (146 bp), SARS-CoV-2 (113 bp), IBV (103 bp) and RNAse P (65 bp) were adequately distinguished in our multiplex. The LoD for SARS-CoV-2, IAV and IBV was 0.02 TCID50/ml, 0.07 TCID50/ml and 10-3 from a pool of positive samples, respectively. All samples positive for SARS-CoV-2 (n=70, Ct 17.2-36.9), IAV (n=53, Ct 14-34.9) and IBV (n=12, Ct 23.9-31.9) remained positive in our multiplex assay. RNAse P from negative samples (n=40, Ct 25.2-30.2) was also amplified in the multiplex. Overall, our assay is a timely and alternative tool for detecting SARS-CoV-2 and influenza viruses in laboratories with limited access to supplies/equipment.

Use of strips of rapid diagnostic tests as a source of ribonucleic acid for genomic surveillance of viruses: an example of SARS-CoV-2

BACKGROUND

This study aimed to demonstrate that the genomic material of SARS-CoV-2 can be isolated from strips of COVID-19 rapid diagnostic test cassettes.

METHOD

It was a prospective cross-sectional study involving patients admitted to treatment centers and sampling sites in the city of Conakry, Guinea. A total of 121 patients were double sampled, and 9 more patients were tested only for RDT. PCR was conducted according to the protocol of the RunMei kit. Sequencing was performed by using the illumina COVIDSeq protocol. Nine COVID-19 RDTs without nasopharyngeal swabs were in addition tested.

RESULT

Among the 130 COVID-19 RDTs, forty-seven were macroscopically positive, whereas seventy-two were positive according to PCR using RDT strip, while among the 121 VTM swabs, sixty-four were positive. Among eighty-three negative COVID-19 RDTs, twenty-seven were positive by PCR using RDT strip with a geometric mean Ct value of 32.49 cycles. Compared to those of PCR using VTM, the sensitivity and specificity of PCR using RDT strip were estimated to be 100% and 85.96%, respectively, with 93.39% test accuracy. Among the fifteen COVID-19 RDT extracts eligible for sequencing, eleven had sequences identical to those obtained via the standard method, with coverage between 75 and 99.6%.

CONCLUSION

These results show that COVID-19 RDTs can be used as biological material for the genomic surveillance of SARS-CoV-2.

Prevalence and influencing factors of sleep disorders in medical students after the COVID-19 pandemic

BACKGROUND

The prevalence of sleep disorders among medical students was high during the COVID-19 pandemic. However, fewer studies have been conducted on sleep disorders among medical students after the COVID-19 pandemic. This study investigated the prevalence and factors influencing sleep disorders among Chinese medical students after COVID-19.

METHODS

A total of 1,194 Chinese medical students were included in this study from 9th to 12th July 2023. We used the Self-administered Chinese scale to collect the demographic characteristics. In addition, we used the Chinese versions of the Self-rating Depression Scale (SDS), the Self-rating Anxiety Scale (SAS), and the Pittsburgh Sleep Quality Index (PSQI) to assess subjects' depression, anxiety, and sleep disorders, respectively. The chi-square test and binary logistic regression were used to identify factors influencing sleep disorders. The receiver operating characteristic (ROC) curve was utilized to assess the predictive value of relevant variables for sleep disorders.

RESULTS

We found the prevalence of sleep disorders among medical students after COVID-19 was 82.3%. According to logistic regression results, medical students with depression were 1.151 times more likely to have sleep disorders than those without depression (OR = 1.151, 95% CI 1.114 to 1.188). Doctoral students were 1.908 times more likely to have sleep disorders than graduate and undergraduate students (OR = 1.908, 95% CI 1.264 to 2.880).

CONCLUSION

The prevalence of sleep disorders among medical students is high after COVID-19. In addition, high academic levels and depression are risk factors for sleep disorders. Therefore, medical colleges and administrators should pay more attention to sleep disorders in medical students after the COVID-19 pandemic. Regular assessment of sleep disorders and depression is essential.

COVID-19 Related Acute Respiratory Distress Syndrome versus Classical Acute Respiratory Distress Syndrome Patients: Inflammatory Biomarkers as Predictors of Mortality in Pulmonary Septic Shock

Introduction and Objectives

Coronavirus disease-2019 (COVID-19)-related severe acute respiratory distress syndrome (ARDS) differs pathophysiological from other pulmonary septic shock-related ARDS. Thus, we assessed whether all-cause in-hospital mortality differs for severe COVID-19-related and classical severe ARDS and which inflammatory biomarkers can predict mortality among these patients.

Material and Methods

This single-center, retrospective, observational cohort study included pulmonary septic shock patients (n = 114) with COVID-19-related and classical severe ARDS admitted in the Intensive Care Unit.

Results

Patients with a mean age of 73 (IQR 62-82), predominantly male (63%), were divided into two groups based on outcomes: survivors (n = 50) and non-survivors (n = 64). COVID-19-related severe ARDS (n = 48) accounts for 75% of deaths. Present comorbidities like heart disease (p = 0.043), neurologic disorders (p = 0.018), and liver disease (p = 0.038) were associated with in-hospital mortality, as well. Regarding inflammatory biomarkers, the AUC/c-statistic was 0.656 (95% CI: 0.53-0.759) for leukocytes, 0.613 (95% CI: 0.509-0.717) C-reactive protein (CRP) and 0.651 (95% CI: 0.548-0.753) for procalcitonin in predicting all-cause in-hospital mortality among patients with pulmonary septic shock and severe ARDS.

Conclusion

Patients with pulmonary septic shock and with COVID-19-related severe ARDS had a higher incidence of in-hospital mortality than those with classical severe ARDS. The high value of leukocytes, C-reactive protein, and procalcitonin were predictive for all-cause in-hospital mortality in patients with pulmonary septic shock and ARDS. Infection with COVID-19 was an independent predictor of in-hospital mortality in the presence of ARDS.

Comprehensive Study of the IBMP ELISA IgA/IgM/IgG COVID-19 Kit for SARS-CoV-2 Antibody Detection

COVID-19 laboratory diagnosis primarily relies on molecular tests, highly sensitive during early infection stages with high viral loads. As the disease progresses, sensitivity decreases, requiring antibody detection. Since the beginning of the pandemic, serological tests have been developed and made available in Brazil, but their diagnostic performance varies. This study evaluated the IBMP ELISA IgA/IgM/IgG COVID-19 kit performance in detecting SARS-CoV-2 antibodies. A total of 90 samples, including 64 from COVID-19 patients and 26 pre-pandemic donors, were assessed based on time post symptom onset (0-7, 8-14, and 15-21 days). The kit showed 61% sensitivity, 100% specificity, and 72% accuracy overall. Sensitivity varied with time, being 25%, 57%, and 96% for 0-7, 8-14, and 15-21 days, respectively. Similar variations were noted in other commercial tests. The Gold ELISA COVID-19 (IgG/IgM) had sensitivities of 31%, 71%, and 100%, while the Anti-SARS-CoV-2 NCP ELISA (IgG) and Anti-SARS-CoV-2 NCP ELISA (IgM) showed varying sensitivities. The IBMP ELISA kit displayed high diagnostic capability, especially as the disease progressed, complementing COVID-19 diagnosis. Reproducibility assessment revealed minimal systematic and analytical errors. In conclusion, the IBMP ELISA IgA/IgM/IgG COVID-19 kit is a robust tool for detecting anti-SARS-CoV-2 antibodies, increasing in efficacy over the disease course, and minimizing false negatives in RT-PCR COVID-19 diagnosis.

Phenylboronic Acid-Modified Membrane-Like Magnetic Quantum Dots Enable the Ultrasensitive and Broad-Spectrum Detection of Viruses by Lateral Flow Immunoassay

Although lateral flow immunochromatographic assay (LFIA) is an effective point-of-care testing technology, it still cannot achieve broad-spectrum and ultrasensitive detection of viruses. Herein, we propose a multiplex LFIA platform using a two-dimensional graphene oxide (GO)-based magnetic fluorescent nanofilm (GF@DQD) as a multifunctional probe and 4-aminophenylboronic acid (APBA) as a broad-spectrum recognition molecule for viral glycoprotein detection. GF@DQD-APBA with enhanced magnetic/fluorescence properties and universal capture ability for multiple viruses was easily prepared through the electrostatic adsorption of one layer of density-controlled Fe3O4 nanoparticles (NPs) and thousands of small CdSe/ZnS-MPA quantum dots (QDs) on a monolayer GO sheet followed by chemical coupling with APBA on the QD surface. The GF@DQD-APBA probe enabled the universal capture and specific determination of different target viruses on the test strip through an arbitrary combination with the antibody-modified LFIA strip, thus greatly improving detection efficiency and reducing the cost and difficulty of multiplex LFIA for viruses. The proposed technique can simultaneously and sensitively diagnose three newly emerged viruses within 20 min with detection limits down to the pg/mL level. The excellent practicability of GF@DQD-APBA-LFIA was also demonstrated in the detection of 34 clinical specimens positive for SARS-CoV-2, revealing its potential for epidemic control and on-site viral detection.

Accuracy improvement enzyme-linked immunosorbent assay using superparamagnetic/polyethylene glycol) nanoparticles for leishmaniasis diagnostic

Serodiagnosis methods have been used as platforms for diagnostic tests for many diseases. Due to magnetic nanoparticles' properties to quickly detach from an external magnetic field and particle size effects, these nanomaterials' functionalization allows the specific isolation of target analytes, enhancing accuracy parameters and reducing serodiagnosis time. Superparamagnetic iron oxide nanoparticles (MNPs) were synthesized and functionalized with polyethylene glycol (PEG) and then associated with the synthetic Leishmaniosis epitope. This nano-peptide antigen showed promising results. Regarding Tegumentary leishmaniasis diagnostic accuracy, the AUC was 0.8398 with sensibility 75% (95CI% 50.50 - 89.82) and specificity 87.50% (95CI% 71.93 - 95.03), and Visceral leishmaniasis accuracy study also present high performance, the AUC was 0.9258 with sensibility 87.50% (95CI% 63.98 - 97.78) and specificity 87.50% (95CI% 71.93 - 95.03). Our results demonstrate that the association of the antigen with MNPs accelerates and improves the diagnosis process. MNPs could be an important tool for enhancing serodiagnosis.

Pooling of samples to optimise SARS-CoV-2 detection in nasopharyngeal swabs and gargle lavage self-samples for covid-19 diagnostics and surveillance

BACKGROUND

Testing of pooled samples is an effective strategy for increasing testing capacity while saving resources and time. This study aimed to validate pooled testing and gather real-life data on its use for Covid-19 surveillance with a gargle lavage (GL) self-sampling strategy.

METHODS

Two-stage pooled testing with pools of 6 and 12 samples was used for preventive testing of an asymptomatic population and Covid-19 surveillance in Czech schools. Both GL and nasopharyngeal swabs were used for sampling.

RESULTS

In total, 61,111 samples were tested. The use of pooled testing for large-scale Covid-19 surveillance reduced consumable costs by almost 75% and increased testing capacity up to 3.8-fold compared to standard methods. RT-PCR experiments revealed a minimal loss of sensitivity (0-2.2%) when using pooled samples, enabling the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes with Ct values >35. The minor loss of sensitivity was counterbalanced by a significantly increased throughput and the ability to substantially increase testing frequencies.

CONCLUSIONS

Pooled testing is considerably more cost-effective and less time-consuming than standard testing for large-scale Covid-19 surveillance even when the prevalence of SARS-CoV-2 is fluctuating. Gargle lavage self-sampling is a non-invasive technique suitable for sample collection without a healthcare worker's assistance.

Capillarity-Driven Enrichment and Hydrodynamic Trapping of Trace Nucleic Acids by Plasmonic Cavity Membrane for Rapid and Sensitive Detections

Small-reactor-based polymerase chain reaction (PCR) has attracted considerable attention. A significant number of tiny reactors must be prepared in parallel to capture, amplify, and accurately quantify few target genes in clinically relevant large volume, which, however, requires sophisticated microfabrication and longer sample-to-answer time. Here, single plasmonic cavity membrane is reported that not only enriches and captures few nucleic acids by taking advantage of both capillarity and hydrodynamic trapping but also quickly amplifies them for sensitive plasmonic detection. The plasmonic cavity membrane with few nanoliters in a void volume is fabricated by self-assembling gold nanorods with SiO2 tips. Simulations reveal that hydrodynamic stagnation between the SiO2 tips is mainly responsible for the trapping of the nucleic acid in the membrane. Finally, it is shown that the plasmonic cavity membrane is capable of enriching severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes up to 20 000-fold within 1 min, amplifying within 3 min, and detecting the trace genes as low as a single copy µL-1. It is anticipated that this work not only expands the utility of PCR but also provides an innovative way of the enrichment and detection of trace biomolecules in a variety of point-of-care testing applications.

Clinical impact of rapid molecular diagnostic tests in patients presenting with viral respiratory symptoms: A systematic literature review

BACKGROUND

Molecular tests can detect lower concentrations of viral genetic material over a longer period of respiratory infection than antigen tests. Delays associated with central laboratory testing can result in hospital-acquired transmission, avoidable patient admission, and unnecessary use of antimicrobials, all which may lead to increased cost of patient management. The aim of this study was to summarize comparisons of clinical outcomes associated with rapid molecular diagnostic tests (RMDTs) versus other diagnostic tests for viral respiratory infections.

METHODS

A systematic literature review (SLR) conducted in April 2023 identified studies evaluating clinical outcomes of molecular and antigen diagnostic tests for patients suspected of having respiratory viral infections.

RESULTS

The SLR included 21 studies, of which seven and 14 compared RMDTs (conducted at points of care or at laboratories) to standard (non-rapid) molecular tests or antigen tests to detect SARS-CoV-2 and influenza, respectively. In studies testing for SARS-CoV-2, RMDTs led to reductions in time to test results versus standard molecular tests (range of the reported medians: 0.2-3.8 hours versus 4.3-35.9 hours), with similar length of emergency department stay (3.2-8 hours versus 3.7-28.8 hours). Similarly, in studies testing for influenza, RMDTs led to reductions in time to test results versus standard molecular tests (1-3.5 hours versus 18.2-29.2 hours), with similar length of emergency department stay (3.7-11 hours versus 3.8-11.9 hours). RMDTs were found to decrease exposure time of uninfected patients, rate of hospitalization, length of stay at the hospitals, and frequency of unnecessary antiviral and antibacterial therapy, while improving patient flow, compared to other tests.

CONCLUSIONS

Compared to other diagnostic tests, RMDTs improve clinical outcomes, test turnaround time, and stewardship by decreasing unnecessary use of antibiotics and antivirals. They also reduce hospital admission and length of stay, which may, in turn, reduce unnecessary exposure of patients to hospital-acquired infections and their associated costs.

Microfluidic Chip-Assisted Upconversion Luminescence Biosensing Platform for Point-of-Care Virus Diagnostics

Epidemics caused by multiple viruses continue to emerge, which have brought a terrible impact on human society. Identification of viral infections with high sensitivity and portability is of significant importance for the screening and management of diseases caused by viruses. Herein, a microfluidic chip (MFC)-assisted upconversion luminescence biosensing platform is designed and fabricated for point-of-care virus detection. Upconversion nanoparticles with excellent stability are successfully synthesized as luminescent agents for optical signal generation in the portable virus diagnostic platform. The relevant investigation results illustrate that the MFC-assisted virus diagnostic platform possesses outstanding performance such as good integration, high sensitivity (1.12 pg mL-1), ease of use, and portability. In addition, clinical sample test result verifies its more prominent virus diagnostic properties than commercially available rapid test strips. All of these thrilling capabilities imply that the designed portable virus diagnostic platform has great potential for future virus detection applications.

Impact of SARS-CoV-2 Vaccination or Infection on the Safety and Efficacy of Aesthetic Injections: A Systematic Review

BACKGROUND

Aesthetic injections have become increasingly popular for maintaining a youthful appearance. However, with the rise of SARS-CoV-2, there have been concerns about potential complications. This study aims to summarize and understand the complications that occur in individuals who have received cosmetic injections after SARS-CoV-2 infection or vaccination. By doing so, we hope to provide recommendations to minimize these complications and ensure the safety of aesthetic treatments in the current COVID-19 era.

METHODS

The PRISMA guidelines, the Preferred Reporting Program for Systematic Reviews and Meta-Analyses, were used for this review. Databases including PubMed, EMBASE, Medline, Web of Science and ScienceDirect were searched. The last search time of each database was May 10, 2023. In addition, relevant references were manually searched.

RESULTS

A total of 26 studies containing 139 patients were searched. The complication with the highest percentage of reported patients was delayed inflammatory response (DIR) (n = 68; 48.92%), followed by diminished efficacy (n = 45; 32.37%) and filler reaction (n = 12; 8.63%). The remaining complications include hypersensitivity reactions, symptomatic hypercalcemia, sub-acute hypersensitive reactions, hyperalgesia, infection, fat necrosis and granulomatous reaction.

CONCLUSIONS

Cosmetic injectable procedures are generally safe but may have adverse effects, particularly during the pandemic. It is important for individuals to fully understand these risks beforehand. Clinicians should be knowledgeable about adverse event mechanisms and management to prevent issues. Industry leaders should strengthen risk management efforts to ensure safe and steady development of cosmetic injections. Overall, a comprehensive understanding, effective communication and risk management are crucial for the safe use of cosmetic injectable procedures.

LEVEL OF EVIDENCE III

This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors at www.springer.com/00266 .

Vaccination status and self-reported side effects after SARS-CoV-2 vaccination in relation to psychological and clinical variables in patients with multiple sclerosis

The recent SARS-CoV-2 pandemic and the vaccination campaign posed a challenge to patients with autoimmune disease, such as multiple sclerosis (MS). We aimed for investigating whether psychological/sociodemographic/clinical characteristics of MS patients are associated with SARS-CoV-2 vaccination status and self-reported vaccination side effects (SEs). We have asked patients with MS about their willingness to receive recommended standard vaccinations pre-pandemically since June 2019. Between 10/2021 and 01/2022, we surveyed 193 of these MS patients about their current SARS-CoV-2 vaccination status, their perception of vaccination-related SEs, and reasons for and against SARS-CoV-2 vaccination. 75.6% of the patients declared their willingness to receive standard vaccinations before the pandemic. 84.5%, 78.2%, and 13.0% of the patients had received the first, second, and third SARS-CoV-2 vaccination, respectively, until the follow-up survey. The most common reason for not getting vaccinated against SARS-CoV-2 was concern about possible side effects (82.1%), followed by the belief that the vaccines had not been adequately tested (64.3%). Vaccination-related SEs were reported by 52.8% of the patients. Younger age, higher education, lower degree of disability, relapsing disease course, shorter disease duration, not receiving a disease-modifying therapy and higher anxiety and depression levels were associated with the occurrence of certain vaccination-related SEs. Concerns about novel vaccines are widespread among MS patients and necessitate targeted education of the patients, especially to those with more severe psychopathological symptoms (anxiety or depression) and those who are generally skeptical of vaccination.

Advances in Nucleic Acid Assays for Infectious Disease: The Role of Microfluidic Technology

Within the fields of infectious disease diagnostics, microfluidic-based integrated technology systems have become a vital technology in enhancing the rapidity, accuracy, and portability of pathogen detection. These systems synergize microfluidic techniques with advanced molecular biology methods, including reverse transcription polymerase chain reaction (RT-PCR), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR), have been successfully used to identify a diverse array of pathogens, including COVID-19, Ebola, Zika, and dengue fever. This review outlines the advances in pathogen detection, attributing them to the integration of microfluidic technology with traditional molecular biology methods and smartphone- and paper-based diagnostic assays. The cutting-edge diagnostic technologies are of critical importance for disease prevention and epidemic surveillance. Looking ahead, research is expected to focus on increasing detection sensitivity, streamlining testing processes, reducing costs, and enhancing the capability for remote data sharing. These improvements aim to achieve broader coverage and quicker response mechanisms, thereby constructing a more robust defense for global public health security.

Mental health and insomnia problems in healthcare workers after the COVID-19 pandemic: A multicenter cross-sectional study

BACKGROUND

Healthcare workers (HCWs) are at increased risk of contracting coronavirus disease 2019 (COVID-19) as well as worsening mental health problems and insomnia. These problems can persist for a long period, even after the pandemic. However, less is known about this topic.

AIM

To analyze mental health, insomnia problems, and their influencing factors in HCWs after the COVID-19 pandemic.

METHODS

This multicenter cross-sectional, hospital-based study was conducted from June 1, 2023 to June 30, 2023, which was a half-year after the end of the COVID-19 emergency. Region-stratified population-based cluster sampling was applied at the provincial level for Chinese HCWs. Symptoms such as anxiety, depression, and insomnia were evaluated by the Generalized Anxiety Disorder-7, Patient Health Questionnaire-9, and Insomnia Severity Index. Factors influencing the symptoms were identified by multivariable logistic regression.

RESULTS

A total of 2000 participants were invited, for a response rate of 70.6%. A total of 1412 HCWs [618 (43.8%) doctors, 583 (41.3%) nurses and 211 (14.9%) nonfrontline], 254 (18.0%), 231 (16.4%), and 289 (20.5%) had symptoms of anxiety, depression, and insomnia, respectively; severe symptoms were found in 58 (4.1%), 49 (3.5%), and 111 (7.9%) of the participants. Nurses, female sex, and hospitalization for COVID-19 were risk factors for anxiety, depression, and insomnia symptoms; moreover, death from family or friends was a risk factor for insomnia symptoms. During the COVID-19 outbreak, most [1086 (76.9%)] of the participating HCWs received psychological interventions, while nearly all [994 (70.4%)] of them had received public psychological education. Only 102 (7.2%) of the HCWs received individual counseling from COVID-19.

CONCLUSION

Although the mental health and sleep problems of HCWs were relieved after the COVID-19 pandemic, they still faced challenges and greater risks than did the general population. Identifying risk factors would help in providing targeted interventions. In addition, although a major proportion of HCWs have received public psychological education, individual interventions are still insufficient.

Programmable Gravity Self-Driven Microfluidic Chip for Point-of-Care Multiplied Immunoassays

Point-of-care testing (POCT) is experiencing a groundbreaking transformation with microfluidic chips, which offer precise fluid control and manipulation at the microscale. Nevertheless, chip design or operation for existing platforms is rather cumbersome, with some even heavily depending on external drivers or devices, impeding their broader utilization. This study develops a unique programmable gravity self-driven microfluidic chip (PGSMC) capable of simultaneous multi-reagent sequential release, multi-target analysis, and multi-chip operation. All necessary reagents are introduced in a single step, and the process is initiated simply by flipping the PGSMC vertically, eliminating the need for additional steps or devices. Additionally, it demonstrates successful immunoassays in less than 60 min for antinuclear antibodies testing, compared to more than 120 min by traditional methods. Assessment using 25 clinically diagnosed cases showcases remarkable sensitivity (96%), specificity (100%), and accuracy (99%). These outcomes underscored its potential as a promising platform for POCT with high accuracy, speed, and reliability, highlighting its capability for automated fluid control.

Design and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein to Validate the Viral Quality Assurance Panels

The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for the calibration and quality assurance of inactivated SARS-CoV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. A heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)-C-terminal domain (CTD) across all SARS-CoV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprised of UV-inactivated SARS-CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (limit of detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a 20 amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust 'pan-variant' antigen-based assays for viruses prone to high mutational rates.

The characteristics of microbiome in the upper respiratory tract of COVID-19 patients

BACKGROUND

Co-infection with other pathogens in coronavirus disease 2019 (COVID-19) patients exacerbates disease severity and impacts patient prognosis. Clarifying the exact pathogens co-infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is premise of the precise treatment for COVID-19 patients.

METHODS

Sputum samples were collected from 17 patients in the COVID-19 positive group and 18 patients in the COVID-19 negative group. DNA extraction was performed to obtain the total DNA. Sequencing analysis using 16S and ITS rRNA gene was carried out to analyze the composition of bacterial and fungal communities. Meanwhile, all the samples were inoculated for culture.

RESULTS

We did not observe significant differences in bacterial composition between the COVID-19 positive and negative groups. However, a significantly higher abundance of Candida albicans was observed in the upper respiratory tract samples from the COVID-19 positive group compared to the COVID-19 negative group. Moreover, the Candida albicans strains isolated from COVID-19 positive group exhibited impaired secretion of aspartyl proteinases.

CONCLUSION

COVID-19 positive patients demonstrate a notable increase in the abundance of Candida albicans, along with a decrease in the levels of aspartyl proteinases, indicating the alteration of microbiota composition of upper respiratory tract.

Organic Fluorophores with Large Stokes Shift for the Visualization of Rapid Protein and Nucleic Acid Assays

Organic small-molecule fluorophores, characterized by flexible chemical structure and adjustable optical performance, have shown tremendous potential in biosensing. However, classical organic fluorophore motifs feature large overlap between excitation and emission spectra, leading to the requirement of advanced optical set up to filter desired signal, which limits their application in scenarios with simple settings. Here, a series of wavelength-tunable small-molecule fluorescent dyes (PTs) bearing simple organic moieties have been developed, which exhibit Stokes shift up to 262 nm, molar extinction coefficients ranged 30,000-100,000 M-1 cm-1, with quantum yields up to 54.8 %. Furthermore, these dyes were formulated into fluorescent nanoparticles (PT-NPs), and applied in lateral flow assay (LFA). Consequently, limit of detection for SARS-CoV-2 nucleocapsid protein reached 20 fM with naked eye, a 100-fold improvement in sensitivity compared to the pM detection level for colloidal gold-based LFA. Besides, combined with loop-mediated isothermal amplification (LAMP), the LFA system achieved the visualization of single copy level nucleic acid detection for monkeypox (Mpox).

Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance

Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.

Nanobody engineering for SARS-CoV-2 neutralization and detection

In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases.

IMPORTANCE

Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.

Biomarkers of early SARS-CoV-2 infection before the onset of respiratory symptoms

OBJECTIVES

Currently, limited data exist regarding the pathological changes occurring during the incubation phase of SARS-CoV-2 infection. We utilized proteomic analysis to explore changes in the circulatory host response in individuals with SARS-CoV-2 infection before the onset of symptoms.

METHODS

Participants were individuals from a randomized clinical trial of prophylaxis for COVID-19 in a workers' dormitory. Proteomic signatures of blood samples collected within 7 days before symptom onset (incubation group) were compared with those collected >21 days (non-incubation group) to derive candidate biomarkers of incubation. Candidate biomarkers were assessed by comparing levels in the incubation group with both infected individuals (positive controls) and non-infected individuals (negative controls).

RESULTS

The study included men (mean age 34.2 years and standard deviation 7.1) who were divided into three groups: an incubation group consisting of 44 men, and two control groups-positive (n = 56) and negative (n = 67) controls. Through proteomic analysis, we identified 49 proteins that, upon pathway analyses, indicated an upregulation of the renin-angiotensin and innate immune systems during the virus incubation period. Biomarker analyses revealed increased concentrations of plasma angiotensin II (mean 731 vs. 139 pg/mL), angiotensin (1-7) (302 vs. 9 pg/mL), CXCL10 (423 vs. 85 pg/mL), CXCL11 (82.7 vs. 32.1 pg/mL), interferon-gamma (0.49 vs. 0.20 pg/mL), legumain (914 vs. 743 pg/mL), galectin-9 (1443 vs. 836 pg/mL), and tumour necrosis factor (20.3 vs. 17.0 pg/mL) during virus incubation compared with non-infected controls (all p < 0.05). Plasma angiotensin (1-7) exhibited a significant increase before the onset of symptoms when compared with uninfected controls (area under the curve 0.99, sensitivity 0.97, and specificity 0.99).

DISCUSSION

Angiotensin (1-7) could play a crucial role in the progression of symptomatic COVID-19 infection, and its assessment could help identify individuals who would benefit from enhanced monitoring and early antiviral intervention.

Whole Blood as a Sample Matrix in Homogeneous Time-Resolved Assay-Förster Resonance Energy Transfer-Based Antibody Detection

The protein-L-utilizing Förster resonance energy transfer (LFRET) assay enables mix-and-read antibody detection, as demonstrated for sera from patients with, e.g., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Zika virus, and orthohantavirus infections. In this study, we compared paired serum and whole blood (WB) samples of COVID-19 patients and SARS-CoV-2 vaccine recipients. We found that LFRET also detects specific antibodies in WB samples. In 44 serum-WB pairs from patients with laboratory-confirmed COVID-19, LFRET showed a strong correlation between the sample materials. By analyzing 89 additional WB samples, totaling 133 WB samples, we found that LFRET results were moderately correlated with enzyme-linked immunosorbent assay results for samples collected 2 to 14 months after receiving COVID-19 diagnosis. However, the correlation decreased for samples >14 months after receiving a diagnosis. When comparing the WB LFRET results to neutralizing antibody titers, a strong correlation emerged for samples collected 1 to 14 months after receiving a diagnosis. This study also highlights the versatility of LFRET in detecting antibodies directly from WB samples and suggests that it could be employed for rapidly assessing antibody responses to infectious agents or vaccines.

Magnetic-responsive upconversion luminescence resonance energy transfer (LRET) biosensor for ultrasensitive detection of SARS-CoV-2 spike protein

Upconversion nanoparticles (UCNPs) are ideal donors for luminescence resonance energy transfer (LRET)-based biosensors due to their excellent upconversion luminescence properties. However, the relatively large size of antibodies and proteins limits the application of UCNPs-based LRET biosensors in protein detection because the large steric hindrance of proteins leads to low energy transfer efficiency between UCNPs and receptors. Herein, we developed a magnetic responsive UCNPs-based LRET biosensor to control the coupling distance between antibody-functionalized UCNPs (Ab-UCNPs) as donors and antibody-PEG linker-magnetic gold nanoparticles (Ab-PEG-MGNs) as acceptors for ultrasensitive and highly selective detection of SARS-CoV-2 spike proteins. Our results showed that this platform reversibly shortened the coupling distance between UCNPs and MGNs and enhanced the LRET signal with a 10-fold increase in the limit of detection (LOD) from 20.6 pg/mL without magnetic modulation to 2.1 pg/mL with magnetic modulation within 1 h. The finite-difference time-domain (FDTD) simulation with cyclic distance change confirmed the distance-dependent LRET efficiency under magnetic modulation, which supported the experimental results. Moreover, the applications of this magnetic-responsive UCNP-based LRET biosensor could be extended to other large-size biomolecule detection.

On the impact of mass screening for SARS-CoV-2 through self-testing in Greece

Background

Screening programs that pre-emptively and routinely test population groups for disease at a massive scale were first implemented during the COVID-19 pandemic in a handful of countries. One of these countries was Greece, which implemented a mass self-testing program during 2021. In contrast to most other non-pharmaceutical interventions (NPIs), mass self-testing programs are particularly attractive for their relatively small financial and social burden, and it is therefore important to understand their effectiveness to inform policy makers and public health officials responding to future pandemics. This study aimed to estimate the number of deaths and hospitalizations averted by the program implemented in Greece and evaluate the impact of several operational decisions.

Methods

Granular data from the mass self-testing program deployed by the Greek government between April and December 2021 were obtained. The data were used to fit a novel compartmental model that was developed to describe the dynamics of the COVID-19 pandemic in Greece in the presence of self-testing. The fitted model provided estimates on the effectiveness of the program in averting deaths and hospitalizations. Sensitivity analyses were used to evaluate the impact of operational decisions, including the scale of the program, targeting of sub-populations, and sensitivity (i.e., true positive rate) of tests.

Results

Conservative estimates show that the program reduced the reproduction number by 4%, hospitalizations by 25%, and deaths by 20%, translating into approximately 20,000 averted hospitalizations and 2,000 averted deaths in Greece between April and December 2021.

Conclusion

Mass self-testing programs are efficient NPIs with minimal social and financial burden; therefore, they are invaluable tools to be considered in pandemic preparedness and response.

Usefulness of receptor binding domain protein-based serodiagnosis of COVID-19

Objectives

This study evaluated the performance of recombinant receptor binding domain (RBD) protein-based enzyme-linked immunosorbent assays (RBD-ELISAs) for detecting anti-SARS-CoV-2 immunoglobulin (Ig) G and IgM antibodies.

Methods

In this study, 705 sera from SARS-CoV-2-infected individuals and 315 sera from healthy individuals were analyzed.

Results

The RBD-ELISA IgG exhibited high specificity (99.1%) and moderate sensitivity (48.0%), with an overall diagnostic accuracy of 73.5%. RBD-ELISA IgM demonstrated specificity at 94.6% and sensitivity at 51.1%, with an accuracy of 72.8%. Both assays displayed improved performance when analyzing samples collected 15-21 days post-symptom onset, achieving sensitivity and accuracy exceeding 88% and 90%, respectively. Combining RBD-ELISA IgG and IgM in parallel analysis enhanced sensitivity to 98.6% and accuracy to 96.2%. Comparing these RBD-ELISAs with commercially available tests, the study found overlapping sensitivity and similar specificity values. Notably, the combined RBD-ELISA IgG and IgM showed superior performance. Cross-reactivity analysis revealed low false-positive rates (4.4% for IgG, 3.7% for IgM), primarily with viral infections.

Conclusion

This research underscores the potential of RBD-based ELISAs for COVID-19 diagnosis, especially when assessing samples collected 15-21 days post-symptom onset and utilizing a parallel testing approach. The RBD protein's immunogenicity and specificity make it a valuable tool for serodiagnosis, offering an alternative to polymerase chain reaction-based methods, particularly in resource-limited settings.

Ginseng and ginsenosides on cardiovascular and pulmonary diseases; Pharmacological potentials for the coronavirus (COVID-19)

Since its outbreak in late 2019, the Coronavirus disease 2019 (COVID-19) pandemic has profoundly caused global morbidity and deaths. The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has major complications in cardiovascular and pulmonary system. The increased rate of mortality is due to delayed detection of certain biomarkers that are crucial in the development of disease. Furthermore, certain proteins and enzymes in cellular signaling pathways play an important role in replication of SARS-CoV-2. Most cases are mild to moderate symptoms, however severe cases of COVID-19 leads to death. Detecting the level of biomarkers such as C-reactive protein, cardiac troponin, creatine kinase, creatine kinase-MB, procalcitonin and Matrix metalloproteinases helps in early detection of the severity of disease. Similarly, through downregulating Renin-angiotensin system, interleukin, Mitogen-activated protein kinases and Phosphoinositide 3-kinases pathways, COVID-19 can be effectively controlled and mortality could be prevented. Ginseng and ginsenosides possess therapeutic potential in cardiac and pulmonary complications, there are several studies performed in which they have suppressed these biomarkers and downregulated the pathways, thereby inhibiting the further spread of disease. Supplementation with ginseng or ginsenoside could act on multiple pathways to reduce the level of biomarkers significantly and alleviate cardiac and pulmonary damage. Therefore, this review summarizes the potential of ginseng extract and ginsenosides in controlling the cardiovascular and pulmonary diseases by COVID-19.

Machine learning-driven SERS fingerprinting of disintegrated viral components for rapid detection of SARS-CoV-2 in environmental dust

Surveillance of airborne viruses in crowded indoor spaces is crucial for managing outbreaks, as highlighted by the SARS-CoV-2 pandemic. However, the rapid and on-site detection of fast-mutating viruses, such as SARS-CoV-2, in complex environmental backgrounds remains challenging. Our study introduces a machine learning (ML)-driven surface-enhanced Raman spectroscopy (SERS) approach for detecting viruses within environmental dust matrices. By decomposing intact virions into individual structural components via a Raman-background-free lysis protocol and concentrating them into nanogap SERS hotspots, we significantly enhance the SERS signal intensity and fingerprint information density from viral structural components. Utilizing Principal Component Analysis (PCA), we establish a robust connection between the SERS data of these structural components and their biological sequences, laying a solid foundation for virus detection through SERS. Furthermore, we demonstrate reliable quantitative detection of SARS-CoV-2 using identified SARS-CoV-2 peaks at concentrations down to 102 pfu/ml through Gaussian Process Regression (GPR) and a digital SERS methodology. Finally, applying a Principal Component Analysis-Linear Discriminant Analysis (PCA-LDA) algorithm, we identify SARS-CoV-2, influenza A virus, and Zika virus within an environmental dust background with over 86% accuracy. Therefore, our ML-driven SERS approach holds promise for rapid environmental virus monitoring to manage future outbreaks.

SARS-CoV-2 Variants Genotyping and Diagnostic Performance of a 2-Genes Detection Assay

BACKGROUND

The emergence of the COVID-19 pandemic resulted in the unprecedented expansion of molecular testing technologies. This study aimed at evaluating the performance of the FluoroType® SARS-CoV-2 plus assay for SARS-CoV-2 detection as well as describing the detection of SARS-CoV-2 variants using the FluoroType® SARS-CoV-2 varID Q kit.

METHODS

The study utilized 679 archived nasopharyngeal samples. Analytical performance and the diagnostic performance of the FluoroType® SARS-CoV-2 plus assay were determined using 320 samples and reference material. Variants identification on the FluoroType® SARS-CoV-2 varID Q assay was performed on 359 samples. The study was approved by the Aga Khan University Hospital Institutional Review Board.

RESULTS

The FluoroType® SARS-CoV-2 plus assay's limit of detection was verified as 1.2 copies/µL. The repeatability SD and %CV were 2.45 and 9.8% while reproducibility had an SD and %CV of 1.39 and 5.68%, respectively, for the RdRP gene. The positive and negative percent agreement were determined to be 99.4% (95% CI; 98.1%-100%) and 99.4% (95% CI; 98.2%-100%) respectively. In the variants identification, samples from the original wave had no mutations identified while 12.3%, 49%, and more than 90% of the samples during the Alpha, Delta, and Omicron waves, respectively, had detectable mutations.

CONCLUSIONS

The FluoroType® SARS-CoV-2 plus assay demonstrated analytical performance comparable to the reference method with a diagnostic sensitivity and specificity of >99%. The FluoroType® SARS-CoV-2 varID Q assay achieved rapid detection of circulating variants.

Smart and emerging point of care electrochemical sensors based on nanomaterials for SARS-CoV-2 virus detection: Towards designing a future rapid diagnostic tool

In the recent years, researchers from all over the world have become interested in the fabrication of advanced and innovative electrochemical and/or biosensors for respiratory virus detection with the use of nanotechnology. These fabricated sensors demonstrated a number of benefits, including precision, affordability, accessibility, and miniaturization which makes them a promising test method for point-of-care (PoC) screening for SARS-CoV-2 viral infection. In order to comprehend the principles of electrochemical sensing and the role of various types of sensing interfaces, we comprehensively explored the underlying principles of electroanalytical methods and terminologies related to it in this review. In addition, it is addressed how to fabricate electrochemical sensing devices incorporating nanomaterials as graphene, metal/metal oxides, metal organic frameworks (MOFs), MXenes, quantum dots, and polymers. We took an effort to carefully compile current developments, advantages, drawbacks, possible solutions in nanomaterials based electrochemical sensors.

Disease diagnosis and application analysis of molecularly imprinted polymers (MIPs) in saliva detection

Saliva has significantly evolved as a diagnostic fluid in recent years, giving a non-invasive alternative to blood analysis. A high protein concentration in saliva is delivered directly from the bloodstream, making it a "human mirror" that reflects the body's physiological state. It plays an essential role in detecting diseases in biomedical and fitness monitoring. Molecularly imprinted polymers (MIPs) are biomimetic materials with custom-designed synthetic recognition sites that imitate biological counterparts renowned for sensitive analyte detection. This paper reviews the progress made in research about MIP biosensors for detecting saliva biomarkers. Specifically, we investigate the link between saliva biomarkers and various diseases, providing detailed insights into the corresponding biosensors. Furthermore, we discuss the principles of molecular imprinting for disease diagnostics and application analysis, including recent advances in integrated MIP-sensor technologies for high-affinity analyte detection in saliva. Notably, these biosensors exhibit high discrimination, allowing for the detection of saliva biomarkers linked explicitly to chronic stress disorders, diabetes, cancer, bacterial or viral-induced illnesses, and exposure to illicit toxic substances or tobacco smoke. Our findings indicate that MIP-based biosensors match and perhaps surpass their counterparts featuring integrated natural antibodies in terms of stability, signal-to-noise ratios, and detection limits. Additionally, we highlight the design of MIP coatings, strategies for synthesizing polymers, and the integration of advanced biodevices. These tailored biodevices, designed to assess various salivary biomarkers, are emerging as promising screening or diagnostic tools for real-time monitoring and self-health management, improving quality of life.

Comparative analysis of aptamers binding to SARS-CoV-2 N protein using capillary electrophoresis and bio-layer interferometry

Aptamers are increasingly employed in SARS-CoV-2 theragnostics in recent years. Characterization of aptamers, testing affinity and kinetic parameters (e.g., equilibrium dissociation constant (KD), kon, and koff), can be done by several methods and influenced by many factors. This study aims to characterize the binding of aptamers to SARS-CoV-2 nucleocapsid (N) protein using capillary electrophoresis (CE) and bio-layer interferometry (BLI). These two analytical methods differ by how the aptamer binds to its target protein once the aptamer, as a capture ligand, is partitioned in solution (CE) or immobilized on the biosensor (BLI). With CE, the KD values of the N-binding aptamers (tNSP1, tNSP2, and tNSP3) were determined to be 18 ± 4 nM, 45 ± 11 nM, and 32 ± 7 nM, respectively, while the KD measurements by BLI yielded 4.8 ± 0.6, 4.5 ± 0.5, and 2.9 ± 0.3 nM, respectively. CE results showed a higher KD across all aptamers tested. The differences in the steric hindrance and confirmational structures of the aptamers immobilized on the BLI biosensors versus those suspended in the CE sample solution affect the molecular interactions between aptamers and the target proteins. Moreover, the buffer composition including pH and ionic strength can influence the stability of aptamer structures, or aptamer-protein complexes. All these variables affect the binding and calculated KD. In this sense, a KD value alone is not sufficient to make comparisons between aptamers; instead, the entire experimental setup should also be considered. This is particularly important when implementing aptamers in different bioanalytical systems.

Advances and Challenges in SARS-CoV-2 Detection: A Review of Molecular and Serological Technologies

The urgent need for accurate COVID-19 diagnostics has led to the development of various SARS-CoV-2 detection technologies. Real-time reverse transcriptase polymerase chain reaction (RT-qPCR) remains a reliable viral gene detection technique, while other molecular methods, including nucleic acid amplification techniques (NAATs) and isothermal amplification techniques, provide diverse and effective approaches. Serological assays, detecting antibodies in response to viral infection, are crucial for disease surveillance. Saliva-based immunoassays show promise for surveillance purposes. The efficiency of SARS-CoV-2 antibody detection varies, with IgM indicating recent exposure and IgG offering prolonged detectability. Various rapid tests, including lateral-flow immunoassays, present opportunities for quick diagnosis, but their clinical significance requires validation through further studies. Challenges include variations in specificity and sensitivity among testing platforms and evolving assay sensitivities over time. SARS-CoV-2 antigens, particularly the N and S proteins, play a crucial role in diagnostic methods. Innovative approaches, such as nanozyme-based assays and specific nucleotide aptamers, offer enhanced sensitivity and flexibility. In conclusion, ongoing advancements in SARS-CoV-2 detection methods contribute to the global effort in combating the COVID-19 pandemic.

A novel saliva-based miRNA profile to diagnose and predict oral cancer

Oral cancer (OC) is the most common form of head and neck cancer. Despite the high incidence and unfavourable patient outcomes, currently, there are no biomarkers for the early detection of OC. This study aims to discover, develop, and validate a novel saliva-based microRNA signature for early diagnosis and prediction of OC risk in oral potentially malignant disorders (OPMD). The Cancer Genome Atlas (TCGA) miRNA sequencing data and small RNA sequencing data of saliva samples were used to discover differentially expressed miRNAs. Identified miRNAs were validated in saliva samples of OC (n = 50), OPMD (n = 52), and controls (n = 60) using quantitative real-time PCR. Eight differentially expressed miRNAs (miR-7-5p, miR-10b-5p, miR-182-5p, miR-215-5p, miR-431-5p, miR-486-3p, miR-3614-5p, and miR-4707-3p) were identified in the discovery phase and were validated. The efficiency of our eight-miRNA signature to discriminate OC and controls was: area under curve (AUC): 0.954, sensitivity: 86%, specificity: 90%, positive predictive value (PPV): 87.8% and negative predictive value (NPV): 88.5% whereas between OC and OPMD was: AUC: 0.911, sensitivity: 90%, specificity: 82.7%, PPV: 74.2% and NPV: 89.6%. We have developed a risk probability score to predict the presence or risk of OC in OPMD patients. We established a salivary miRNA signature that can aid in diagnosing and predicting OC, revolutionising the management of patients with OPMD. Together, our results shed new light on the management of OC by salivary miRNAs to the clinical utility of using miRNAs derived from saliva samples.