Search Results (591)

The overlap between the geographic distribution of COVID-19 outbreaks and pollution levels suggested a strong correlation between exposure to atmospheric particulate matter and an increased risk of developing severe forms of disease. This correlation has been highlighted by several epidemiological studies, indicating the existence of shared molecular mechanisms. Emerging evidence has highlighted the important role of lipid rafts in facilitating viral entry into cells. Specifically, the receptor binding domain of the SARS-CoV-2 spike protein interacts with sialylated glycans of the monosialic ganglioside GM1 and GM2 that are particularly enriched in lipid rafts. This interaction has been proposed to facilitate ACE2 recognition by the spike protein and may contribute to early events involved in viral attachment and entry. Here, we reveal that A549 alveolar lung cells, after DEP exposure, exhibit a significant shift in ACE2 into lipid rafts, accompanied by an increase in the immature form of ADAM17, the sheddase responsible for ACE2 cleavage. Additionally, DEP exposure results in a significant increase in IL-6 release, while no changes were observed in IL-8 and sACE2 release. This treatment does not cause significant alterations in protein levels or membrane redistribution of COX-2 and HO-1, proteins involved in the inflammatory response and oxidative stress following exposure to air pollution, and linked to COVID-19 pathogenesis. Finally, lipidomic analysis by UHPLC-MS revealed that DEP exposure induces a significant increase in GM2 levels, and a concomitant decrease in GM1 and GM3 levels. Together, these results indicate that DEP exposure remodels lipid raft-associated molecular features in A549 cells, including ACE2 membrane redistribution, altered ganglioside composition, and increased IL-6 release. Although these changes may be relevant to cellular mechanisms associated with SARS-CoV-2 susceptibility, the present study does not directly assess viral binding, viral entry, or infection, and further functional studies are required. Full article

Identifying antigens that elicit protective immunity is the key step for vaccine development. Here, we describe the use of the MS2 VLP platform to identify epitopes of SARS-CoV-2 structural proteins recognized by antibodies from COVID-19 patients, and to present those epitopes to the immune system as vaccines. We constructed an MS2 virus-like particle (VLP) library covering all four structural proteins of SARS-CoV-2 and affinity-selected vaccine candidates by biopanning on antibodies from infected humans. We focused on the structural proteins, reasoning that they are the most likely targets of a protective antibody response. The epitopes we found map almost entirely to the spike and nucleocapsid proteins. The VLPs displaying such epitopes were produced individually in E. coli and then tested for their potential as vaccines. While none of the affinity-selected spike-specific VLPs elicited neutralizing antibodies, VLPs displaying nucleocapsid epitopes induced protective immunity in a hamster model. This work illustrates the MS2 VLP platform’s capacity for the identification of new vaccine candidates and raises the possibility that VLPs displaying nucleocapsid epitopes could provide long-lasting protection against a range of virus variants. Full article

This study investigated the antiviral potential of silver nanoparticles (AgNPs) synthesized from Senna italica and Vepris reflexa plant extracts, rich in saponins and flavonoids. The aim was to explore the synthesis of AgNPs through green chemistry, followed by assessing their inhibitory activity against SARS-CoV-2 papain-like protease (PLpro) and evaluating cytotoxicity. The synthesized AgNPs were predominantly spherical in shape, with an average particle size in the nanoscale range (12–55 nm), as conformed by the transmission electron microscopy (TEM) and dynamic light scattering (DLS) analyses. A dose-dependent inhibition of SARS-CoV-2 PLpro was observed, with IC₅₀ values ranging from 0.12 to 0.48 mg/mL for different formulations. Cytotoxicity tests on Vero-76 cells revealed a high viability (>75%) at concentrations below 0.5 mg/mL for all AgNP samples. The findings suggest that the plant-derived AgNPs exhibit significant antiviral activity and minimal cytotoxicity, supporting their potential for further development as therapeutic agents. Full article

In this article, we formulated a mathematical model to describe SARS-CoV-2 development in humans, accounting for the dynamics of susceptible and infected epithelial cells, viral particles, ACE2 receptors, cytotoxic T lymphocytes (CTLs), and antibodies. The basic reproduction number and equilibrium points are derived, with stability analysis showing that the disease-free equilibrium is maintained when ${\mathcal{R}}_0<1$, while an endemic equilibrium arises for ${\mathcal{R}}_0>1$. Additionally, Hopf bifurcating periodic solutions are observed under elevated viral replication and infection rates. To capture therapeutic intervention, an impulsive control framework based on antibody-mediated drug administration is introduced. The existence and stability of a disease-free periodic orbit are established through the impulsive reproduction number ${\mathcal{R}}_0^{imp}$, with stability ensured when ${\mathcal{R}}_0^{imp}<1$. The findings from numerical simulations support the analytical outcomes, proving the efficacy of impulsive control in suppressing viral persistence. The current research work offers important knowledge on the interaction between immune system and impulsive control mechanisms, which serves as a basis to develop therapies against SARS-CoV-2. Full article

The molecular mechanisms governing the efficient packaging of the large SARS-CoV-2 RNA genome into progeny virions remain incompletely understood, with the role of untranslated regions (UTRs) being particularly enigmatic. Leveraging proximity ligation sequencing data, we identified direct, high-frequency interactions between the viral packaging signal PS9 and both the 5′ and 3′ UTRs during intracellular replication stages. Functional validation using an infectious virus-like particle (iVLP) system demonstrated that genomes incorporating SARS-CoV-2 UTRs exhibited significantly enhanced packaging efficiency, yielding an increase in both packaged RNA copies and reporter gene expression post-infection. Competitive packaging assays confirmed the UTRs confer a selective advantage during particle assembly. Mechanistically, Western blot and digital Western analysis revealed that UTR-containing iVLPs incorporated approximately 2-fold more nucleocapsid (N) proteins, suggesting enhanced N recruitment or retention. The deletion of specific core sequences within the UTRs predicted to form a base pair with PS9 abrogated this enhancement, suggesting the functional significance of the UTR-PS9 interaction interface. Collectively, these results establish that the 5′ and 3′ UTRs act synergistically through direct RNA-RNA interactions with PS9 to promote N protein recruitment and enhance packaging efficiency in a PS9-dependent iVLPs system. This UTR-PS9 regulatory axis presents a novel target for therapeutic intervention against SARS-CoV-2 and related coronaviruses. Full article

Aerosol-generating procedures (AGPs) expose healthcare personnel to airborne pathogens and require portable engineering controls that can be integrated into routine clinical workflows. We developed a portable, foldable negative-pressure aerosol-containment system (FNPACS) combining adaptive fan control, an H14 high-efficiency particulate air (HEPA) filter, and a disposable metal-oxide prefilter in a mobile filtration module. Bench performance was evaluated using pressure-flow testing in accordance with National Environmental Balancing Bureau (NEBB) procedures and International Organization for Standardization (ISO) 14644-3, polyalphaolefin aerosol challenge testing, and smoke visualization, while an exploratory clinical study assessed environmental contamination via real-time reverse-transcription PCR (rRT-PCR) in 11 patients (31 assay analyses). Bench testing demonstrated HEPA filtration efficiencies of 99.994–99.997%, stable negative-pressure generation across fan duty cycles, no detectable downstream breakthrough beyond the HEPA filter under the tested conditions, and effective inward airflow on smoke testing. A Lagrangian discrete phase model (DPM) particle-tracking simulation further characterized size-dependent aerosol-surrogate transport. Under HEPA-ON active-extraction conditions, 73.0–86.1% of simulated 0.3–10 µm water-equivalent particles were transported to the HEPA suction pathway, while 13.9–27.0% were deposited on internal wall surfaces. In the clinical evaluation, SARS-CoV-2 RNA detection on environmental swabs was limited and predominantly low level. The clearest reproducible signal occurred on the top interior surface under HEPA-OFF conditions, whereas HEPA-ON detections were isolated or presumptive high-Ct signals without reproducible confirmation. These findings provide preliminary engineering and usability support for FNPACS as a feasible near-source aerosol-control platform for AGPs. The patient swab component should be interpreted as an exploratory, proof-of-concept assessment rather than confirmatory evidence of clinical containment efficiency because several clinical cases had non-supportive patient-related controls and were therefore not used in the primary containment interpretation. Full article

Objectives: Membrane-enveloped virus-like particles (VLPs) constitute a versatile vaccine platform allowing for the display of heterologous viral surface antigens. The density of displayed antigens is paramount for the efficient elicitation of a strong cellular and humoral immune response. SARS-CoV-2 spike protein variants with engineered cytoplasmic tails (CTs) were generated to enhance decoration efficiency on the surface of VLPs formed by the HIV core protein Gag. These HIV (SARS-CoV-2) chimeric particles serve as a vaccine component prototype. Methods: Spike variants were first analyzed for cellular and surface expression as well as incorporation into extracellular vesicles (EVs) and VLPs using flow cytometric analysis and Western blot analysis. Receptor binding, fusogenicity, i.e., mediating the fusion of spike-positive with receptor-containing membranes, and the proteins’ potential to mediate lentiviral vector gene transduction into susceptible target cells was examined by employing syncytia-formation assays and vector titration experiments. The display of a neutralization-sensitive epitope was examined utilizing immuno-precipitation using a neutralizing antibody. Results: All four variants were shown to be cell-surface expressed, to recruit the cognate receptor, to mediate membrane fusion and cell entry of lentiviral pseudotype vector particles and to decorate VLPs and EVs. However, the spike variant encompassing a truncated CT derived from the gibbon ape leukemia virus (GaLV) transmembrane (TM) envelope protein was most efficiently incorporated into HIV Gag-formed VLPs. All variants exposed a neutralization-sensitive epitope in the receptor binding domain. Conclusions: Engineering of the CTs of viral surface antigens can enhance VLP decoration, while required functionality of the ecto-domain such as receptor recognition, fusogenicity and neutralization-sensitive epitope presentation are not abrogated. This indicates the preservation of the structural integrity of the antigen required to elicit a neutralizing humoral immunity upon vaccination. The identified truncated CT of GaLV TM may be of utility to improve the incorporation of other viral surface antigens into a variety of membrane-enveloped VLPs derived from a range of different parental viruses. Full article

Although SARS-CoV-2 has been extensively studied from clinical, virological, and diagnostic perspectives, the problem of accurate automatic semantic segmentation of SARS-CoV-2 particles in electron microscopy images remains inadequately explored. Existing studies have largely focused on virus detection, classification, morphometry, or conventional image analysis, while comparatively little attention has been paid to pixel-level delineation of viral structures using specialised deep learning segmentation frameworks. To address this gap, we propose here a deep learning system based on convolutional neural networks (CNNs) combined with image processing techniques to establish semantic segmentation tools for the automatic identification of SARS-CoV-2. Our approach utilises the super-Euclidean pixels method as an intermediate layer within the CNN for semantic segmentation. We then compare its performance against the gradient vector flow (GVF) and Poisson inverse gradient (PIG) segmenters. The proposed CNN model surpassed the traditional GVF and PIG segmentation models, achieving the following metrics (mean ± variance): Dice similarity coefficient (DSC) = 0.9345 ± 0.0006; intersection over union (IoU) = 0.8782 ± 0.0018; sensitivity/true positive rate (TPR) = 0.9373 ± 0.0018; specificity/true negative rate (SPC) = 0.9517 ± 0.0012; accuracy = 0.9449 ± 0.0004; area under the ROC curve (AUC) = 0.9446 ± 0.0431; and Cohen’s Kappa = 0.9137 ± 0.0011. This method enables virologists to employ an automatic CNN-based segmentation tool for detecting SARS-CoV-2 and demonstrates superiority over GVF and PIG. Full article

Salivary gland infection by SARS-CoV-2 requires viral entry via routes and mechanisms that remain unresolved. This study examined the expression of the angiotensin-converting enzyme 2 (ACE2) receptor in salivary tissues and basal cell-derived human salivary progenitor cells (hS/PCs), an unstudied potential entry point for SARS-CoV-2. Multiple detection modalities, including immunocytochemistry, Western blotting, flow cytometry and RT-PCR, demonstrated a consistent lack of ACE2 protein and transcript in both tissue specimens and primary salivary epithelial cells. Antigen retrieval at pH 9 was determined to be optimal for immunodetection protocols, yet ACE2 remained undetectable. Small intestine tissue served as a positive control, confirming the validity of the methods and reagents we used. Considering there can be other receptors for SARS-CoV-2, flow cytometric analyses demonstrated that recombinant SARS-CoV-2 spike protein failed to bind to salivary epithelial cells, in contrast to HEK293 cells engineered to overexpress ACE2, which showed robust spike binding. Additional studies showed that patient-derived salivary cells, negative for ACE2, are not infected by the SARS-CoV-2 pseudovirus, while ACE2-positive cells are readily infected. These findings strongly support our conclusion that salivary cells do not serve as major targets for SARS-CoV-2 infection via ACE2, spike protein, or an alternate receptor. Thus, salivary cells are unlikely major targets for SARS-CoV-2 infection, either through direct exposure to viral particles in ductal fluids or via access to basal cells across the basement membrane. Full article

The surface spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key target for the development of Coronavirus Disease 2019 (COVID-19) vaccines. Nevertheless, the mutations in the S protein, particularly in its receptor-binding domain region, have resulted in a reduced or complete loss of immunogenicity and/or protective efficacy in early vaccines against the Omicron variant and subvariants. Accordingly, continuous efforts are required to develop effective vaccines against multiple Omicron subvariants to reduce current and future threats. In this study, we designed an mRNA vaccine targeting the S protein of a recent Omicron-XEC subvariant (XEC-S-mRNA) and assessed its immunogenicity, including its broad neutralizing activity, and its protective efficacy against multiple Omicron subvariants. Our results demonstrated that the lipid nanoparticle-formulated mRNA vaccine formed an appropriate particle size with strong stability and successful antigen expression. It elicited durable cellular immune responses and broad neutralizing antibodies against multiple early and recent Omicron subvariants, thereby cross-protecting transgenic mice from challenge with a heterologous Omicron strain (KP.3). Moreover, the vaccine-induced neutralizing antibodies alone were sufficient to prevent Omicron-KP.3 infection. Overall, this study shows promise for further development of the candidate vaccine against current and future Omicron infections. Full article

The aim of the study was to modify polylactide with zinc oxide nanoparticles (ZnO), raspberry leaf extract (E), and a combined ZnO/extract system (EZnO) in order to prepare novel packaging materials via a solvent-free method, namely cast extrusion. Physicochemical properties: Morphology (GPC, SEM, FTIR), mechanical (tensile tests, puncture), barrier (WVTR, OTR, UV-Vis) and water contact angle for PLA-based films with two thickness ranges were investigated. Additionally, antimicrobial (antibacterial, antifungal and antiviral) tests were performed. GPC results revealed that the presence of the extract counteracted biopolyester degradation during hot melt processing. The best mechanical properties (TS ca. 50 MPa, EB ca. 18%) were obtained for PLA modified with raspberry leaf extract (PLA/E). EZnO addition led to the highest increase in oxygen (with 25%) and water vapor (up to ca. 28%) barrier properties. The material with EZnO addition was also found to be the only one to demonstrate antibacterial effectiveness, although the activity was insignificant. However, the incorporation of EZnO into the biopolymer matrix enhanced its antiviral properties, resulting in the complete inactivation of Φ6 bacteriophage particles used as a surrogate of SARS-CoV-2 virus. Full article

Background/Objectives: This investigation aims to assess the potential for repurposing nitazoxanide (NIT) as a treatment for COVID-19. NIT was loaded into terpene-enriched chondrosomes (TECs) to assess its anti-hCoV-19 activity through pulmonary delivery. Methods: NIT-TECs were then fabricated utilizing the ethanol injection method. Using a D-optimal design, the effects of factors on entrapment efficiency (EE%), particle size (PS), and zeta potential (ZP) were determined, and the optimal formulation was selected. Results: The optimum TEC exhibited an EE% of 98.87 ± 0.69, a PS of 129.43 ± 5.43 nm, a polydispersity index (PDI) of 0.433 ± 0.022, and a ZP of −25.99 ± 0.99 mV. The optimum TEC was lyophilized to attain a dry powder. Further, the differential scanning calorimetry test confirmed that NIT was transformed from crystalline to amorphous form inside the optimum TEC. In addition, the mucoadhesion test confirmed the ability of the optimum TECs to adhere to pulmonary tissues. Additionally, NIT binding to the active site of SARS-CoV-2 enzymes was investigated using in silico analysis. When compared to NIT, the aerodynamic characteristics of the lyophilized optimum TECs employing the cascade impactor showed superior residence in the lungs. Conclusions: These findings suggest that loading NIT into TECs enhanced its antiviral activity, as indicated by the in vitro cytotoxicity study. Overall, the results point to NIT-loaded TECs as a potentially effective pulmonary delivery system for COVID-19 treatment. Full article

The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for antivirals that are resilient to resistance. Current Food and Drug Administration (FDA)-approved therapies primarily target single viral mechanisms, leaving gaps in efficacy. Here, we developed a Deep Learning-based Activity Screening Model (DLASM), which integrates graph convolutional network with machine learning to identify SARS-CoV-2 inhibitors, using experimental 3-chymotrypsin-like (3CL) main protease assay data. The optimized DLASMs virtually screened ~170,000 compounds from diverse in-house collections and yielded novel hits, several of which not only inhibited the 3CL protease but also blocked viral entry by interfering with heparan sulfate-mediated host interactions. These activities were validated through multiple assays, including 3CL enzymatic inhibition, SARS-CoV-2 pseudotyped particle entry, α-synuclein fibril uptake as a proxy for endocytosis, live virus cytopathic effect, heparan sulfate-dependent entry assay, and a 3D human lung mucociliary tissue model. Molecular docking studies elucidated binding modes at the 3CL protease active site, while molecular dynamics simulations provided insights into compound–heparan sulfate interactions. The identified compounds represent early-stage hits with moderate potency that demonstrate dual-mechanism antiviral activity. Together, these findings establish dual-target inhibition as a promising antiviral strategy, offering not only enhanced potency but also reduced risk of resistance. Moreover, our DLASM framework provides a generalizable pipeline for identifying chemically diverse scaffolds and for broader applications beyond SARS-CoV-2. Full article

As SARS-CoV-2 continues to evolve with increased transmissibility and immune evasion, the need for vaccines that provide broader and more durable protection has become increasingly urgent. The extensive research spurred by the pandemic has accelerated the development of diverse vaccine platforms, including mRNA, DNA, virus-like particles (VLPs), recombinant proteins, and mosaic mono- and polyvalent vaccines. While several of these platforms have reached regulatory approval and widespread clinical employment, others remain under evaluation or in various stages of clinical development. These vaccines have significantly reduced infection rates, severe disease, and hospitalizations, particularly among high-risk group. Nevertheless, the ongoing emergence of novel variants and subvariants has challenged the efficacy of both existing and newly developed vaccines. This evolving landscape underscores the urgent need for a universal SARS-CoV-2 vaccine platform capable of providing comprehensive and long-lasting immunity. In this review, we evaluate current and emerging strategies for SARS-CoV-2 universal vaccine development, with a focus on antigen design, breadth of immune protection, and clinical feasibility. Attention is given to various universal vaccine platforms such as the mosaic polyvalent spike construct, multi-epitope vaccines targeting the receptor-binding domain (RBD), and approaches centered on the conserved S2 subunit of the spike protein. We also discuss strategies leveraging additional conserved viral proteins and T helper (Th) and cytotoxic T lymphocyte (CTL) epitopes from across coronaviruses. By highlighting the advances in these areas, this review provides a framework to guide the rational design of next-generation universal vaccines capable of delivering broad and durable protection against SARS-CoV-2 variants. Full article

In the post-pandemic era, monitoring adaptive immunity of the population to emerging SARS-CoV-2 variants remains an important public health priority. To address this need, we developed a test that can simultaneously assess the neutralization ability of three SARS-CoV-2 variants. A panel of lentiviral pseudoviruses, each bearing the S-protein of different SARS-CoV-2 variants (Wuhan-Hu-1, BA.1, and XBB.1.5) and expressing a unique fluorescent protein (Clover, mRhubarb713, or mRuby3) was generated and used to transduce hACE2-overexpressing cells. The percentage of infected target cells for each variant was quantified via flow cytometry. Co-infection led to a minor reduction in the percentage of infected cells compared to mono-infection controls, confirming the robustness of the assay. We then applied the test to the analysis of human sera samples, which were collected in the Sirius Federal Territory (Russian Federation) and revealed the following: (1) sera collected in 2021 neutralized the Wuhan-Hu-1 variant and demonstrated cross-specificity to the BA.1 variant, but not to the XBB.1.5 variant; (2) sera collected after the Omicron emergence point neutralized Wuhan-Hu-1 and BA.1, and possessed a weak ability to neutralize the XBB.1.5. This assay provides a valuable tool for efficient profiling of humoral immunity and monitoring its development in response to ongoing viral diversity. Full article