Search Results (444)

Background/Objectives: Concurrent outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A and B viruses (IAV/IBV), and respiratory syncytial virus (RSV) necessitate rapid and precise differential laboratory diagnostic methods. This study aimed to evaluate the multiplex molecular diagnostic performance of the geneLEAD VIII system (Precision System Science Co., Ltd., Matsudo, Japan), a fully automated sample-to-result precision instrument, in conjunction with the VIASURE SARS-CoV-2, Flu & RSV Real Time PCR Detection Kit (CerTest Biotec, S.L., Zaragoza, Spain). Methods: The specific detection capabilities of SARS-CoV-2, IAV/IBV, and RSV genes were evaluated using virus-spiked saliva and nasal swab samples. Using saliva samples, the viral titer detection limits of geneLEAD/VIASURE and manual referent singleplex RT-qPCR assays were compared. The performance of geneLEAD/VIASURE in analyzing single- and multiple-infection models was scrutinized. The concordance between the geneLEAD/VIASURE and the manual assays was assessed. Results: The geneLEAD/VIASURE successfully detected all the virus genes in the saliva and nasal swab samples despite some differences in the Ct values. The viral titer detection limits in the saliva samples for SARS-CoV-2, IAV, IBV, and RSV using geneLEAD/VIASURE were 10⁰, ≤10⁻², 10⁰, and 10² TCID₅₀/mL, respectively, compared to ≤10⁻¹, ≤10⁰, ≤10⁰, and ≤10⁴ TCID₅₀/mL, respectively, in the manual assays. geneLEAD/VIASURE yielded similar Ct values in the single- and multiple-infection models, with some exceptions noted in the triple-infection models when low titers of RSV were spiked with high titers of the other viruses. The concordance between geneLEAD/VIASURE and the manual assays was high, with Pearson’s R² values of 0.90, 0.85, 0.92, and 0.95 for SARS-CoV-2, IAV, IBV, and RSV, respectively. Conclusions: geneLEAD/VIASURE is a reliable diagnostic tool for detecting SARS-CoV-2, IAV/IBV, and RSV in single- and multiple-infection scenarios. Full article

Wastewater-based epidemiology (WBE) has historically proven to be a powerful surveillance tool, particularly during the SARS-CoV-2 pandemic. Effective WBE depends on the sensitive detection of pathogens in wastewater. However, determining the process limit of detection (PLOD) of WBE through a comprehensive evaluation that accounts for pathogen concentration, nucleic acid extraction, and molecular analysis has rarely been documented. We prepared dilution series with known concentrations of S. Typhi, V. cholerae, rotavirus, and SARS-CoV-2 in surface water and wastewater. Pathogen concentration was performed using Nanotrap particles with the KingFisher™ Apex robotic platform, followed by nucleic acid extraction. Quantitative real-time PCR (qPCR) and digital PCR (dPCR) were used to detect the extracted nucleic acids of the pathogens. The PLODs and recovery efficiencies for each of the four pathogens in surface water and wastewater were determined. Overall, the observed PLODs for S. Typhi, V. cholerae, and rotavirus in surface water and wastewater were approximately 3 log₁₀ loads (2.1–2.8 × 10³/10 mL) using either qPCR or dPCR as the detection method. For SARS-CoV-2, the PLOD in surface water was 2.9 × 10⁴/10 mL with both RT-qPCR and dPCR, one log₁₀ higher than the PLODs of the other three pathogens. In wastewater, the PLOD for SARS-CoV-2 was 2.9 × 10⁴/10 mL using RT-qPCR and 2.9 × 10³/10 mL using dPCR. The mean recovery rates of S. Typhi, V. cholerae, rotavirus, and SARS-CoV-2 for dPCR in both surface water and wastewater were below 10.4%, except for S. Typhi and V. cholerae in wastewater, which showed significantly higher recoveries, from 26.5% at 4.6 × 10⁵/10 mL for S. Typhi to 58.8% at 4.8 × 10⁵/10 mL for V. cholerae. Our study demonstrated that combining qPCR or dPCR analysis with automated Nanotrap particle concentration and nucleic acid extraction using the KingFisher™ platform enables the sensitive detection of S. Typhi, V. cholerae, rotavirus, and SARS-CoV-2 in surface water and wastewater. Full article

The Bacillus Calmette-Guérin (BCG) vaccine confers broad, non-specific immunity that may bolster defenses against respiratory viruses. While NOD2 (nucleotide-binding oligomerization domain-containing protein 2)-driven pathways are central to innate immune responses, the contribution of surface receptor modulation on monocytes to shaping these responses remains underexplored. We analyzed whole-blood cultures from BCG-vaccinated Polish children, stratified by serostatus to SARS-CoV-2 and RSV, and stimulated for 48 h with live BCG, purified viral antigens, or both. RT-qPCR quantified mRNA levels of NOD2 and key cytokines (IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, TNF), while flow cytometry assessed CD14, HLA-DR, CD11b, and CD206 expression. Co-stimulation with BCG + RSV elicited the strongest transcriptional response, notably a 2–4-fold upregulation of NOD2, IL-1β, and IL-6 versus RSV alone. In SARS-CoV-2(+) donors, RSV alone induced higher NOD2 expression than BCG or BCG + RSV, while IL-2 peaked following BCG + SARS-CoV-2. Across conditions, NOD2 positively correlated with IL-4 and IL-6 but negatively correlated with IL-1β in SARS-CoV-2 cultures. Viral antigens increased CD14 and HLA-DR on monocytes, suggesting activation; CD206 rose only in dual-seropositive children. Our findings indicate that BCG stimulation affects pediatric antiviral immunity through NOD2-related cytokine production and induction of a CD14⁺HLA-DR⁺ phenotype, supporting its potential role in boosting innate defenses against respiratory pathogens. Full article

(1) Background: The ongoing global health threat posed by SARS-CoV-2 requires reliable and accessible diagnostic tools, especially in resource-limited settings where RT-qPCR may be impractical. This study describes the development and validation of two enzyme-linked immunosorbent assays (ELISA) designed to detect anti-SARS-CoV-2 IgG antibodies employing recombinant S1 and S2 spike protein subunits. (2) Methods: The assays were optimized and validated using serum samples from 354 RT-qPCR-confirmed hospitalized patients and 337 pre-pandemic blood donors. (3) Results: The S1-based ELISA achieved a 52.8% sensitivity and a specificity of 93.5%, with an area under the ROC curve (AUC) of 71.6%. In contrast, the S2-based ELISA demonstrated superior diagnostic performance, with a sensitivity of 63.7%, a specificity of 99.7%, and an AUC of 83.1%. Cross-reactivity analysis using sera from individuals with unrelated infectious diseases confirmed the high specificity of the S2-ELISA. Time-stratified analysis revealed that sensitivity increased with time, peaking between 15 and 21 days post-symptom onset. Compared to commercial serological assays, the S2-ELISA demonstrated comparable or improved performance, particularly in specificity and diagnostic odds ratio. (4) Conclusions: The S2-ELISA offers a robust, highly specific, and operationally simple tool for serological detection of SARS-CoV-2 infection. Its strong diagnostic performance and accessibility make it well-suited for implementation in diverse epidemiological settings, particularly where molecular testing is limited. The development of affordable, validated serological assays such as this is critical for strengthening surveillance, understanding transmission dynamics, and informing public health responses. Full article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is known to affect multiple organ systems, including the respiratory tract and nervous and ocular systems. This retrospective study aimed to characterize the spatiotemporal distribution of viral antigen and associated pathological changes in the nose, lungs, brain, and eyes of K18-hACE2 mice intranasally infected with SARS-CoV-2. Using histology and immunohistochemistry, tissues were examined at 3, 6, and 7/8 days post-infection (dpi). In addition, lung and brain tissues were analyzed by means of RT-qPCR to determine viral RNA titers. Viral antigen was most pronounced in the nose, brain, and lung at 3, 6, and 7/8 dpi, respectively, whereas viral antigen was detected at 6 and 7/8 dpi in the retina. Quantitative PCR confirmed increasing viral RNA levels in both lung and brain, peaking at 7/8 dpi. Nasal and lung inflammation mirrored viral antigen distribution and localization. In the brain, the predominantly basal viral spread correlated with lymphohistiocytic meningoencephalitis, neuronal vacuolation, and altered neurofilament immunoreactivity. Retinal ganglion cells showed viral antigen expression without associated lesions. Microglial activation was evident in both the optic chiasm and the brain. These findings highlight the K18-hACE2 model’s utility for studying extrapulmonary SARS-CoV-2 pathogenesis. Understanding the temporal and spatial dynamics of viral spread enhances insights into SARS-CoV-2 neurotropism and its clinical manifestations. Full article

The recent COVID-19 pandemic has prompted the scientific community to prioritize the discovery of preventive methods and new therapeutics, including the investigation of natural compounds with antiviral potential. Fungal secondary metabolites (SMs) represent a promising source of antiviral drugs due to their structural diversity and intrinsic biocompatibility. Herein, the antiviral activity of 6-pentyl-α-pyrone (6PP) against bovine coronavirus (BCoV) has been evaluated in vitro. Considering that BCoV and SARS-CoV-2 are both members of the Betacoronavirus genus and share several key features, BCoV represents a valuable reference model for human coronavirus research. A non-cytotoxic dose of 6PP was used on MDBK cells to evaluate its antiviral activity against BCoV. Different experimental conditions were employed to examine cell monolayer protection both pre- and post-infection, as well as the potential inhibition of viral internalization. Overall, post-infection 6PP treatment reduced viral load and decreased viral internalization. Results were analyzed using viral titration and quantitative PCR, while data interpretation was performed by statistical software tools. This study presents a novel fluorescence quantification approach with high confidence demonstrated by its significant concordance with RT-qPCR results. These data suggest that 6PP could be an effective antiviral agent for BCoV, warranting further investigation of its role in coronavirus inhibition. Full article

SARS-CoV-2, a β-coronavirus, primarily affects the lungs, with non-specific lesions and no cytopathic viral effect in the skin. Cutaneous antiviral mechanisms include activation of TLR/IRF pathways and production of type I IFN. We evaluated the antiviral mechanisms involved in the skin of COVID-19 patients, including skin samples from 35 deceased patients who had contracted COVID-19 before the launch of the vaccine. Detection of SARS-CoV-2 in the skin was performed using transmission electron microscopy and RT-qPCR. Microscopic and molecular effects of the virus in skin were evaluated by histopathology, RT-qPCR, and immunohistochemistry (IHC). The results revealed the presence of SARS-CoV-2 and microscopic changes, including microvascular hyaline thrombi, perivascular dermatitis, and eccrine gland necrosis. There was increased transcription of TBK1 and a reduction in transcription of TNFα by RT-qPCR in the COVID-19 group. IHC revealed reduced expression of ACE2, TLR7, and IL-6, and elevated expression of IFN-β by epidermal cells. In the dermis, there was decreased expression of STING, IFN-β, and TNF-α and increased expression of IL-6 in sweat glands. Our results highlight the role of type I IFN in the skin of COVID-19 patients, which may modulate the cutaneous response to SARS-CoV-2. Full article

Background: Dental professionals were thought to have the most significant risk of coronavirus infection during the pandemic. Since the first Coronavirus Disease 2019 (COVID-19) patient was detected in Japan in January 2020, Japan has faced several waves of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections. However, no cluster of SARS-CoV-2 infections associated with dental procedures has been reported in Japan. In this study, we aimed to investigate the actual status of SARS-CoV-2 infection during the pandemic through antibody testing for dental professionals. We further investigated saliva and oral management-related aerosol to estimate the risk of virus transmission during dental procedures. Methods: SARS-CoV-2 antibody titer in the blood of dental professionals and their families was determined during the pre-vaccinated period of the SARS-CoV-2 wave to see the history of infection in Japan. Viral loads in saliva and in the aerosol generated during the oral management of COVID-19 patients were detected by RT-qPCR. Results: The antibody testing of dental healthcare providers during the early phases of the pandemic in Japan revealed low antibody positivity, which supported the low incidence of infection clusters among dental clinics. The aerosol generated during dental procedures may contain trace levels of SARS-CoV-2, indicating the risk of transmission through dental procedures is limited. Therefore, SARS-CoV-2 did not spread through dental clinics. Conclusions: Very few SARS-CoV-2 infections were observed in dental professionals who took appropriate infection control measures in the early period of the pandemic. Performing dental procedures using standard precautions seems to be sufficient to prevent SARS-CoV-2 infections. Full article

The high variability of human leukocyte antigen (HLA) genes results in each molecule having distinct antigenic peptide binding capacities, potentially influencing the immune response to SARS-CoV-2. This study aimed to investigate associations between HLA class I (A, B) and class II (DRB1) polymorphisms and COVID-19 severity in a South Brazilian population, and to evaluate the binding affinity of alleles to viral peptides. A cross-sectional study included 503 unvaccinated patients with RT-qPCR-confirmed COVID-19: 145 non-severe, 129 severe, and 229 critical. HLA typing was performed using PCR-SSO and Luminex™ technology. The DRB1*11 allelic group was significantly associated with protection against severe and critical cases, while DRB1*15 was associated with increased risk; both remained significant after Bonferroni correction. Other allelic groups were associated with disease outcomes but lost significance after correction: B*49 and B*08 (risk); and B*37, B*50, and A*03 (protection). In silico analysis revealed that the DRB1*15 allele group showed a higher proportion of strong binders, mostly from non-structural proteins, while DRB1*11:01 binders, though fewer in number, were concentrated in the M protein. These results suggest functional differences in antigen presentation and reinforce the relevance of class II HLA, particularly DRB1, in modulating COVID-19 severity. Full article

The aim of this study is to ascertain whether qRT-PCR (reverse transcriptase real-time PCR) or RT-ddPCR (reverse transcriptase digital droplet PCR) is more effective for detecting SARS-CoV-2 RNA (severe acute respiratory syndrome coronavirus 2 RNA) in blood plasma from COVID-19 (coronavirus infectious disease-19) patients. The E-gene of SARS-CoV-2 RNA was quantified using both methods in 128 plasma samples from 70 hospitalized patients, followed by a statistical analysis to compare the sensitivity and concordance between the methods. Out of the 128 samples, 89 yielded consistent results irrespective of the method used, whereas 39 samples showed discrepancies between the two different methods. RT-ddPCR frequently registered higher viral quantities compared to qRT-PCR; however, the results did not demonstrate a clear superiority in sensitivity for RT-ddPCR. Although RT-ddPCR registered higher viral quantities, this study concludes that both methods provide comparable results for detecting SARS-CoV-2 E-gene RNA in plasma. Full article

Wastewater surveillance has proven to be a cost-effective, non-invasive method for monitoring the spread and evolution of SARS-CoV-2, yet its value during today’s low-incidence phase is still being defined. Between August 2023 and July 2024, 42 composite wastewater samples were collected in Perugia, Italy and analyzed using RT-qPCR and whole-genome sequencing to identify circulating SARS-CoV-2 lineages. In parallel, clinical samples (respiratory tract samples) were collected and analyzed, allowing for direct comparisons to confirm the robustness of the wastewater findings. The sewage viral loads ranged from 8.9 × 10⁵ to 4.9 × 10⁷ genome copies inhabitant⁻¹ day⁻¹, outlining two modest community waves (September–December 2023 and May–July 2024). Sequencing resolved 403 Omicron lineages and revealed three successive subvariant phases: (i) XBB.* dominance (August–October 2023), when late-Omicron XBB subvariants (mainly EG.5.* and XBB.1.5) accounted for almost all genomes; (ii) a BA.2.86/JN surge (November 2023–March 2024), during which the BA.2.86 subvariant, driven mainly by its JN descendants (especially JN.1), rapidly displaced XBB.* and peaked at 89% in February 2024; and (iii) KP.* takeover (April–July 2024), with JN.1-derived KP subvariants rising steadily and KP.3 reaching 81% by July 2024, thereby becoming the dominant lineage. Comparisons of data from wastewater and clinical surveillance demonstrated how the former presented a much higher diversity of circulating viral lineages. Importantly, some subvariants (including BA.2.86*) were detected in wastewater weeks to months prior to clinical identification, and for longer periods. Taken together, the obtained data validated wastewater surveillance as an effective early warning system, especially during periods of low infection prevalence and/or limited molecular testing efforts. This methodology can thus complement clinical surveillance by offering valuable insights into viral dynamics at the community level and enhancing pandemic preparedness. Full article

Background: Respiratory droplets are the main way in which the COVID-19 pandemic’s causal agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), spreads. Angiotensin-converting enzyme 2 (ACE2) receptors, especially in lung cells, allow the virus to enter host cells. However, ACE2 expression in intestinal cells has sparked worries about possible fecal transfer, particularly in poor-sanitation areas like India. Methods: Between July 2021 and July 2024, clinical (nasopharyngeal, saliva, and stool samples) and sewage samples were collected from outpatient departments and sewage treatment plants (STPs), respectively, from the high-population-density area under study in order to investigate SARS-CoV-2 transmission. Results: This proof-of-concept study analyzed clinical samples from n = 60 COVID-19-positive patients at a central Indian tertiary care hospital and n = 156 samples from hospital STPs. Variants of SARS-CoV-2 were found using qRT-PCR and Next-Generation Sequencing (NGS). Of the n = 37 qRT-PCR-positive patients who gave their assent, 30% had stool samples that tested positive for viral RNA. In 70% of positive NP and 65% of positive saliva samples, along with two stool samples from immunocompromised patients, the live virus was identified using Vero E6 cell lines. Although 18% of the tests reported qRT-PCR-positive results, no live virus was detected in sewage samples despite NGS validation. The detection of SARS-CoV-2 in the absence of confirmed clinical cases may indicate the silent circulation of the virus within the community, suggesting that sewage surveillance can serve as an early warning system before an outbreak occurs. Conclusions: These findings provide critical insights into the importance of continuous environmental surveillance, silent virus circulation, changes in viral epidemiology throughout the years, and strategies to mitigate coronavirus outbreaks. Full article

Neurological symptoms involving the central nervous system (CNS) and peripheral nervous system (PNS) are common complications of acute COVID-19 as well as post-COVID conditions. Most research into these neurological sequalae focuses on the CNS, disregarding the PNS. Guinea pigs were previously shown to be useful models of disease during the SARS-CoV-1 epidemic. However, their suitability for studying SARS-CoV-2 has not been experimentally demonstrated. To assess the suitability of guinea pigs as models for SARS-CoV-2 infection and the impact of SARS-CoV-2 infection on the PNS, and to determine routes of CNS invasion through the PNS, we intranasally infected wild-type Dunkin-Hartley guinea pigs with ancestral SARS-CoV-2 USA-WA1/2020. We assessed PNS sensory neurons (trigeminal ganglia, dorsal root ganglia), autonomic neurons (superior cervical ganglia), brain regions (olfactory bulb, brainstem, cerebellum, cortex, hippocampus), lungs, and blood for viral RNA (RT-qPCR), protein (immunostaining), and infectious virus (plaque assay) at three- and six-days post infection. We show that guinea pigs, which have previously been used as a model of SARS-CoV-1 pulmonary disease, are not susceptible to intranasal infection with ancestral SARS-CoV-2, and are not useful models in assessing neurological impacts of infection with SARS-CoV-2 isolates from the early pandemic. Full article

SARS-CoV-2 is a highly contagious virus that infects humans, wildlife, domesticated and farmed animals. An increase in SARS-CoV-2 variants and human–animal interactions could have implications for the global maintenance and perpetuation of the virus. This study aimed to detect SARS-CoV-2 infection in dogs and cats living in households with and without SARS-CoV-2-positive owners by real-time reverse transcription polymerase chain reaction (qRT-PCR) in Grenada. This cross-sectional study was conducted from August 2020 to April 2022 from dogs (139) and cats (22) in households (96) in Grenada. Nasopharyngeal and oropharyngeal swabs were taken from the dogs and cats to detect SARS-CoV-2. qRT-PCR tests were performed targeting the E and RdRP genes, respectively. Notably, 12% (17/139) of dogs and 23% (5/22) of cats tested positive for SARS-CoV-2. The positive animals were found in 17 (18%) households, all with at least one positive individual. No positive cases of pets were detected in households without infected humans. A statistically significant association (p < 0.0001) was observed between humans with SARS-CoV2 and their pets. Phylogenetic tree analysis showed evidence of a relationship between the Grenadian SARS-CoV-2 E gene and other SARS-CoV-2 E gene sequences available in the NCBI database. This study confirmed the concurrent SARS-CoV-2 human/companion animal infection from households in Grenada. Humans and pet animals were positive synchronously; however, the direction of transmission from pets to humans or vice versa remains unknown. This study suggests that pets could play a role in the maintenance, transmission, and prolongation of infection of human-adapted pathogens such as SARS-CoV-2. Full article

Background/Objectives: Gene therapy has emerged as a promising strategy for treating a wide range of diseases. However, a major challenge remains in developing efficient and safe delivery systems for genetic material. Nanoparticles, particularly chitosan nanoparticles (CNPs), have gained significant attention as a potential solution. This study focuses on designing a SARS-CoV-2 plasmid DNA (pDNA) conjugated with CNPs and evaluating its in vitro delivery efficiency. Methods: The Omicron Spike DNA sequence was inserted into the pIRES2-eGFP expression vector, and CNPs were synthesized with optimized physicochemical properties to enhance stability, cellular uptake, and transfection efficiency. The conjugate was characterized using UV-Vis, FT-IR, DLS, and TEM techniques. Transfection efficiency was assessed and compared to the commercially available TurboFect reagent as a control. Results: CNPs-pDNA polyplexes with an average size of 159.0 ± 33.1 nm (TEM), a zeta potential of +19.7 ± 0.3 mV, and 100% ± 0.0 encapsulation efficiency were developed as a non-viral delivery system. CNPs efficiently serve as a delivery vehicle for the constructed pDNA without altering cell morphology, achieving transfection efficiencies of 62–74%, compared to 55–70% for TurboFect. Furthermore, RT-qPCR confirmed the expression of Spike mRNA, and Western blot assays validated the expression of Spike protein. Notably, Spike protein expression from CNPs was found to be two-fold higher than the control at 96 h post-transfection. Conclusions: These findings suggest that CNPs are a promising and versatile platform for delivering genetic material. Importantly, this study highlights the intrinsic properties of chitosan, without the use of additional ligands, as a key factor in achieving efficient gene delivery. Full article