Search Results (72)

The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its impact on public health continue to demand attention as the virus continues to evolve, demonstrating a remarkable ability to adapt to diverse selective pressures including immune responses, therapeutic treatments, and prophylactic interventions. The SARS-CoV-2 variant landscape remains dynamic, with new subvariants continuously emerging, many harboring spike protein mutations linked to immune evasion. In this study, we characterized a panel of live SARS-CoV-2 strains, including those key subvariants implicated in recent waves of infection. Our findings revealed a significant variability in mutation patterns in the spike protein across the strains analyzed. Commercial antibodies and human convalescent plasma (HCoP) samples from unvaccinated donors were ineffective in neutralizing the most recent Omicron subvariants, particularly after the emergence of JN.1 subvariant. Using human airway epithelial cells derived from healthy bronchiolar tissue (hBAEC), we established both monoinfections and coinfections involving SARS-CoV-2, Influenza A virus H1N1 (IFAV_H1N1) and Respiratory Syncytial Virus (RSV). Assessments were conducted to compare viral infectivity and the production and release of immune mediators in the apical and basolateral compartments. Notably, Omicron KP.3.1.1 subvariant induced a more pronounced cytopathic effect in hBAEC compared to its parental strain JN.1 and even surpassed the impact observed with the ancestral wild-type virus (WA1/2020, Washington strain). Furthermore, the coinfection of KP.3.1.1 subvariant with IFAV_H1N1 or RSV did not attenuate SARS-CoV-2 infectivity; instead, it significantly exacerbated the pathogenic synergy in the lung epithelium. Our study demonstrated that pro-inflammatory cytokines IL-6, IFN-β, and IL-10 were upregulated in hBAEC following SARS-CoV-2 monoinfection with recent Omicron subvariants as well as during coinfection with IFAV_H1N1 and RSV. Taken together, our findings offer new insights into the immune evasion strategies and pathogenic potential of evolving SARS-CoV-2 Omicron subvariants, as well as their interactions with other respiratory viruses, carrying important implications for therapeutic development and public health preparedness. Full article

Conventional diagnostic methods (CDMs) for lower respiratory infections (LRIs) have limitations in detecting causative pathogens. This study evaluates the utility of shotgun metagenomic sequencing (SMS) as a complementary diagnostic tool using bronchoalveolar lavage (BAL) fluid. Sixteen BAL fluid samples from pneumonia patients with positive CDM results—including bacterial/fungal cultures; PCR for Mycobacterium tuberculosis or cytomegalovirus; and the BioFire^® FilmArray^® Pneumonia Panel (BioFire Diagnostics LLC, Salt Lake City, UT, USA)—underwent 10 Gb SMS on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Reads were aligned to the NCBI RefSeq database; with fungal identification further supported by internal transcribed spacer (ITS) analysis. Antibiotic resistance genes (ARGs) were annotated using the Comprehensive Antibiotic Resistance Database. Microbial reads accounted for 0.00002–0.04971% per sample. SMS detected corresponding bacteria in 63% of cases, increasing to 69% when subdominant taxa were included. Fungal reads were low; however, Candida species were identified in four samples via ITS. No viral reads were detected. ARGs meeting perfect match criteria were found in two cases. This is the first real-world study comparing SMS with CDMs, including semiquantitative PCR, in BAL fluid for LRI. SMS shows promise as a supplementary diagnostic method, with further research needed to optimize its performance and cost-effectiveness. Full article

The aim of the study was to determine the prevalence rates of respiratory pathogens using syndromic tests and also to show which respiratory viruses were detected in suspected cases, especially during and after the pandemic period. A total of 1984 different respiratory tract samples from various departments were included and studied with the QIAstat-Dx device in 2021–2023. The samples were studied with the QIAstat-Dx1 Respiratory SARS-CoV-2 Panel. The kit used was a fully automated, multiplex syndromic test that detected SARS-CoV-2 and 21 other respiratory tract pathogens. As a result of the study, the prevalence of Rhinovirus/Enterovirus (RV/EV) (18.59%), RV/EV-SARS-CoV-2 (42.74%), SARS-CoV-2 (5.04%), and Influenza A Virus (IAV) (5.59%) agents was found to be higher than other agents during the period investigated. Among the 1984 patients examined, 959 (48.33%) had a single viral agent, 156 (7.86%) had double coinfection, 11 (0.55%) had triple coinfection and 1 patient had quadruple coinfection. Nearly half of the patients had a straightforward infection, which helps clinicians in directing specific treatment methods. The study results demonstrate that during the pandemic period, the detection of respiratory pathogens such as SARS-CoV-2 and RV/EV was not only critical for accurate diagnosis but also served as an important indicator of the broader epidemiological trends in respiratory infections. The seasonal distribution showed that while RV/EV was frequently present, its coinfection with SARS-CoV-2 was notably observed only in the first trimester. In light of our findings showing high rates of SARS-CoV-2 and RV/EV detection, along with diverse patterns of coinfection in clinical samples, such comprehensive testing not only assists in rapid diagnosis but also informs public health strategies by reflecting the evolving landscape of respiratory infections in the pandemic and post-pandemic era. Full article

Respiratory infections are the most common infectious diseases among children, representing a cause of death and generating a significant number of hospitalisations. The aim of the study was to analyse the epidemiological and clinical characteristics of viral pathogens causing respiratory tract infections in newborns and young children admitted to Galati pediatric hospital between October 2022 and December 2023. The diagnosis was performed using multiplex RT-PCR panels, which allowed simultaneous identification of respiratory pathogens (viruses and bacteria). From a total of 803 hospitalised patients with respiratory diseases, 607 (75.6%) children had a positive result for at least one respiratory virus and 96 patients (11.9%) were identified with bacterial infections. Mixed coinfections were found in almost half of the patients (44.5%). Most of RSV positive children had an increased length of stay, more than 7 days. It was shown a decline in severe cases of viral respiratory infections with prolonged hospitalisation as patients age up to 5 years. Full article

Objectives: We aimed to analyze the landscape of viral respiratory illnesses (VRIs) in a large metropolitan area in Southern California with a focus on the COVID-19 pandemic. Methods: We conducted a retrospective cohort study within the UCLA Health System, which evaluated children aged 0–5 years who received comprehensive respiratory viral panel (cRVP) testing during August–February of 2018–2023. The patient demographics, disease severity, and clinical course were specifically compared during the pandemic. Predictors of significant VRI were determined by multivariate logistic regression. Results: A total of 1321 children underwent cRVP testing, and 753 positive subjects were identified during the study period. Rhinovirus (RV) was by far the most frequent virus detected across 5 years, even during the COVID-19 pandemic, followed by respiratory syncytial virus (RSV). Along with RSV and human metapneumovirus, RV was identified as an independent risk for significant disease and occurred irrespective of co-infection with other viruses. Conclusions: RV was the most common viral pathogen in young children, even during the height of the COVID-19 pandemic, and was an independent driver of moderate-to-severe disease, particularly in children with comorbidities. Ethnic disparities were also observed as a risk for significant disease, underscoring the need for targeted interventions and heightened clinical vigilance in pediatric populations. Full article

Background: Human metapneumovirus (HMPV) is a significant cause of respiratory infections, particularly in children, the elderly, and immunocompromised individuals. However, data on HMPV infection in people living with HIV (PLWH) are limited, and cases of co-infection with influenza A virus in this population have not been previously described. Case Presentation: We reported the case of a 73-year-old HIV-positive man with multiple comorbidities, including insulin-dependent diabetes mellitus, who presented with fever, asthenia, and glycometabolic decompensation. Despite an initially unremarkable chest computed tomography (CT) scan, the patient developed progressive respiratory failure, requiring high-flow oxygen therapy. Molecular testing using the BIOFIRE^® FILMARRAY^® Pneumonia Panel Plus identified HMPV and influenza A virus as the causative pathogens. Bacterial cultures were negative, allowing for the discontinuation of empirical antibiotic therapy. The patient was successfully weaned off oxygen therapy and discharged after clinical improvement. Conclusions: This case highlights the potential severity of HMPV and influenza A co-infection in PLWH, emphasizing the importance of molecular diagnostics in distinguishing viral from bacterial infections. Rapid and accurate pathogen identification is essential for guiding appropriate antimicrobial stewardship and optimizing patient outcomes in community-acquired pneumonia. Full article

Background and Objectives: Childhood asthma represents a significant global public health issue and is the most common chronic disease among children. Hospitalization costs, especially for intensive care, are quite high. This study aimed to evaluate the characteristics, prognosis, and preventable risk factors of patients admitted to the Pediatric Intensive Care Unit (PICU) due to severe asthma exacerbations. Materials and Methods: We assessed patients admitted to the Ankara Bilkent City Hospital PICU from January 2013 to December 2022 diagnosed with asthma based on The Global Initiative for Asthma (GINA) criteria. The collected data encompassed demographic and clinical characteristics, intensive care treatments, hospitalization duration, atopic conditions, and respiratory viral panel results. The current clinical status was assessed using hospital records and caregiver interviews, with a focus on recent emergency admissions, ongoing treatments, exacerbation frequency, and asthma control based on GINA guidelines. Results: The study comprised 83 patients with a mean age of 72.9 (±45.5) months, predominantly male (63.9%). The average follow-up duration post-discharge was 40.7 ± 26.9 months. Patients received respiratory support in the PICU for a mean of 3.8 (±2.8) days and systemic steroid therapy for 4 (±1.5) days. Respiratory viral panel results identified pathogens in 42 patients, with rhinovirus being the most frequent. Post-discharge, 72.3% of patients continued follow-up at pediatric allergy clinics. Of the 60 patients contacted, 67.5% were on current asthma treatment and 48.2% had experienced an exacerbation in the past year. Asthma management steps remained unchanged for 33 patients, decreased for 13, and increased for 47 (44.6%). Asthma maintenance treatments pre-admission and post-discharge showed that 44.6% (n = 47) of the patients required an increase in their GINA treatment step after PICU admission, which was statistically significant (p < 0.001). History of atopic dermatitis was a significant risk factor for escalating treatment steps in both univariate and multivariate analyses (p = 0.018, p = 0.03). Conclusions: We found that admission to the PICU due to severe asthma exacerbation not only increases the risk of recurrent asthma exacerbations but also serves as a risk factor for stepping up maintenance treatment according to GINA guidelines during long-term follow-up. Full article

Background: The impact of respiratory viral infections associated with Kawasaki Disease (KD) cases on KD’s clinical presentation and initial response to treatment has not been clearly determined. Objective: This study aimed to evaluate respiratory viral infections using FilmArray Respiratory Panel (FARP) testing and analyze the effect of the concurrent presence of pathogens on clinical presentations of KD. Methods: Between January 2021 and June 2023, we conducted a retrospective, single-center observational study of 105 Japanese children with KD. KD was diagnosed and treated according to RAISE study guidelines, and the cases’ clinical information was assessed. FARP testing was performed in 71 out of 105 KD cases with fever and/or respiratory symptoms. Results: In 38 (53.5%) out of 71 cases, at least one virus was detected. The FARP-positive cases tended to have a higher frequency of Kobayashi scores (K-scores) ≥ 5 than the negative cases (42.1% vs. 21.2%), and lower initial treatment failure (7.89% vs. 21.2%). The most common virus detected was rhino/enterovirus (RV/EV: 27 cases), followed by seven cases of respiratory syncytial virus (RSV). RV/EV-positive KD cases did not differ significantly in their clinical data or the frequency of K-scores ≥ 5, and RSV-positive cases showed significantly elevated liver enzyme (AST:59 U/L (43.5–150.5) vs. 35 U/L (27–41), ALT:40 U/L (28.5–244.5) vs. 18 U/L (14–27)) and CRP levels (12 mg/dL (7.3–14.2) vs. 6.5 mg/dL (4.1–8.5)), and an increased frequency of K-scores ≥ 5 (71.4% vs. 21.2%) compared to FARP-negative cases. KD cases that were also RSV-positive or RV/EV-positive showed favorable responses to initial treatments. Conclusions: Concurrent respiratory virus infection could affect the clinical manifestation and initial treatment response of KD. Full article

Background/Objectives: Standard-of-care influenza vaccines contain antigens that are typically derived from components of wild type (WT) influenza viruses. Often, these antigens elicit strain-specific immune responses and are susceptible to mismatch in seasons where antigenic drift is prevalent. Thanks to advances in viral surveillance and sequencing, influenza vaccine antigens can now be optimized using computationally derived methodologies and algorithms to enhance their immunogenicity. Methods: Mice and ferrets that had been previously exposed to historical H1N1 and H3N2 influenza viruses were vaccinated intramuscularly with bivalent mixtures of H1 and H3 recombinant hemagglutinin (rHA) proteins, which were generated using a computationally optimized broadly reactive antigen (COBRA) design methodology. The vaccine antigens were mixed with a cationic lipid nanoparticle adjuvant, Infectimune^®, which promotes both humoral and cellular immune responses. Results: Mice and ferrets vaccinated with Infectimune^® and COBRA rHAs elicited protective antibody titers against panels of H1N1 and H3N2 influenza viruses isolated over the past 10 years. These animals also had antibodies that neutralized numerous modern H1N1 and H3N2 influenza viruses in vitro. When challenged with the A/Victoria/2570/2019 H1N1 influenza virus, the COBRA rHA vaccinated animals had minimal weight loss, and no detectable virus was present in their respiratory tissues on day 3 post-infection. Conclusions: These results demonstrate that COBRA rHA vaccines formulated with Infectimune^® elicit protective antibody responses against influenza strains, which were isolated across periods of time when standard-of-care vaccines were frequently reformulated, thus reducing the need to update vaccines on a nearly annual basis. Full article

Acute respiratory infection is one of the leading causes of morbidity and mortality among children in low- and middle-income countries. Due to limited diagnostic capability, many respiratory pathogens causing influenza-like illness go undetected. This study aims to detect enterovirus, respiratory syncytial virus, seasonal coronavirus and respiratory pathogens other than influenza in patients with influenza-like illness. A total of 997 (54.3%) respiratory samples (collected in the years 2016–2018) were randomly selected from 1835 influenza-negative samples. The xTAG Respiratory Viral Panel (RVP) FAST v2 panel was used to detect respiratory pathogens including enterovirus/rhinovirus (EV/RV), respiratory syncytial virus (RSV) and seasonal coronavirus (HKU1, OC43, NL63 and 229E). A total of 78.7% (785/997) were positive for respiratory viruses. Of these viruses, EV/RV was detected in 36.3% (362/997), which is the highest number, followed by RSV in 13.7% (137/997). The seasonal coronaviruses HKU1 and OC43 (1.5%, 15/997), NL63 (1.2%, 12/997) and 229E (1%, 10/997) were also detected. The EV/RV-positive samples were sequenced, of which 16.7% (5/30) were confirmed as EVs and were identified as coxsackievirus (CV) types CVB5, CVB3, CV21 and CVB2. The findings of this study highlight the importance of strengthening influenza-like illness surveillance programs in the region by including other respiratory viruses in their scope besides seasonal human influenza viruses. Full article

Objectives: Following the COVID-19 pandemic, global epidemiological trends demonstrate a return to pre-pandemic levels of respiratory syncytial virus (RSV) and influenza (Flu) A/B viruses. For the appropriate clinical management of viral infections, reliable and timely diagnosis is crucial. The clinical presentation of these respiratory viral infections shows significant overlaps; thus, the syndromic diagnosis of these infections becomes challenging. The goal of this study was to compare the performance of three multiplex real-time PCR-based platforms for the detection of SARS-CoV-2, Flu A, Flu B, and RSV. Materials and Methods: A retrospective study was performed on 200 de-identified nasopharyngeal and oropharyngeal specimens. All samples were tested simultaneously on three PCR-based platforms for the detection of SARS-CoV-2, Flu A, Flu B, and RSV: HealthTrackRx’s real-time PCR Open Array^® respiratory panel, TrueMark™ SARS-CoV-2, Flu A, Flu B, RSV Select Panel, and BioFire^® RP2.1 Panel. The positive and negative predictive value of each test was evaluated at a 95% confidence interval. Results: Among the 200 tested samples, the TrueMark™ and OpenArray^® laboratory-developed tests (LDTs) showed a 100% concordance for the detection of SARS-CoV-2, Flu A, Flu B, and RSV. Overall agreement of 100% was observed for nasopharyngeal samples between the laboratory-developed tests and FDA-approved BioFire^® RP2.1 Panel. Diagnostic results for these four respiratory viruses, in clinical samples, between the LDTs and the FDA-approved comparator demonstrated full concordance. Conclusions: Respiratory viral infections represent one of the major global healthcare burdens. Consequently, the accurate detection and surveillance of these viruses are critical, particularly when these viruses are known to co-circulate. The excellent performance and full concordance of the LDTs, with the BioFire^® Respiratory RP2.1 panel, in detecting SARS-CoV-2, Flu A, Flu B, and RSV shows that these tests can be confidently implemented for the clinical testing of respiratory viral infections. Full article

The emergence of novel pathogens, exemplified recently by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need for rapidly deployable and adaptable diagnostic assays to assess their impact on human health and guide public health responses in future pandemics. In this study, we developed an automated multiplex microscopy assay coupled with machine learning-based analysis for antibody detection. To achieve multiplexing and simultaneous detection of multiple viral antigens, we devised a barcoding strategy utilizing a panel of HeLa-based cell lines. Each cell line expressed a distinct viral antigen, along with a fluorescent protein exhibiting a unique subcellular localization pattern for cell classification. Our robust, cell segmentation and classification algorithm, combined with automated image acquisition, ensured compatibility with a high-throughput approach. As a proof of concept, we successfully applied this approach for quantitation of immunoreactivity against different variants of SARS-CoV-2 spike and nucleocapsid proteins in sera of patients or vaccinees, as well as for the study of selective reactivity of monoclonal antibodies. Importantly, our system can be rapidly adapted to accommodate other SARS-CoV-2 variants as well as any antigen of a newly emerging pathogen, thereby representing an important resource in the context of pandemic preparedness. Full article

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) continues to be a global threat due to its ability to evolve and generate new subvariants, leading to new waves of infection. Additionally, other coronaviruses like Middle East respiratory syndrome coronavirus (MERS-CoV, formerly known as hCoV-EMC), which first emerged in 2012, persist and continue to present a threat of severe illness to humans. The continued identification of novel coronaviruses, coupled with the potential for genetic recombination between different strains, raises the possibility of new coronavirus clades of global concern emerging. As a result, there is a pressing need for pan-CoV therapeutic drugs and vaccines. After the extensive optimization of an HCV protease inhibitor screening hit, a novel 3CLPro inhibitor (MK-7845) was discovered and subsequently profiled. MK-7845 exhibited nanomolar in vitro potency with broad spectrum activity against a panel of clinical SARS-CoV-2 subvariants and MERS-CoV. Furthermore, when administered orally, MK-7845 demonstrated a notable reduction in viral burdens by >6 log orders in the lungs of transgenic mice infected with SARS-CoV-2 (K18-hACE2 mice) and MERS-CoV (K18-hDDP4 mice). Full article

In Sicily (Italy), respiratory syncytial virus (RSV), rhinovirus (HRV), and influenza virus triggered epidemics among children, resulting in an increase in acute respiratory tract infections (ARTIs). Our objective was to capture the epidemiology of respiratory infections in children, determining which pathogens were associated with respiratory infections following the lockdown and whether there were changes in the epidemiological landscape during the post-SARS-CoV-2 pandemic era. Materials and Methods: We analyzed multiplex respiratory viral PCR data (BioFire^® FilmArray^® Respiratory Panel 2.1 Plus) from 204 children presenting with respiratory symptoms and/or fever to our Unit of Pediatrics and Pediatric Emergency. Results: Viruses were predominantly responsible for ARTIs (99%), with RSV emerging as the most common agent involved in respiratory infections, followed by human rhinovirus/enterovirus and influenza A. RSV and rhinovirus were also the primary agents in coinfections. RSV predominated during winter months, while HRV/EV exhibited greater prevalence than RSV during the fall. Some viruses spread exclusively in coinfections (human coronavirus NL63, adenovirus, metapneumovirus, and parainfluenza viruses 1–3), while others primarily caused mono-infections (influenza A and B). SARS-CoV-2 was detected equally in both mono-infections (41%) and coinfections (59%). Conclusions: Our analysis underlines the predominance of RSV and the importance of implementing preventive strategies for RSV. Full article

Elevated immunoglobulin E (IgE) levels are commonly associated with allergies. However, high IgE levels are also found in several other infectious and non-infectious disorders. Elevated IgE levels typically suggest allergies, eczema, or recurrent skin infections. Hyperimmunoglobulin E (hyper-IgE) levels typically reflect a monogenic atopic condition or inborn immune defects with an atopic phenotype. The aim of our research is to investigate and observe the clinical characteristics of children with increased IgE levels who have previously manifested infectious diseases. Furthermore, the retrospective study considers other factors, such as demographic characteristics (sex, area/environment, and age), and their effect on IgE serum levels. To answer this question, we conducted a one-year hospital-based retrospective study that included 200 hospitalized children who had at least two viral or bacterial infections in the six months preceding hospitalization. Measurements of IgE and allergen panels (respiratory and digestive) using blood samples revealed that individuals who tested positive for the body’s synthesis of hyper-IgE were not observably allergic to any potential allergens despite having higher total serum IgE. According to the results, there was a strong correlation between elevated IgE serum levels and a history of infectious diseases among the patients. Full article