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1.
Methods Mol Biol ; 2857: 33-43, 2025.
Article in English | MEDLINE | ID: mdl-39348053

ABSTRACT

Immunosenescence is a well-characterized phenomenon that occurs with increasing age in all immune and somatic cells. In order to best study immunosenescence, it is imperative to develop methods to accurately identify immunosenescent cells. Elderly patients are known to have impaired immune responses to respiratory viruses, and it is hypothesized that this is due, in part, to immunosenescent, terminally exhausted CD8+ T cells. To test this hypothesis, we developed an aged mouse model and a flow cytometry protocol using the Cytek® Aurora to assess the CD8+ T-cell response during respiratory viral infection and identify immunosenescent CD8+ T cells. This protocol and our aged mouse model have great potential to be incredibly valuable for future studies elucidating how to rejuvenate and possibly reverse immunosenescent CD8+ T cells, which could improve the immune response to respiratory viruses in this at-risk population.


Subject(s)
CD8-Positive T-Lymphocytes , Flow Cytometry , Immunosenescence , Respiratory Tract Infections , CD8-Positive T-Lymphocytes/immunology , Animals , Mice , Respiratory Tract Infections/immunology , Respiratory Tract Infections/virology , Flow Cytometry/methods , Immunosenescence/immunology , Disease Models, Animal , Virus Diseases/immunology , Humans
2.
Rev Med Suisse ; 20(889): 1747-1750, 2024 Oct 02.
Article in French | MEDLINE | ID: mdl-39359214

ABSTRACT

Recurrent respiratory papillomatosis is a chronic infection of the airway mucosa by the human papilloma virus, in the form of recurrent exophytic papilloma. Two clinical forms are distinguished: juvenile and adult onset. Depending on their size and location, papilloma can cause dysphonia, pharyngeal discomfort, until obstruction of the airway. There is no curative treatment. The management strategy is to surgically remove symptomatic disease by transoral approach, but some recurrent disease require multiple interventions and -adjuvant therapies. The symptoms caused by the disease as well as treatments' side effects have a major impact on patient's quality of life. Vaccination against HPV currently represents the best strategy to prevent disease.


La papillomatose respiratoire récurrente est une infection chronique de la muqueuse des voies aériennes par le virus du papillome humain sous forme de papillomes exophytiques récidivants. Deux formes cliniques sont décrites : juvénile et adulte. Selon leurs taille et localisation, les papillomes peuvent être responsables d'une dysphonie, d'une gêne pharyngée, jusqu'à l'obstruction des voies respiratoires. Il n'y a pas de traitement curatif définitif. La stratégie est chirurgicale par l'ablation des lésions symptomatiques par voie endoscopique, mais certaines maladies récidivantes nécessitent de multiples interventions en plus des thérapies adjuvantes. L'impact sur la qualité de vie est majeur, à travers les symptômes occasionnés et les séquelles des traitements. La vaccination représente le meilleur espoir d'éradication de la maladie.


Subject(s)
Papillomavirus Infections , Respiratory Tract Infections , Humans , Papillomavirus Infections/diagnosis , Papillomavirus Infections/complications , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Respiratory Tract Infections/therapy , Papillomavirus Vaccines/administration & dosage , Quality of Life
4.
Ann Clin Microbiol Antimicrob ; 23(1): 88, 2024 Sep 30.
Article in English | MEDLINE | ID: mdl-39350160

ABSTRACT

BACKGROUND: Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited. METHODS: To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis. RESULTS: In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS. CONCLUSION: In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS.


Subject(s)
Bronchoalveolar Lavage Fluid , High-Throughput Nucleotide Sequencing , Immunocompromised Host , Metagenomics , Respiratory Tract Infections , Humans , High-Throughput Nucleotide Sequencing/methods , Male , Female , Metagenomics/methods , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/microbiology , Middle Aged , Bronchoalveolar Lavage Fluid/microbiology , Aged , Adult , Sensitivity and Specificity , Bacteria/genetics , Bacteria/isolation & purification , Bacteria/classification , Young Adult
5.
Virol J ; 21(1): 237, 2024 Sep 30.
Article in English | MEDLINE | ID: mdl-39350296

ABSTRACT

Respiratory pathogens infecting the human respiratory system are characterized by their diversity, high infectivity, rapid transmission, and acute onset. Traditional detection methods are time-consuming, have low sensitivity, and lack specificity, failing to meet the needs of rapid clinical diagnosis. Nucleic acid aptamers, as an emerging and innovative detection technology, offer novel solutions with high specificity, affinity, and broad target applicability, making them particularly promising for respiratory pathogen detection. This review highlights the progress in the research and application of nucleic acid aptamers for detecting respiratory pathogens, discussing their selection, application, potential in clinical diagnosis, and future development. Notably, these aptamers can significantly enhance the sensitivity and specificity of detection when combined with detection techniques such as fluorescence, colorimetry and electrochemistry. This review offers new insights into how aptamers can address the limitations of traditional diagnostic methods and advance clinical diagnostics. It also highlights key challenges and future research directions for the clinical application of nucleic acid aptamers.


Subject(s)
Aptamers, Nucleotide , Respiratory Tract Infections , Sensitivity and Specificity , Humans , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Respiratory Tract Infections/microbiology , Viruses/isolation & purification , Viruses/genetics , Viruses/classification , Bacteria/isolation & purification , Bacteria/genetics , SELEX Aptamer Technique/methods , Virus Diseases/diagnosis , Virus Diseases/virology , Molecular Diagnostic Techniques/methods
6.
Front Immunol ; 15: 1443665, 2024.
Article in English | MEDLINE | ID: mdl-39355253

ABSTRACT

Introduction: Respiratory viral infections (RVIs) are a major global contributor to morbidity and mortality. The susceptibility and outcome of RVIs are strongly age-dependent and show considerable inter-population differences, pointing to genetically and/or environmentally driven developmental variability. The factors determining the age-dependency and shaping the age-related changes of human anti-RVI immunity after birth are still elusive. Methods: We are conducting a prospective birth cohort study aiming at identifying endogenous and environmental factors associated with the susceptibility to RVIs and their impact on cellular and humoral immune responses against the influenza A virus (IAV), respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The MIAI birth cohort enrolls healthy, full-term neonates born at the University Hospital Würzburg, Germany, with follow-up at four defined time-points during the first year of life. At each study visit, clinical metadata including diet, lifestyle, sociodemographic information, and physical examinations, are collected along with extensive biomaterial sampling. Biomaterials are used to generate comprehensive, integrated multi-omics datasets including transcriptomic, epigenomic, proteomic, metabolomic and microbiomic methods. Discussion: The results are expected to capture a holistic picture of the variability of immune trajectories with a focus on cellular and humoral key players involved in the defense of RVIs and the impact of host and environmental factors thereon. Thereby, MIAI aims at providing insights that allow unraveling molecular mechanisms that can be targeted to promote the development of competent anti-RVI immunity in early life and prevent severe RVIs. Clinical trial registration: https://drks.de/search/de/trial/, identifier DRKS00034278.


Subject(s)
COVID-19 , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Tract Infections , Female , Humans , Infant , Infant, Newborn , Male , Birth Cohort , COVID-19/immunology , Germany/epidemiology , Influenza, Human/immunology , Prospective Studies , Respiratory Tract Infections/immunology , Respiratory Tract Infections/virology , Respiratory Syncytial Virus Infections/immunology , Research Design
7.
Arch Virol ; 169(11): 219, 2024 Oct 10.
Article in English | MEDLINE | ID: mdl-39387930

ABSTRACT

Acute lower respiratory tract infections (ALRTIs) are a leading cause of mortality in young children worldwide due to human respiratory syncytial virus (RSV). The aim of this study was to monitor genetic variations in RSV and provide genomic data support for RSV prevention and control. A total of 105 complete RSV genome sequences were determined during 2017-2020. Phylogenetic analysis showed that all of the RSVA sequences were of genotype ON1, and all of the RSVB sequences were of genotype BA9. Notably, a phylogenetic tree based on the whole genome had more branches than a tree based on the G gene. In comparison to the RSV prototype sequences, 71.43% (50/70) of the ON1 sequences had five amino acid substitutions (T113I, V131N, N178G, H258Q, and H266L) that occurred simultaneously, and 68.57% (24/35) of the BA9 genotype sequences had 12 amino acid substitutions, four of which (A131T, T137I, T288I, and T310I) occurred simultaneously. In the F gene, there were 19 amino acid substitutions, which were mainly located in the antigenic sites Ø, II, V, and VII. Other amino acid substitutions were found in the NS1, NS2, P, SH, and L proteins. No significant evidence of recombination was found in any of the sequences. These findings provide important data that will be useful for prevention, control, and vaccine development against RSV.


Subject(s)
Genome, Viral , Genotype , Phylogeny , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Humans , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/classification , Respiratory Syncytial Virus, Human/isolation & purification , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus Infections/epidemiology , China/epidemiology , Genome, Viral/genetics , Amino Acid Substitution , Child , Genetic Variation , Child, Preschool , Infant , Genomics , Respiratory Tract Infections/virology , Respiratory Tract Infections/epidemiology
8.
Euro Surveill ; 29(41)2024 Oct.
Article in English | MEDLINE | ID: mdl-39392006

ABSTRACT

We report a considerable increase in enterovirus D68 (EV-D68) cases since July 2024, culminating in an ongoing outbreak of acute respiratory infections in northern Italy, accounting for nearly 90% of all enterovirus infections. The outbreak was identified by community- and hospital-based surveillance systems, detecting EV-D68 in individuals with mild-to-severe respiratory infections. These strains belonged to B3 and a divergent A2 lineage. An increase in adult cases was observed. Enhanced surveillance and molecular characterisation of EV-D68 across Europe are needed.


Subject(s)
Disease Outbreaks , Enterovirus D, Human , Enterovirus Infections , Respiratory Tract Infections , Humans , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Respiratory Tract Infections/diagnosis , Enterovirus Infections/epidemiology , Enterovirus Infections/diagnosis , Enterovirus Infections/virology , Italy/epidemiology , Enterovirus D, Human/isolation & purification , Enterovirus D, Human/genetics , Adult , Adolescent , Child , Male , Child, Preschool , Female , Middle Aged , Infant , Aged , Young Adult , Population Surveillance , Phylogeny
9.
BMC Complement Med Ther ; 24(1): 359, 2024 Oct 07.
Article in English | MEDLINE | ID: mdl-39375630

ABSTRACT

INTRODUCTION: When young children experience recurrent respiratory infections, caregivers face the challenge of preventing new episodes whilst maintaining close rapport with their children. Pediatric massage, such as pediatric Tuina, entails soft massage of the skin, administered by trained providers. This non-pharmaceutical measure is used to prevent new respiratory infections in China. The aim of this study is to deepen our understanding of caregivers' experiences and perceptions of providing pediatric Tuina treatment to their children with recurrent respiratory tract infections. METHODS: A qualitative study, based on semi-structured interviews, was conducted in accordance with the Consolidated Criteria for Reporting Qualitative Research checklist. Sixteen mothers from Southern China, whose children had received pediatric Tuina for recurrent respiratory tract infections, participated online. Analysis was conducted according to the principles of reflexive thematic analysis, using the NVivo qualitative research software. RESULTS: The overarching theme was "Fostering embodied care with children". Caregivers assessed pediatric Tuina by hearing others' experiences of pediatric Tuina, as well as observing the manipulations on their child's body and their bodily reactions during pediatric Tuina sessions. Caregivers also closely observed children's bodily changes after pediatric Tuina sessions. Embodied attachment between children and adults was nurtured through the pediatric Tuina. Compared to other treatments or medical consultations, children were more relaxed and more involved in embodied care, which involved direct skin touching and verbal communication from the pediatric Tuina provider. Children also took the initiative to bring pediatric Tuina into their family life, by asking caregivers to perform it on them and mimicking the manipulations on the caregivers' hand. CONCLUSIONS: Pediatric Tuina served as a means of interaction between children and adults, fostering an embodied care on both a physical and emotional level. Beyond its potentially preventive effect on recurrent respiratory tract infections, pediatric Tuina could be a support for parents of children with recurrent or chronic disease at home.


Subject(s)
Qualitative Research , Respiratory Tract Infections , Humans , Respiratory Tract Infections/therapy , China , Female , Child, Preschool , Male , Adult , Massage/methods , Child , Infant , Caregivers/psychology , Mothers/psychology
10.
J Med Virol ; 96(10): e29954, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39377494

ABSTRACT

Transmembrane protein 176B (TMEM176B), localized mainly on the endosomal membrane, has been reported as an immune regulatory factor in malignant diseases. However, the biological function of this molecule remains undetermined during respiratory viral infections. To investigate the functions and prognostic value of this gene, six gene sets were selected from the Gene Expression Omnibus database for research. First, the function of TMEM176B and its co-expressed genes were evaluated at different levels (cell, peripheral blood, lung tissue). Afterwards, a machine learning algorithm was utilized to analyze the relationship between TMEM176B and its interacting genes with prognosis. After importance evaluation and variable screening, a prognostic model was established. Finally, the reliability of the model was further verified through external data sets. In vitro experiments were conducted to validate the function of TMEM176B. TMEM176B and its co-expressed genes are involved in multiple processes such as inflammasome activation, myeloid immune cell development, and immune cell infiltration. Machine learning further screened 27 interacting gene modules including TMEM176B as prognostic models for severe respiratory viral infections, with the area under the ROC curve (AUCs) of 0.986 and 0.905 in derivation and external validation sets, respectively. We further confirmed that viral load as well as NLRP3 activation and cell death were significantly enhanced in TMEM176B-/- THP-1-differentiated macrophages via in vitro experiments. Our study revealed that TMEM176B is involved in a wide range of biological functions in respiratory viral infections and has potential prognostic value, which is expected to bring new insights into the clinical management of severe respiratory viral infection hosts.


Subject(s)
Membrane Proteins , Respiratory Tract Infections , Single-Cell Analysis , Humans , Membrane Proteins/genetics , Respiratory Tract Infections/virology , Respiratory Tract Infections/genetics , Respiratory Tract Infections/immunology , Prognosis , Single-Cell Analysis/methods , Machine Learning , Sequence Analysis, RNA , Gene Expression Profiling
11.
BMC Infect Dis ; 24(1): 1128, 2024 Oct 09.
Article in English | MEDLINE | ID: mdl-39385077

ABSTRACT

BACKGROUND: Identifying risk factors for respiratory syncytial virus (RSV)-associated severe acute respiratory illness (SARI) will assist with targeting vaccine interventions. METHODS: Using surveillance data from South Africa (2012-2018), we compared the characteristics of individuals with RSV-associated influenza-like illness (ILI) (reference group) to those with RSV-associated SARI to describe factors associated with SARI using a multivariable analysis. RESULTS: RSV was detected in 6% (483/7792) of ILI cases and 15% (844/5672) of SARI cases. Factors associated with SARI in children included age < 2 months, compared to age 2-4 years (adjusted odds ratio (aOR) 54.4; 95% confidence interval (CI) 23.5-125.8), malnutrition (aOR 1.9; 95% CI 1.2-3.2), prematurity (aOR 2.4; 95% CI 1.3-4.6) and living with HIV (LWH) (aOR 22.5; 95% CI 2.9-174.3). In individuals ≥ 5 years, factors associated with SARI included age ≥ 65 years compared to age 5-24 years (aOR 10.7; 95% CI 1.1-107.5), symptom duration ≥ 5 days (aOR 2.7; 95% CI 1.1-6.3), underlying illness (aOR 2.7; 95% CI 1.5-26.1) and LWH (aOR 16.8, 95% CI: 4.8-58.2). CONCLUSION: Individuals at the extremes of age and those with identified risk factors might benefit most from RSV prevention interventions. CLINICAL TRIAL NUMBER: Not applicable, this is not a clinical trial.


Subject(s)
HIV Infections , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Humans , South Africa/epidemiology , Respiratory Syncytial Virus Infections/epidemiology , Risk Factors , Female , Infant , Child, Preschool , Male , HIV Infections/epidemiology , HIV Infections/complications , Adult , Child , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Prevalence , Adolescent , Young Adult , Middle Aged , Infant, Newborn , Aged
12.
BMC Infect Dis ; 24(1): 1129, 2024 Oct 09.
Article in English | MEDLINE | ID: mdl-39385082

ABSTRACT

OBJECTIVE: To investigate the epidemiological characteristics and infections of respiratory syncytial virus (RSV) and influenza viruses in hospitalized elderly patients with respiratory tract infections in Suzhou City, China, and to compare the differences in clinical characteristics and economic burden associated with these two infections. METHODS: In this prospective study, pathogenetic testing and clinical data for hospitalized patients aged 60 years and older with respiratory tract infections were collected in five hospitals through stratified cluster sampling from December 2023 to May 2024. Comparative study on epidemic characteristics, clinical features and costs of cases who infected RSV alone and influenza alone were conducted. RESULTS: Among 1,894 cases included, the RSV positivity rate was 5.91% during the 2023-2024 winter-spring season, while the influenza positivity rate was 9.61%. RSV-B was the predominant subtype of RSV, and influenza A (primarily H3N2) was the dominant strain among the influenza-positive cases. Compared with cases infected influenza virus alone, those infected RSV alone had lower occurrence frequency of fever (18.8% vs. 35.7%, P = 0.004), higher occurrence frequency of complications of lower respiratory tract infections (70.8% vs. 54.8%, P = 0.011), higher direct medical costs ($996.2 vs. $841.1, P = 0.017) and total costs ($1019.7 vs. $888.1, P = 0.036). RSV single infection is more common in female cases (P = 0.007) and diabetic cases (P = 0.007) than influenza virus single infection. CONCLUSIONS: During the winter and spring months, RSV is the second most common pathogen after influenza virus among older adults hospitalized for respiratory infections in Suzhou, China. Patients infected RSV are more likely to develop complications with lower respiratory tract infections and have higher medical costs than the influenza. RSV infection in the elderly should be emphasized, especially in female patients and diabetic patients.


Subject(s)
Influenza, Human , Respiratory Syncytial Virus Infections , Humans , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/economics , Influenza, Human/epidemiology , Influenza, Human/economics , Influenza, Human/virology , Aged , Female , Male , China/epidemiology , Prospective Studies , Middle Aged , Aged, 80 and over , Hospitalization/statistics & numerical data , Seasons , Respiratory Syncytial Virus, Human/isolation & purification , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology
14.
PLoS One ; 19(10): e0307322, 2024.
Article in English | MEDLINE | ID: mdl-39361667

ABSTRACT

BACKGROUND: Respiratory viruses have clinical and epidemiological importance. With the COVID-19 pandemic, interest has focused on SARS-CoV-2, but as a result, the number of samples available for the differential diagnosis of other respiratory viruses has increased. STUDY DESIGN: Cross-sectional study. OBJECTIVE: To describe the epidemiological behavior of respiratory viruses based on a laboratory-based epidemiological surveillance system using data from 2017 to 2023. METHODS: Univariate, bivariate and multivariate analyses of data from a laboratory database of respiratory viruses detected by multiplex RT‒qPCR were performed. RESULTS: A total of 4,632 samples with positive results for at least 1 respiratory virus, not including influenza or SARS-CoV-2, were analyzed. The most common virus detected was respiratory syncytial virus in 1,467 (26.3%) samples, followed by rhinovirus in 1,384 (24.8%) samples. Most of the samples were from children under 5 years of age. The age-adjusted odds ratio (OR) of death for patients infected with parainfluenza virus 4 was 4.1 (95% confidence interval [95% CI] 2.0-8.2). CONCLUSION: Respiratory syncytial virus and rhinovirus had the highest frequency and proportion of coinfections, whereas parainfluenza virus 4 was associated with an increased risk of death.


Subject(s)
Respiratory Tract Infections , Humans , Child, Preschool , Infant , Child , Middle Aged , Female , Adult , Adolescent , Male , Cross-Sectional Studies , Aged , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Young Adult , Epidemiological Monitoring , COVID-19/epidemiology , COVID-19/virology , Coinfection/epidemiology , Coinfection/virology , Rhinovirus/isolation & purification , Rhinovirus/genetics , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus Infections/diagnosis , Infant, Newborn , SARS-CoV-2/isolation & purification
15.
J Med Virol ; 96(10): e29957, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39370869

ABSTRACT

This study aimed to assess the impact of COVID-19 on the prevalence of adenovirus (AdV) infection in children. This study retrospectively analyzed the changes in the epidemiological and clinical features of AdV-associated respiratory infections in children in Hangzhou, China, between January 2019 and July 2024. A total of 771 316 samples were included in the study, and the positive rate was 6.10% (47 050/771 316). Among them, the positive rate of AdV infection was highest in 2019, reaching 11.29% (26 929/238 333), while the positive rates in the remaining years were between 2% and 9%. In terms of seasonal epidemic characteristics, the summer of 2019 was the peak of AdV incidence, with the positive rate peaking at around 16.95% (7275/45 268), followed by a gradual decline and a low-level epidemic in winter, with a positive rate of 8.79% (8094/92 060). However, during the period 2020-2024, the AdV epidemic season did not show any significant regularity. Gender analysis revealed that the positive rate of male patients was generally greater than that of female patients. In different age groups, the population susceptible to AdV changed before and after the epidemic. In the early and middle stages of the COVID-19 epidemic, the susceptible population was mainly 2-5 years old, whereas in the later stages of the epidemic, the susceptible population was 5-18 years old. In addition, the main clinical symptoms of AdV-positive children from 2019-2024 were respiratory tract symptoms and fever. In summary, the COVID-19 epidemic has had a certain impact on the prevalence of AdV. These findings provide an important basis and reference for the prevention and diagnosis of AdV, especially in the context of increasing age- and gender-specific public health strategies.


Subject(s)
COVID-19 , Respiratory Tract Infections , Seasons , Humans , China/epidemiology , Male , Female , Child, Preschool , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Child , Infant , Retrospective Studies , Adolescent , COVID-19/epidemiology , COVID-19/virology , Adenovirus Infections, Human/epidemiology , Adenovirus Infections, Human/virology , Prevalence , Infant, Newborn , SARS-CoV-2 , Incidence , Adenoviridae Infections/epidemiology , Adenoviridae/isolation & purification , Adenoviridae/genetics , Adenoviruses, Human/isolation & purification , Adenoviruses, Human/genetics , Adenoviruses, Human/classification
16.
BMC Res Notes ; 17(1): 291, 2024 Oct 03.
Article in English | MEDLINE | ID: mdl-39363203

ABSTRACT

OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment. RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.


Subject(s)
Metagenomics , Respiratory Tract Infections , Metagenomics/methods , Humans , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/diagnosis , Metagenome/genetics , Computational Biology/methods , Reproducibility of Results , Nasopharynx/microbiology , Nasopharynx/virology
17.
BMJ Paediatr Open ; 8(1)2024 Oct 04.
Article in English | MEDLINE | ID: mdl-39366747

ABSTRACT

INTRODUCTION: Febrile infants under 3 months of age are at risk of invasive bacterial infection (IBI). It is currently unclear if testing for respiratory viruses may have a role in IBI risk stratification. If found to be associated with the likelihood of IBI, respiratory viral point-of-care testing may improve patient and caregiver experience, reduce costs and enhance antimicrobial stewardship. METHODS AND ANALYSIS: This is a study protocol for a systematic review and meta-analysis that aims to answer the following question: In young febrile infants presenting to emergency care settings does a positive respiratory viral test for RSV, Influenza or SARS-CoV2 (relative to a negative test) add value to current risk stratification pathways for the exclusion of invasive bacterial infection, subsequently enabling safe de-escalation of investigation and treatment?A search strategy will include MEDLINE, EMBASE, Web of Science, The Cochrane Library and grey literature. Abstracts and then full texts will be independently screened for selection. Data extraction and quality assessment will be completed by two independent authors.The primary objective is to analyse the ability of a positive respiratory viral test to identify the overall risk of IBI. The secondary objective is to perform a subgroup analysis to investigate how the risk stratification alters based on other variables including virus type, patient characteristics and the presence of an identified source of fever.Bivariate random-effects meta-analysis will be undertaken. Diagnostic odds ratios (OR), sensitivity, specificity and positive and negative likelihood ratios will be calculated. The degree of heterogeneity and publication bias will be investigated and presented. ETHICS AND DISSEMINATION: Ethical approval is not required. We will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to disseminate the study results through publication and conference presentations. PROSPERO REGISTRATION NUMBER: This protocol is registered in PROSPERO-ID number: CRD42023433716.


Subject(s)
Fever , Meta-Analysis as Topic , Systematic Reviews as Topic , Humans , Infant , Fever/diagnosis , Fever/virology , Risk Assessment/methods , Research Design , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , COVID-19/diagnosis , Influenza, Human/diagnosis , Influenza, Human/virology , Bacterial Infections/diagnosis , Respiratory Syncytial Virus Infections/diagnosis , Point-of-Care Testing
18.
Clin Respir J ; 18(10): e70011, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39367675

ABSTRACT

OBJECTIVE: Researches on the epidemiology of various respiratory pathogens at multiple testing points in the pediatric population are limited, and these are crucial for the prevention of respiratory tract infections in children. METHODS: We obtained 1788 upper respiratory tract swabs from children exhibiting symptoms of respiratory infection (notably fever with a body temperature exceeding 38.5°C) across five hospitals in Guangdong between November 2020 and June 2022. We used the multiplex probe amplification (MPA) PCR testing to identify 11 respiratory viruses and subsequently analyzed the prevalence characteristics of these pathogens among febrile children in hospitals. RESULTS: The overall detection rate of the pathogens was 58.1% (1039/1788). Human rhinovirus (HRV) exhibited the highest detection rate at 19.0% (339/1788), succeeded by human parainfluenza virus (HPIV), human adenovirus (HAdV), and respiratory syncytial virus (RSV). The positivity and coinfection rates were higher in children aged 5 years and below compared to those above 5 years. Moreover, a distinct pathogen spectrum was observed across different age groups. Hospitalized patients demonstrated a significantly higher positivity and coinfection rate compared to outpatients. During COVID-2019, RSV appeared a counter-seasonal trend. CONCLUSION: Respiratory viral infections in children display distinct characteristics concerning age, hospitalization status, and seasonality. Children under the age of 5 and minor patients admitted to hospitals at least be tested for RSV, HRV, HPIV, and HAdV. The epidemiological patterns of RSV in the post-epidemic period require ongoing surveillance.


Subject(s)
Respiratory Tract Infections , Humans , Child, Preschool , China/epidemiology , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Male , Female , Child , Infant , Prevalence , Coinfection/epidemiology , Rhinovirus/isolation & purification , Rhinovirus/genetics , Adolescent , Hospitalization/statistics & numerical data , Seasons , Multiplex Polymerase Chain Reaction , COVID-19/epidemiology , Adenoviruses, Human/isolation & purification , Adenoviruses, Human/genetics , Infant, Newborn
19.
Ter Arkh ; 96(8): 797-803, 2024 Sep 14.
Article in Russian | MEDLINE | ID: mdl-39404725

ABSTRACT

AIM: To evaluate the clinical effectiveness, safety and compare the incidence of hospitalization during treatment with antiviral drugs with a direct mechanism of action (riamilovir and umifenovir) in people with acute respiratory viral infections (ARVI) in an outpatient setting. MATERIALS AND METHODS: The study included 150 outpatients with ARVI aged 18-27 years: 50 patients received riamilovir 250 mg 3 times a day for 5 days, the second group included 50 patients who received umifenovir 200 mg 4 times a day for 5 days, 50 individuals received only pathogenetic treatment. RESULTS: The use of direct-acting antiviral drugs was characterized by the least severity of pain and aches in the body, general weakness, and in the group of patients receiving riamilovir, the lowest severity of rhinitis, cough, and the lowest morning body temperature were recorded compared to other groups. In riamilovir group reduction in the duration of the disease was observed. The lowest frequency of ARVI pathogens detection was observed on the 6th day in riamilovir group. Outpatient treatment with riamilovir was accompanied by a minimal number of cases of the disease requiring hospitalization. CONCLUSION: The use of direct antiviral drugs contributes to the rapid relief of ARVI symptoms in patients receiving medical care on an outpatient basis. The antiviral drug riamilovir showed the most pronounced effectiveness (clinical and laboratory).


Subject(s)
Antiviral Agents , Respiratory Tract Infections , Humans , Antiviral Agents/administration & dosage , Antiviral Agents/therapeutic use , Male , Female , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/virology , Adult , Young Adult , Treatment Outcome , Outpatients , Virus Diseases/drug therapy , Acute Disease , Adolescent , Indoles , Sulfides
20.
J Tradit Chin Med ; 44(5): 871-884, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39380218

ABSTRACT

OBJECTIVE: To evaluate and summarise the evidence from published Meta-analyses/systematic reviews (MAs/SRs) of Traditional Chinese Medicine (TCM) in the treatment of recurrent respiratory tract infections (RRTIs) and to provide a scientific basis for the clinical treatment of RRTIs with TCM. METHODS: Studies were retrieved from Chinese and English databases including the China National Knowledge Infrastructure, Wanfang database, China Science and Technology Journal Database, SinoMed, PubMed, Web of Science, the Cochrane Library and EMbase from their establishment date to March 2023. Involved studies were screened, extracted, and evaluated for quality by two researchers independently. The a measurement tool to assess systematic reviews (AMSTAR) 2 scale was used for methodological quality evaluation, as well as the preferred reporting items for systematic reviews and Meta-analyses (PRISMA) 2020 statement for report quality evaluation, the risk of bias in systematic reviews (ROBIS) tool for risk of bias, and the grading of recommendations, assessment, development and evaluation (GRADE) quality assessment tool for evidence quality. RESULTS: Twenty MAs/SRs studies were included, including analyses of 274 original studies involving 38 335 patients with RRTIs. The AMSTAR 2 scale evaluation results showed that 19 studies were of very low quality and one of moderate quality. The ROBIS evaluation results showed that 11 MAs/SRs were at high risk and nine at low risk of bias. The PRISMA 2020 report quality showed the included studies had scores between 23.5 and 35.5, among them one with high quality, 17 with moderate quality and two with low quality. The GRADE system results showed that among 126 outcome indicators, only 17 had moderate quality of evidence, 27 had low quality, 82 had very low quality, and none had high quality. CONCLUSIONS: The MAs/SRs methodological quality of using TCM for treatment RRTIs is generally poor, the quality of reports as well as of evidence is generally low, and the risk of bias is high; therefore we should treat these results with caution.


Subject(s)
Drugs, Chinese Herbal , Medicine, Chinese Traditional , Respiratory Tract Infections , Humans , Respiratory Tract Infections/drug therapy , Child , Medicine, Chinese Traditional/methods , Drugs, Chinese Herbal/therapeutic use , Meta-Analysis as Topic , Systematic Reviews as Topic , Child, Preschool , Adolescent , Infant
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