Presence Of Respiratory Viruses Research Articles

2644. Presence of Respiratory Viruses in the Upper Respiratory Tract of Febrile Infants ≤90 Days Old is Associated with Lower Prevalence of Invasive Bacterial Infection

Abstract Background Infants ≤ 90 days old are at increased risk of severe disease from both viral and bacterial pathogens. Differentiating between these two etiologies has long presented a diagnostic challenge and has resulted in many risk algorithms to determine which infants are infected by bacteria and require antibiotics. The increased availability of rapid molecular diagnostics presents an opportunity to refine these algorithms. While the prevalence of urinary tract infection in the presence of a respiratory virus has been described, large-scale studies with comprehensive viral testing describing the prevalence of invasive bacterial infection (IBI), defined as bacteremia or bacterial meningitis, are lacking. Methods The CDC’s New Vaccine Surveillance Network (NVSN) enrolls children < 18 years old with acute respiratory illness in the emergency department or inpatient setting of 7 hospitals. Upper respiratory specimens are collected and tested for respiratory viruses by real-time PCR. In this analysis respiratory viral positivity is described in febrile and non-febrile infants ≤ 90 days old. We then compared the prevalence of IBI (based on blood and CSF cultures obtained for clinical testing) among febrile infants with and without a respiratory virus detected. IBIs were defined as a positive blood or CSF culture with bacteria unlikely to be a contaminant. Results From December 2016 to March 2020, 3,731 infants (n=2,138 febrile, n=1,593 non-febrile) were enrolled. Respiratory viral positivity was 68% for febrile infants and 78% for non-febrile infants. Among febrile infants, 68% (n=1,461) had either a blood or CSF culture obtained; 3% (n=41) had an IBI. Febrile infants in whom a respiratory virus was detected, were significantly less likely to have an IBI (OR: 0.26 [95% CI: 0.13–0.52]) than febrile infants with negative viral testing (Table). Conclusion Detection of a respiratory virus in febrile infants ≤90 days is associated with significantly lower odds of an IBI (bacteremia or bacterial meningitis). These findings may help develop future risk algorithms for bacterial infection in febrile infants aged ≤90 days aiming to decrease unnecessary antibiotic use in this population. Disclosures Erin G. Nicholson, MD, MS, Blue Lake Biotechnology Inc.: Grant/Research Support|Novavax: Advisor/Consultant Pedro A. Piedra, MD, Ark Bioscience: Advisor/Consultant|Ark Bioscience: Grant/Research Support|GSK: Grant/Research Support|Icosavax: Advisor/Consultant|Icosavax: Grant/Research Support|Mapp Biologics: Grant/Research Support|Meissa Vaccines: Grant/Research Support|Moderna: Advisor/Consultant|Novavax: Advisor/Consultant|Novavax: Grant/Research Support|Sanofi-Pasteur: Grant/Research Support|Shionogi: Advisor/Consultant|Shionogi: Grant/Research Support|Takeda: Advisor/Consultant Janet A. Englund, MD, Ark Biopharma: Advisor/Consultant|AstraZeneca: Advisor/Consultant|AstraZeneca: Grant/Research Support|GlaxoSmithKline: Grant/Research Support|Meissa Vaccines: Advisor/Consultant|Merck: Grant/Research Support|Moderna: Advisor/Consultant|Moderna: Grant/Research Support|Pfizer: Advisor/Consultant|Pfizer: Grant/Research Support|Sanofi Pasteur: Advisor/Consultant John V. Williams, MD, Merck: Grant/Research Support|Quidel: Board Member Marian G. Michaels, MD, MPH, Merck: Grant/Research Support|Viracor: Grant/Research Support Geoffrey A. Weinberg, MD, Merck & Co: Honoraria Rangaraj Selvarangan, BVSc, PhD, D(ABMM), FIDSA, FAAM, Abbott: Honoraria|Altona Diagnostics: Grant/Research Support|Baebies Inc: Advisor/Consultant|BioMerieux: Advisor/Consultant|BioMerieux: Grant/Research Support|Bio-Rad: Grant/Research Support|Cepheid: Grant/Research Support|GSK: Advisor/Consultant|Hologic: Grant/Research Support|Lab Simply: Advisor/Consultant|Luminex: Grant/Research Support Mary A. Staat, MD, MPH, CDC: Grant/Research Support|Cepheid: Grant/Research Support|Merck: Grant/Research Support|NIH: Grant/Research Support|Pfizer: Grant/Research Support|Up-To-Date: Honoraria Elizabeth P. Schlaudecker, MD, MPH, Pfizer: Grant/Research Support|Sanofi Pasteur: Advisor/Consultant Natasha B. Halasa, MD, MPH, Merck: Grant/Research Support|Quidell: Grant/Research Support|Quidell: donation of kits|Sanofi: Grant/Research Support|Sanofi: vaccine support

Understanding the risk of transmission of respiratory viral infections in childcare centres: protocol for the DISeases TrANsmission in ChildcarE (DISTANCE) multicentre cohort study

IntroductionChildcare centre is considered a high-risk setting for transmission of respiratory viruses. Further evidence is needed to understand the risk of transmission in childcare centres. To this end, we established...

Febrile Children with Pneumonia Have Higher Nasopharyngeal Bacterial Load Than Other Children with Fever.

Febrile episodes are common in children and the most frequent reason for attending emergency services. Although most infections have a benign and self-limiting course, severe and sometimes life-threatening infections occur. This prospective study describes a cohort of children presenting to a single-centre pediatric emergency department (ED) with suspected invasive bacterial infection, and explores the relationships between nasopharyngeal microbes and outcomes. All children attending the ED who had a blood culture taken were offered to participate over a two-year period. In addition to conventional medical care, a nasopharyngeal swab was obtained., which was analysed for respiratory viruses and three bacterial species using a quantitative PCR. Fisher's exact test, Wilcoxon rank sum, and multivariable models were used for statistical analyses of the 196 children (75% younger than four years) who were enrolled and had sufficient data for analysis; 92 had severe infections according to the study protocol, while five had bloodstream infections. Radiologically confirmed pneumonia was the most common severe infection found in 44/92 patients. The presence of respiratory viruses and the carriage of Streptococcus pneumoniae and Haemophilus influenzae were associated with a higher risk of pneumonia. Higher density colonisation with these bacteria were independent risk factors for pneumonia, whereas Moraxella catarrhalis carriage was associated with lower risk. Our data support the hypothesis that higher nasopharyngeal density of pneumococci and H. influenzae could play a role in the development of bacterial pneumonia in children. A preceding viral infection of the respiratory tract may be a trigger and play a role in the progression to severe lower respiratory tract infection.

Association between early respiratory viral infections and structural lung disease in infants with cystic fibrosis

BackgroundInfants with cystic fibrosis (CF) develop structural lung disease early in life, and viral infections are associated with progressive lung disease. We hypothesized that the presence of respiratory viruses would be associated with structural lung disease on computed tomography (CT) of the chest in infants with CF. MethodsInfants with CF were enrolled before 4 months of age. Multiplex PCR assays were performed on nasal swabs to detect respiratory viruses during routine visits and when symptomatic. Participants underwent CT imaging at approximately 12 months of age. Associations between Perth–Rotterdam Annotated Grid Morphometric Analysis for CF (PRAGMA-CF) CT scores and respiratory viruses and symptoms were assessed with Spearman correlation coefficients. ResultsSixty infants were included for analysis. Human rhinovirus was the most common virus detected, on 28% of tested nasal swabs and in 85% of participants. The median (IQR) extent of lung fields that was healthy based on PRAGMA-CF was 98.7 (0.8)%. There were no associations between PRAGMA-CF and age at first virus, or detection of any virus, including rhinovirus, respiratory syncytial virus, or parainfluenza. The extent of airway wall thickening was associated with ever having wheezed (ρ = 0.31, p = 0.02) and number of encounters with cough (ρ = 0.25, p = 0.0495). ConclusionsInfants with CF had minimal structural lung disease. We did not find an association between respiratory viruses and CT abnormalities. Wheezing and frequency of cough were associated with early structural changes.

Detection of respiratory viruses in primary cholesteatoma tissues

Cholesteatomas are frequent middle ear benign tumors of unknown etiology. Infectious agents have been considered as possible contributing factors in the pathogenesis of cholesteatomas. Aiming to investigate the presence of respiratory viruses in primary cholesteatoma tissues, 26 formalin-fixed paraffin-embedded primary cholesteatoma tissues obtained from patients seen at the of the Clinical Hospital of the University of São Paulo School of Medicine, in Ribeirão Preto, Brazil were tested by real-time polymerase chain reaction (PCR). Considering the PCR results, 35% of the tissues were positive for human rhinovirus (HRV), 15.3% for human enterovirus (EV), 3.8% for human metapneumovirus (HMPV), and 3.8% for human bocavirus (HBoV). Serial immunohistochemistry for virus antigens and cell surface markers evidenced that the viruses were associated with fibroblasts, dendritic cells, macrophages, B lymphocytes, CD4+ , and CD8+ T lymphocytes. These findings indicate for the first time the presence of active respiratory virus infection in primary cholesteatoma tissues, suggesting that persisting virus infection in the middle could play a role in the pathogenesis and evolution of cholesteatomas.

Evolution of the Seroprevalence of Pestivirus and Respiratory Viral Infections in Spanish Feedlot Lambs.

Simple SummaryThe presence of viruses, such as bovine parainfluenza type 3, bovine herpesvirus type 1, bovine respiratory syncytial virus and pestiviruses, has been widely demonstrated in sheep in the past, but it is unknown how these infections may affect the lambs during their fattening period under commercial conditions. In the present study, the exposure to the aforementioned viruses was studied in 120 feedlot lambs throughout the whole fattening period. Seroprevalences were measured by enzyme-linked immunosorbent assays (ELISA), relating their presence to health and production parameters in the studied lambs. During the studied period, the lambs seroconverted against 3 out of the 4 viruses analysed and only 10.8% of the lambs were seronegative for all the tested viruses throughout the entire study. Finally, no associations were found between the seroconversion to one or more viruses and the presence of respiratory clinical signs or lung lesions at the slaughterhouse. In addition, no disturbances were observed in the performance of the lambs, except in the case of pestivirus infections, for which the presence of antibodies in the animals was associated with reduced final weight at the end of the fattening period.The presence of respiratory viruses and pestiviruses in sheep has been widely demonstrated, and their ability to cause injury and predispose to respiratory processes have been proven experimentally. A longitudinal observational study was performed to determine the seroprevalence of bovine parainfluenza virus type 3 (BPIV-3), bovine respiratory syncytial virus (BRSV), bovine herpesvirus type 1 (BHV-1) and pestiviruses in 120 lambs at the beginning and the end of the fattening period. During this time, the animals were clinically monitored, their growth was recorded, and post-mortem examinations were performed in order to identify the presence of pneumonic lesions in the animals. Seroconversion to all viruses tested except BHV-1 was detected at the end of the period. Initially, BPIV-3 antibodies were the most frequently found, while the most common seroconversion through the analysed period occurred to BRSV. Only 10.8% of the lambs showed no detectable levels of antibodies against any of the tested viruses at the end of the survey. In addition, no statistical differences were found in the presentation of respiratory clinical signs, pneumonic lesions nor in the production performance between lambs that seroconverted and those which did not, except in the case of pestiviruses. The seroconversion to pestiviruses was associated with a reduction in the final weight of the lambs.

Macrolide resistance and molecular typing of Mycoplasma pneumoniae infections during a 4 year period in Spain

Background Mycoplasma pneumoniae (MP) causes community-acquired pneumonia affecting mainly children, and tends to produce cyclic outbreaks. The widespread use of macrolides is increasing resistance rates to these antibiotics. Molecular tools can help in diagnosis, typing and resistance detection, leading to better patient management.ObjectivesTo assess the MP genotypes and resistance pattern circulating in our area while comparing serological and molecular diagnosis of MP.MethodsMolecular and serological diagnosis of MP was performed in 821 samples collected in Badalona (Barcelona, Spain) from 2013 to 2017. Multiple locus variable number tandem repeat analysis (MLVA) and macrolide resistance detection by pyrosequencing were performed in those cases positive by PCR. Presence of respiratory viruses and relevant clinical data were also recorded.ResultsMP was detected in 16.8% of cases by PCR, with an overall agreement with serology of 76%. Eleven different MLVA types were identified, with 4-5-7-2 (50.1%) and 3-5-6-2 (29.2%) being the most abundant, with the latter showing a seasonal increase during the study. A total of 8% of the strains harboured a point substitution associated with macrolide resistance, corresponding mainly to an A2063G 23S rRNA mutation and directly related to previous macrolide therapy. Analysis of respiratory viruses showed viral coinfections in most cases.ConclusionsSerological and molecular tools combined could improve MP diagnosis and the analysis of its infection patterns. Macrolide resistance is associated with previous therapy. Given that MP pneumonia usually resolves spontaneously, it should be reconsidered whether antibiotic treatment is suitable for all cases.

Prevalence and clinical implications of respiratory viruses in stable chronic obstructive pulmonary disease (COPD) and exacerbations: a systematic review and meta-analysis protocol

IntroductionBoth stable chronic obstructive pulmonary disease (COPD) and acute exacerbations represent leading causes of death, disability and healthcare expenditure. They are complex, heterogeneous and their mechanisms are poorly understood. The...

Respiratory viruses: What is their role in acute exacerbations in children with cystic fibrosis?

Respiratory viruses (RVs) are frequently present in the airways of patients with cystic fibrosis (CF) during pulmonary exacerbations (PEx). This prospective, longitudinal study was performed to examine the role of RVs in acute exacerbations in children with CF. Sputum samples or additional midturbinate swabs were tested from all children using a polymerase chain reaction panel. The primary aims of the study were to determine the prevalence and etiologic role of RVs in exacerbations of CF and to compare changes with RV-positive and RV-negative infections. The secondary aims were to determine the predictive factors for RV-related exacerbations. From 50 patients with PEx, 23 (48.9%) sputum samples were virus-positive. With a combination of sputum and swab, viral positivity increased to 56%. The virus-positive group presented more frequently with hypoxia (oxygen saturation <93%) than the virus-negative group (P = .048). Virus-positive exacerbations were not associated with an increase in colonization rates or greater lung function decline over 12 months. RVs frequently present during PEx of CF. However, predicting viral infections is difficult in this group. Only the presence of hypoxia may raise the suspicion of an accompanying viral agent. The combination of sputum and nasal swab samples increases the diagnostic yield in viral infections of CF. Despite their high frequency, the presence of RVs had no impact on clinical outcomes, such as a decline in lung function and increased colonization rates.

Respiratory viruses in mechanically ventilated patients: a pilot study

BackgroundRespiratory virome is an integral part of the human microbiome and its characterization may contribute to a better understanding of the changes that arise in the disease and, consequently, influence the approach and treatment of patients with acute lower respiratory infections.The aim of this study was to evaluate the presence of respiratory viruses in the lower airways of individuals undergoing invasive mechanical ventilation, with and without acute lower respiratory infection (respectively WRI and WORI groups).MethodsWe studied 44 mini-bronchoalveolar lavage samples (collected with a double catheter, Combicath® kit) from patients with mean age in the seventh decade, 20 from WORI group and 24 from WRI group, who were hospitalized for acute respiratory failure in Intensive Care Units of two hospitals in the Lisbon area. Real-time PCR was applied to verify analyse the presence of 15 common respiratory viruses (adenovirus, human bocavirus, influenza virus A and B, repiratory syncytial virus, human parainfluenza virus types 1, 2, 3 and 4, human enterovirus, human rhinovirus, human metapneumovirus, human coronavirus group 1 (229E, NL63) and 2 (OC43, HKU1).ResultsRespiratory viruses were detected in six of the 20 patients in the WORI group: influenza AH3 (n = 2), parainfluenza virus 1/3 (n = 2), human rhinovirus (n = 2), respiratory syncytial virus (n = 1) and human metapneumovirus (n = 1).In the WRI group, respiratory viruses were detected in 12 of the 24 patients: influenza AH3 (n = 3), human rhinovirus (n = 3), respiratory syncytial virus (n = 3), human metapneumovirus (n = 3), human bocavirus (n = 2) and human enterovirus (n = 1). Simultaneous detection of two viruses was recorded in two samples in both groups.ConclusionsThe results of this study suggest the presence of common respiratory viruses in the lower respiratory tract without causing symptomatic infection, even in carefully collected lower samples. This may have important implications on the interpretation of the results on the diagnostic setting.

High concentrations of middle ear antimicrobial peptides and proteins and proinflammatory cytokines are associated with detection of middle ear pathogens in children with recurrent acute otitis media.

Recurrent and chronic otitis media (OM) are often refractory to antibiotics due to bacterial persistence in biofilm within the middle ear. In vitro and in vivo studies have demonstrated that antimicrobial proteins and peptides (AMPs) are bactericidal against otopathogens, indicating potential therapeutic value for recalcitrant OM. We measured concentrations of 6 AMPs and 14 cytokines in middle ear effusion (MEE) from 67 children undergoing ventilation tube insertion for recurrent acute OM. Sixty one percent of children had bacterial otopathogens detected in their MEE, 39% by PCR and 22% by PCR and culture. Groups were defined as: PCR-negative/culture-negative (absence of bacterial otopathogen), n = 26; PCR-positive/culture-negative (presence of nonculturable bacterial otopathogen), n = 26; PCR-positive/culture-positive (presence of culturable bacterial otopathogen), n = 15. Age, antibiotic usage, day-care attendance, presence of respiratory viruses in MEE and number of AOM episodes were similar between groups. AMP and cytokine concentrations were higher in children with bacterial otopathogens in their MEE compared to those with no bacterial otopathogens. Median concentrations of AMPs (except HBD2) were 3 to 56-fold higher in MEE from children with bacterial otopathogens detected in their MEE (P ≤ 0.01). Similarly, median cytokine concentrations (except TGFβ) were >16-fold higher in MEE with bacterial otopathogens detected (P ≤ 0.001). This is the first study to measure AMPs in MEE and together with the cytokine data, results suggest that elevated AMPs and cytokines in MEE are a marker of inflammation and bacterial persistence. AMPs may play an important role in OM pathogenesis.

Sputum Microbiome Dynamics in Chronic Obstructive Pulmonary Disease Patients during an Exacerbation Event and Post-Stabilization

Background: Chronic obstructive pulmonary disease (COPD) affects up to 65 million people worldwide, and COPD exacerbation causes tissue damage and subsequent loss of lung function. It is a multifactorial event in which respiratory infections are involved, but little is known about its dynamics. Objectives: The objective of our study was to determine the microbiome composition during an exacerbation event and post-stabilization. Methods: We conducted an observational analytical study of a cohort of 55 COPD patients in which 2 sputum samples (the first taken during an exacerbation event and the second during clinical post-stabilization) were submitted to 16s RNA ribosomal analysis by Illumina Miseq Next Generation Sequencing (NGS). The presence of respiratory viruses was also determined. Results: Our study found a stable microbiome composition in the post-stabilization sputum samples of COPD patients, and 4 additional microbiomes in samples taken during the exacerbation, 3 of which showed a marked dysbiosis by Haemophilus, Pseudomonas, and Serratia. The fourth exacerbation microbiome had a very similar composition to post-stabilization samples, but some pathogens such as Moraxella and respiratory viruses were also found. Conclusions: Our study reveals the main protagonists involved in lung microbiome dynamics during an exacerbation event and post-stabilization in COPD patients by NGS analysis.

Human virome in nasopharynx and tracheal secretion samples.

BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols.OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil.METHODS Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens.FINDINGS The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses.MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.

The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens

The nasopharynx is the primary site of colonization by respiratory pathogen that constitutes the port of entrance in the respiratory tract. The role of mucosal respiratory microbiota in infection has been recently emphasized; therefore, we aimed to assess if a specific respiratory microbiota profile was associated with symptomatic infection and/or with presence of respiratory viruses. We performed a case-control study to characterize the healthy respiratory microbiota and its alteration during acute viral infections. Next-generation sequencing of the 16S rRNA gene was applied to 225 nasopharyngeal samples from 177 patients with viral respiratory infection and 48 matched healthy controls. We evidenced an important decrease of bacterial alpha-diversity in patients with symptomatic respiratory infection and a loss of the healthy core microbiota, specifically anaerobes and Prevotella spp. Moreover, eight respiratory pathogens were enriched in these patients, including Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, Dol osigranulum pigrum and Corynebacterium propinquum/pseudodiphtheriticum, whose role in respiratory infection is unclear. The asymptomatic carrier of influenza harbors a microbiota similar to healthy subjects, suggesting a critical role of microbiota in the clinical expression of viruses. These data suggest that the commensal microbiota plays a significant role in susceptibility to viral infection. The frequent co-detection of virus and bacteria raises the question of a strategy to prevent bacterial disease, focusing on the prevention of nasopharyngeal colonization through effective antibiotic treatment. In addition to antibiotics, further studies should test preventive or therapeutic interventions for maintaining or restoring a healthy nasopharyngeal microbiota.

Comparison of the prevalence of respiratory viruses in patients with acute respiratory infections at different hospital settings in North China, 2012\u20132015

BackgroundAcute respiratory infections (ARIs) are a great public health challenge globally. The prevalence of respiratory viruses in patients with ARIs attending at different hospital settings is fully undetermined.MethodsLaboratory-based surveillance for ARIs was conducted at inpatient and outpatient settings of 11 hospitals in North China. The first 2–5 patients with ARIs were recruited in each hospital weekly from 2012 through 2015. The presence of respiratory viruses was screened by PCR assays. The prevalence of respiratory viruses was determined and compared between patients at different hospital settings.ResultsA total of 3487 hospitalized cases and 6437 outpatients/Emergency Department (ED) patients were enrolled. The most commonly detected viruses in the hospitalized cases were respiratory syncytial virus (RSV, 33.3%) in children less than two years old, adenoviruses (13.0%) in patients 15–34 years old, and influenza viruses (IFVs, 9.6%) in patients ≥65 years. IFVs were the most common virus in outpatient/ED patients across all age groups (22.7%). After controlling for the confounders caused by other viruses and covariates, adenoviruses (adjusted odds ratio [aOR]: 3.97, 99% confidence interval [99% CI]: 2.19–7.20) and RSV (aOR: 2.04, 99% CI: 1.34–3.11) were independently associated with increased hospitalization in children, as well as adenoviruses in adults (aOR: 2.14, 99% CI: 1.19–3.85). Additionally, co-infection of RSV with IFVs was associated with increased hospitalization in children (aOR: 12.20, 99% CI: 2.65–56.18).ConclusionsA substantial proportion of ARIs was associated with respiratory viruses in North China. RSV, adenoviruses, and co-infection of RSV and IFVs were more frequent in hospitalized children (or adenoviruses in adults), which might predict the severity of ARIs. Attending clinicians should be more vigilant of these infections.

Respiratory Viruses in Invasively Ventilated Critically Ill Patients—A Prospective Multicenter Observational Study

The presence of respiratory viruses and the association with outcomes were assessed in invasively ventilated ICU patients, stratified by admission diagnosis. Prospective observational study. Five ICUs in the Netherlands. Between September 1, 2013, and April 30, 2014, 1,407 acutely admitted and invasively ventilated patients were included. None. Nasopharyngeal swabs and tracheobronchial aspirates were collected upon intubation and tested for 14 respiratory viruses. Out of 1,407 patients, 156 were admitted because of a severe acute respiratory infection and 1,251 for other reasons (non-severe acute respiratory infection). Respiratory viruses were detected in 28.8% of severe acute respiratory infection patients and 17.0% in non-severe acute respiratory infection (p < 0.001). In one third, viruses were exclusively detected in tracheobronchial aspirates. Rhinovirus and human metapneumovirus were more prevalent in severe acute respiratory infection patients (9.6% and 2.6% vs 4.5 and 0.2%; p = 0.006 and p < 0.001). In both groups, there were no associations between the presence of viruses and the number of ICU-free days at day 28, crude mortality, and mortality in multivariate regression analyses. Respiratory viruses are frequently detected in acutely admitted and invasively ventilated patients. Rhinovirus and human metapneumovirus are more frequently found in severe acute respiratory infection patients. Detection of respiratory viruses is not associated with worse clinically relevant outcomes in the studied cohort of patients.

The role of respiratory viruses in nasopharynx microbiome in children

The article considers the problem of incidence of respiratory diseases in children, especially of preschool age, preconditioned by the state of Waldeyer’s tonsillar ring and the pharyngeal tonsil in particular. The article provides assessment of the effect of the previous infectious diseases on the state of the nasopharynx microbiome. The authors present their data on frequency of viruses extraction (by PRC method) in the material taken from the surface of pharyngeal tonsil in patients with the inflammatory changes of the tonsil and without it. The article presents numerical materials about the age- and season-specific features of the presence of respiratory viruses in the nasopharynx microbiome of children of various age groups.

Association between secondary thrombocytosis and viral respiratory tract infections in children.

Secondary thrombocytosis (ST) is frequently observed in children with a variety of clinical conditions. The leading cause of ST is respiratory tract infection (RTI) in children. Nasopharyngeal aspirate samples were collected and assessed for common respiratory viruses. The relationships between virus infections and secondary thrombocytosis were analyzed retrospectively. The blood platelet count and the presence of respiratory viruses were determined for 3156 RTI patients, and 817 (25.9%) cases with platelet ≥500 × 109/L were considered as the thrombocytosis group. Compared with the normal group, the detection rates of respiratory syncytial virus (RSV) and human rhinovirus (HRV) were significantly higher in the thrombocytosis group (P = 0.017 and 0.042, respectively). HRV single infection was a risk factor associated with thrombocytosis [odds ratio (OR) = 1.560, 95% confidence interval (CI) = 1.108–2.197]. Furthermore, ST was more likely to occur in younger patients who had clinical manifestations of wheezing and dyspnea and who had been diagnosed with bronchiolitis. Furthermore, the course of disease lasted longer in these patients. ST is associated with viral respiratory tract infections, especially RSV and HRV infections. HRV single infection is a risk factor associated with thrombocytosis.

İki Ardışık Epidemik Sezonda Ülkemizde Dolaşımda Olan İnsan Metapnömovirus Suşlarının Filogenetik Çeşitliliği

Human metapneumovirus (HMPV), classified in Paramyxoviridae family, phylogenetically consists of two major groups namely A and B, with genetic lineages of A1, A2 (comprises of sublineages A2a and A2b) and B1, B2. Although detailed evaluation on phylogenetic analysis of HMPV has been described in other countries, there are no data from Turkey on this subject. The aim of this study was to demonstrate for the first time, the phylogenetic diversity of HMPV strains circulating in Turkey during two consecutive epidemic seasons. A total of 2900 upper respiratory tract samples collected from patients with respiratory illness were evaluated between January 2011 and December 2013, without any special selection criteria. The presence of respiratory viruses in the samples were detected by real-time multiplex polymerase chain reaction (FTD® Respiratory Pathogens 21 Multiplex RT-PCR, Fast Track Diagnostics, Luxemburg), and 76 (2.6%) samples positive for HMPV were included in the study. HPMV nucleocapsid (N) (nt: 454-878) and fusion (F) (nt: 3624-4130) genes were selected for phylogenetic analysis. In sequence analysis, F and N gene sequences could only be obtained successfully from 46 out of 76 HMPV positive samples. According to sequences obtained, 54.3% belonged to B2, 17.4% to B1, 4.3% to A1, 4.3% to A2a, and 20% to A2b. In 2011, the A2b sublineage was predominant, while in 2012 and 2013, B2 lineages were predominant together with the B1 lineage. The A1 lineage was observed only in 2013. For the F gene fragment, nucleotide distance between group A and B was in the range of 0.138-0.168, however aminoacid distance amongst Turkish HMPV sequences were in the range of 0.028-0.042. For the N gene fragment, nucleotide distance between group A and B was in the range of 0.141-0.163, but aminoacid distance between group A and B was in the range of 0.037-0.050. Nucleotide diversity was higher than aminoacid diversity between and within lineages found in this study. This result indicated that the functional constraints on F and N genes prevent dramatic aminoacid changes, and indicated that the evolution of HMPV was slow. The seasonal peaks were observed from April to July in 2011, from January to June in 2012 and from January to May in 2013. In addition, our data emphasized that the HMPV prevalence was high in children 0-5 years old, and coinfections were common with the other respiratory viruses such as respiratory syncytial virus, coronavirus, parainfluenza virus 3, rhinovirus and enterovirus. In conclusion, this study showed that HMPV strains circulating in Turkey were similar to those circulating in Europe.

Clinical analysis of influenza virus-associated acute lower respiratory tract infection in children in Beijing during 2007-2014

Objective To investigate the status of influenza virus (IFV) in children with acute lower respiratory tract infection (ALRTI) in Beijing, and to compare the clinical characteristics of ALRTI with single IFV and respiratory syncytial virus(RSV) in children. Methods Throat swab of nasopharyngeal aspirate specimens were collec-ted from children with ALRTI and tested for the presence of respiratory viruses (such as RSV, parainfluenza virus, rhinovirus and IFV) by reverse transcription-polymerase chain reaction.The epidemiological features of patients with influenza A, B or C virus (IFA, IFB, IFC) infection were analyzed.Clinical features of patients with single IFV and single RSV infection were compared. Results (1) During March 2007 and March 2014, at least one virus was detected in 2 697 (67.2%)of 4 012 children.There were 256 samples positive for IFV (6.4%), including 154 samples for IFA (3.8%), 97 samples for IFB (2.4%), and 6 samples for IFC (0.1%). (2) The IFV positive rate of 6 years groups were 4.1%, 7.6%, 12.0%, 7.8% and 4.8%, respectively.The 1-3 years-old group showed the highest positive rate of IFV.The positive rate of IFV showed no difference between males and females(6.7% vs 5.9%, χ2=2.63, P>0.05) (3) There were 16, 15 and 175 hospitalized children in single IFV, single IFB and single RSV infection group, respectively.The rate of <1-year children in single IFA(43.8% vs 84.0%, χ2 =12.74, P<0.001 or IFB (33.3% vs 84.0%, χ2 =19.11, P<0.001)infection group were both higher than it in single RSV infection group, and there was a significant difference.The incident rate of severe pneumonia in single IFA or IFB infection groups were both higher than that in single RSV infection group significant difference (31.2%, 26.7% vs 4.0%; χ2=18.49, 13.01, all P<0.001). The incident rate of trachea cannula in single IFA and IFB infection groups were higher than in single RSV infection group, and the difference was significant(25.0%, 13.3% vs 1.7%; χ2=22.51, 7.28, P<0.001, P=0.001). There was no significant difference in other clinical features, diagnosis and mechanical ventilation between single IFA infection group and single RSV infection group or single IFB infection group and single RSV infection group. Conclusions IFV is one of the major viral pathogens in children in Beijing.Peaks of influenza infection activity in children were in spring and winter.Children, especially 1-6 years old group, were more susceptible to IFV.The ALRTI children infected with IFV or RSV showed the similar clinical characteristics and severity of disease, but the incident rate of severe pneumonia was higher in children infection with IFV. Key words: Acute lower respiratory tract infection; Influenza virus; Respiratory syncytial virus; Clinical cha-racteristics; Child