The relationship between respiratory viral loads and diagnosis in children presenting to a pediatric hospital emergency department

A single amino acid mutation alters multiple neutralization epitopes in the respiratory syncytial virus fusion glycoprotein

Respiratory syncytial virus (RSV) is the leading cause of infant hospitalization. All current RSV therapeutics, including antibody prophylaxis and adult vaccination, target the RSV fusion glycoprotein (RSV-F). The seven neutralization sites on RSV-F are highly conserved and infrequently mutate. Here, we show that a single amino acid mutation at position 305 in RSV-F significantly alters antigenic recognition of RSV-F binding sites and reduces the susceptibility of RSV to neutralizing antibodies. In an in vitro evolution assay, we show that RSV-F L305I occurs in a majority of RSV quasi-species. Computational modeling predicted that the L305I mutation altered the epitope landscape of RSV-F, resulting in changes to neutralizing antibody sensitivity and affinity towards the RSV-F glycoprotein. Screening of published RSV-F sequences revealed that position 305 in RSV-F was conserved with a leucine and isoleucine in RSV-A and RSV-B subtypes respectively. Our study suggests that select amino acids in RSV-F may act as 'conformational switches' for RSV to evade host serum antibodies. This work has important implications in understanding RSV evolution and resistance as it suggests that mutational resistance to neutralizing antibodies can occur at sites distal to antigenic epitopes, significantly altering antibody sensitivity to viral infection. These unique antigenic landscape changes should be considered in the context of vaccine and therapeutic development in order to better understand viral mechanisms of evasion and resistance.

Respiratory morbidity associated with viral respiratory infections during neonatal stage in premature infants

BACKGROUND AND OBJECTIVE

Very low birth weight (VLBW) infants are highly susceptible to viral respiratory infections (VRIs), even during admission to the neonatal intensive care unit (NICU). Although the role of VRI in childhood in the development of recurrent wheezing and long-term asthma is well known, information on the impact in later morbidity of VRI in the neonatal period is lacking. We aimed to explore the occurrence of recurrent wheezing over the first 2 years of life according to VRI status during NICU admission.

METHODS

During April 2016 and December 2017, infants below 32 weeks of gestation were prospectively studied in VRI surveillance during NICU admission. Families were contacted between September 2018 and May 2019 by a telephone questionnaire.

RESULTS

A total of 99 patients were enrolled. The mean gestational age and birth weight were 28.8 (1.9) weeks and 1118 (329) g, respectively. During the first 2 years of life, neither episodes of wheezing nor the respiratory impairment-related hospital admissions differed between positive and negative VRI infants. Episodes of wheezing and respiratory impairment-related hospital admissions, as well as specific respiratory treatment prescription, were more frequent within the first 2 years in infants who had suffered symptomatic VRI during NICU admission.

CONCLUSION

Symptomatic VRI in VLBW infants is associated with long-term respiratory morbidity. The early surveillance of VRI in the preterm infant during NICU admission is justified for prognostic counseling and closely monitoring after discharge. Routine instruction on asthma-related risk factors and early prescription of antiasthmatic treatments, when indicated, should be established.

Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study

BACKGROUND

Multiplex real-time polymerase chain reaction assays have improved diagnostic sensitivity for a wide range of pathogens. However, co-detection of multiple agents and bacterial colonization make it difficult to distinguish between asymptomatic infection or illness aetiology. We assessed whether semi-quantitative microbial load data can differentiate between symptomatic and asymptomatic states for common respiratory pathogens.

METHODS

We obtained throat and nasal swab samples from military trainees at two Thai Army barracks. Specimens were collected at the start and end of 10-week training periods (non-acute samples), and from individuals who developed upper respiratory tract infection during training (acute samples). We analysed the samples using a commercial multiplex respiratory panel comprising 33 bacterial, viral and fungal targets. We used random effects tobit models to compare cycle threshold (Ct) value distributions from non-acute and acute samples.

RESULTS

We analysed 341 non-acute and 145 acute swab samples from 274 participants. Haemophilus influenzae type B was the most commonly detected microbe (77.4% of non-acute and 64.8% of acute samples). In acute samples, nine specific microbe pairs were detected more frequently than expected by chance. Regression models indicated significantly lower microbial load in non-acute relative to acute samples for H. influenzae non-type B, Streptococcus pneumoniae and rhinovirus, although it was not possible to identify a Ct-value threshold indicating causal etiology for any of these organisms.

CONCLUSIONS

Semi-quantitative measures of microbial concentration did not reliably differentiate between illness and asymptomatic colonization, suggesting that clinical symptoms may not always be directly related to microbial load for common respiratory infections.

Human adenovirus load in respiratory tract secretions are predictors for disease severity in children with human adenovirus pneumonia

Background

Pneumonia is a serious public health issue and is concerned around the world. This study is to investigate the association between viral load in children with human adenovirus (HAdV) pneumonia and disease severity.

Methods

A total of 1313 cases of children hospitalized in Hunan Provincial People’s Hospital due to community acquired pneumonia (CAP) from April 2011 to May 2014 were enrolled in this study. Samples of nasopharyngeal aspirate were collected for the cohort. WHO criteria for CAP grading was emerged for pneumonia severity classification. Real-time fluorescence quantitative PCR (qRT-PCR) was used to detect 12 kinds of respiratory viruses. HAdV types were identified by nested PCR. The relationship between HAdV load and severity of disease was there by analyzed.

Results

Finally, 174 cases (174/1313, 13.3%) were positive for HAdV, and HAdV type 7 (HAdV-7) was the main serotype (76/174, 43.7%). Among the 174 cases, 70 cases were with HAdV infection alone and 104 cases were accompanied by other viruses. The patients were divided into mild pneumonia group (n = 108 cases) and severe pneumonia group (n = 66 cases). HAdV load of children in severe pneumonia group was higher than that in mild pneumonia group. Similar result was obtained in the 70 cases with HAdV infection alone after subgrouping. Relevant factors analysis results showed that severe pneumonia children presented lower onset age, more prone to fever, longer fever time, and longer hospital stay compared with that of mild pneumonia children. Children with HAdV-7 infection developed more frequently severe pneumonia. Multivariate regression analysis showed that HAdV load, age, and fever time were risk factors for pneumonia severity.

Conclusion

The severity of HAdV infection is significantly correlated with viral load and serotype.

Developmental Regulation of Effector and Resident Memory T Cell Generation during Pediatric Viral Respiratory Tract Infection

Viral respiratory tract infections (VRTI) remain a leading cause of morbidity and mortality among infants and young children. In mice, optimal protection to VRTI is mediated by recruitment of effector T cells to the lungs and respiratory tract, and subsequent establishment of tissue resident memory T cells (Trm), which provide long-term protection. These critical processes of T cell recruitment to the respiratory tract, their role in disease pathogenesis, and establishment of local protective immunity remain undefined in pediatric VRTI. In this study, we investigated T cell responses in the upper respiratory tract (URT) and lower respiratory tract (LRT) of infants and young children with VRTI, revealing developmental regulation of T cell differentiation and Trm generation in situ. We show a direct concurrence between T cell responses in the URT and LRT, including a preponderance of effector CD8⁺ T cells that was associated with disease severity. During infant VRTI, there was an accumulation of terminally differentiated effector cells (effector memory RA⁺ T cells) in the URT and LRT with reduced Trm in the early neonatal period, and decreased effector memory RA⁺ T cell and increased Trm formation with age during the early years of childhood. Moreover, human infant T cells exhibit increased expression of the transcription factor T-bet compared with adult T cells, suggesting a mechanism for preferential generation of effector over Trm. The developmental regulation of respiratory T cell responses as revealed in the present study is important for diagnosing, monitoring, and treating VRTI in the critical early life stages.

Clinical and Molecular Epidemiology of Human Parainfluenza Viruses 1-4 in Children from Viet Nam

HPIVs are serologically and genetically grouped into four species that account for up to 10% of all hospitalizations due to acute respiratory infection in children under the age of five. Genetic and epidemiological data for the four HPIVs derived from two pediatric cohorts in Viet Nam are presented. Respiratory samples were screened for HPIV1-4 by real-time PCR. Demographic and clinical data of patients infected with different HPIV were compared. We used a hemi-nested PCR approach to generate viral genome sequences from HPIV-positive samples and conducted a comprehensive phylogenetic analysis. In total, 170 samples tested positive for HPIV. HPIV3 was most commonly detected in our cohort and 80 co-detections of HPIV with other respiratory viruses were found. Phylogenetic analyses suggest local endemic circulation as well as punctuated introductions of new HPIV lineages. Viral gene flow analysis revealed that Viet Nam is a net importer of viral genetic diversity. Epidemiological analyses imply similar disease severity for all HPIV species. HPIV sequences from Viet Nam formed local clusters and were interspersed with sequences from diverse geographic regions. Combined, this new knowledge will help to investigate global HPIV circulation patterns in more detail and ultimately define more suitable vaccine strains.

Exacerbation induces a microbiota shift in sputa of COPD patients

Little is known about the microbiota shift induced by exacerbation in chronic obstructive pulmonary disease (COPD) patients. The sputa microbiota of COPD patients was evaluated when clinically stable and during acute exacerbations of the disease. Sputa microbiota was analyzed using 16S ribosomal RNA gene pyrosequencing and quantitative polymerase chain reaction-based pathogen detection. Nine COPD patients were enrolled. Pyrosequencing of 16S rRNA genes identified 2,267 unique bacterial operational taxonomic units. Principal microbiota shifts during exacerbation were in either Proteobacteria, Firmicutes or Bacteroidetes. Streptococcus and Moraxella levels were detected during exacerbation in severe (Global Initiative for Chronic Obstructive Lung Disease 3) COPD patients. Most of the clinically-important genera found in the sputum with the pyrosequencing of 16S rRNA gene correlated with specific quantitative polymerase chain reactions for bacteria while respiratory viruses were nearly absent. Sputum microbiotas of exacerbated COPD patients are complex. This pilot study shows a clear shift in the microbiota of patients during exacerbation. The nature of this shift varies from patient to patient in such a way that the treatment should be patient-specific. Further studies are needed to establish the impact of microbial exacerbations on the pulmonary microbiota.

Is Higher Viral Load in the Upper Respiratory Tract Associated With Severe Pneumonia? Findings From the PERCH Study

Background.

The etiologic inference of identifying a pathogen in the upper respiratory tract (URT) of children with pneumonia is unclear. To determine if viral load could provide evidence of causality of pneumonia, we compared viral load in the URT of children with World Health Organization–defined severe and very severe pneumonia and age-matched community controls.

Methods.

In the 9 developing country sites, nasopharyngeal/oropharyngeal swabs from children with and without pneumonia were tested using quantitative real-time polymerase chain reaction for 17 viruses. The association of viral load with case status was evaluated using logistic regression. Receiver operating characteristic (ROC) curves were constructed to determine optimal discriminatory viral load cutoffs. Viral load density distributions were plotted.

Results.

The mean viral load was higher in cases than controls for 7 viruses. However, there was substantial overlap in viral load distribution of cases and controls for all viruses. ROC curves to determine the optimal viral load cutoff produced an area under the curve of <0.80 for all viruses, suggesting poor to fair discrimination between cases and controls. Fatal and very severe pneumonia cases did not have higher viral load than less severe cases for most viruses.

Conclusions.

Although we found higher viral loads among pneumonia cases than controls for some viruses, the utility in using viral load of URT specimens to define viral pneumonia was equivocal. Our analysis was limited by lack of a gold standard for viral pneumonia.

A Virological and Phylogenetic Analysis of the Emergence of New Clades of Respiratory Syncytial Virus

The significant burden of Respiratory Syncytial Virus (RSV) in pediatric and elderly populations is well recognized. However, questions remain about transmission and evolution of RSV in the community, between seasons, and the role played by viral genetics in viral replication. Therefore, we integrated next generation sequencing, patient viral load, and viral replication analysis with surveillance of RSV to initiate a better understanding of viral adaptation in communities. RSV type-A and B infections were most closely related to RSV sequences from the USA and Asia, respectfully. The sample titres between RSV types-A and B were not significantly different. However, when the patient sample titre was compared to the phylogenetics of RSV, emergent clades were identified that we termed High Titre (HiT) clades of RSV. In conclusion, the correlation between patient viral load and replication kinetics of RSV patient isolates in culture indicated that viral genetics may determine virus replicative ability within patients. There was evolution or introduction of high-titre RSV type-A and B infections that seeded HiT clades in the subsequent year. Therefore, virological analysis of RSV isolates in conjunction with RSV phylogenetics may be a tool for predicting new clades of RSV in impending seasons.

Respiratory Syncytial Virus: Infection, Detection, and New Options for Prevention and Treatment

Respiratory syncytial virus (RSV) infection is a significant cause of hospitalization of children in North America and one of the leading causes of death of infants less than 1 year of age worldwide, second only to malaria. Despite its global impact on human health, there are relatively few therapeutic options available to prevent or treat RSV infection. Paradoxically, there is a very large volume of information that is constantly being refined on RSV replication, the mechanisms of RSV-induced pathology, and community transmission. Compounding the burden of acute RSV infections is the exacerbation of preexisting chronic airway diseases and the chronic sequelae of RSV infection. A mechanistic link is even starting to emerge between asthma and those who suffer severe RSV infection early in childhood. In this article, we discuss developments in the understanding of RSV replication, pathogenesis, diagnostics, and therapeutics. We attempt to reconcile the large body of information on RSV and why after many clinical trials there is still no efficacious RSV vaccine and few therapeutics.

The Susceptibilities of Respiratory Syncytial Virus to Nucleolin Receptor Blocking and Antibody Neutralization are Dependent upon the Method of Virus Purification

Respiratory Syncytial Virus (RSV) that is propagated in cell culture is purified from cellular contaminants that can confound experimental results. A number of different purification methods have been described, including methods that utilize fast protein liquid chromatography (FPLC) and gradient ultracentrifugation. Thus, the constituents and experimental responses of RSV stocks purified by ultracentrifugation in sucrose and by FPLC were analyzed and compared by infectivity assay, Coomassie stain, Western blot, mass spectrometry, immuno-transmission electron microscopy (TEM), and ImageStream flow cytometry. The FPLC-purified RSV had more albumin contamination, but there was less evidence of host-derived exosomes when compared to ultracentrifugation-purified RSV as detected by Western blot and mass spectrometry for the exosome markers superoxide dismutase [Cu-Zn] (SOD1) and the tetraspanin CD63. Although the purified virus stocks were equally susceptible to nucleolin-receptor blocking by the DNA aptamer AS1411, the FPLC-purified RSV was significantly less susceptible to anti-RSV polyclonal antibody neutralization; there was 69% inhibition (p = 0.02) of the sucrose ultracentrifugation-purified RSV, 38% inhibition (p = 0.03) of the unpurified RSV, but statistically ineffective neutralization in the FPLC-purified RSV (22% inhibition; p = 0.30). The amount of RSV neutralization of the purified RSV stocks was correlated with anti-RSV antibody occupancy on RSV particles observed by immuno-TEM. RSV purified by different methods alters the stock composition and morphological characteristics of virions that can lead to different experimental responses.

Respiratory RNA Viruses

Acute upper and lower respiratory infections are a major public health problem and a leading cause of morbidity and mortality worldwide. At greatest risk are young children, the elderly, the chronically ill, and those with suppressed or compromised immune systems. Viruses are the predominant cause of respiratory tract illnesses and include RNA viruses such as respiratory syncytial virus, influenza virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus. Laboratory testing is required for a reliable diagnosis of viral respiratory infections, as a clinical diagnosis can be difficult since signs and symptoms are often overlapping and not specific for any one virus. Recent advances in technology have resulted in the development of newer diagnostic assays that offer great promise for rapid and accurate detection of respiratory viral infections. This chapter emphasizes the fundamental characteristics and clinical importance of the various RNA viruses that cause upper and lower respiratory tract diseases in the immunocompromised host. It highlights the laboratory methods that can be used to make a rapid and definitive diagnosis for the greatest impact on the care and management of ill patients, and the prevention and control of hospital-acquired infections and community outbreaks.

Pitfalls in interpretation of CT-values of RT-PCR in children with acute respiratory tract infections

Background

The relation between viral load and disease severity in childhood acute respiratory tract infections (ARI) is not fully understood.

Objectives

To assess the clinical relevance of the relation between viral load, determined by cycle threshold (CT) value of real-time reverse transcription-polymerase chain reaction assays and disease severity in children with single- and multiple viral ARI.

Study design

582 children with ARI were prospectively followed and tested for 15 viruses. Correlations were calculated between CT values and clinical parameters.

Results

In single viral ARI, statistically significant correlations were found between viral loads of Respiratory Syncytial Virus (RSV) and hospitalization and between viral loads of Human Coronavirus (HCoV) and a disease severity score. In multiple-viral ARI, statistically significant correlations between viral load and clinical parameters were found. In RSV-Rhinovirus (RV) multiple infections, a low viral load of RV was correlated with a high length of hospital stay and a high duration of extra oxygen use. The mean CT value for RV, HCoV and Parainfluenza virus was significantly lower in single- versus multiple infections.

Conclusion

Although correlations between CT values and clinical parameters in patients with single and multiple viral infection were found, the clinical importance of these findings is limited because individual differences in host-, viral and laboratory factors complicate the interpretation of statistically significant findings. In multiple infections, viral load cannot be used to differentiate between disease causing virus and innocent bystanders.

Consolidation of molecular testing in clinical virology

INTRODUCTION

The development of quantitative methods for the detection of viral nucleic acids have significantly improved our ability to manage disease progression and to assess the efficacy of antiviral treatment. Moreover, major advances in molecular technologies during the last decade have allowed the identification of new host genetic markers associated with antiviral drug response but have also strongly revolutionized the way we see and perform virus diagnostics in the coming years. Areas covered: In this review, we describe the history and development of virology diagnostic methods, dedicating particular emphasis on the gradual evolution and recent advances toward the introduction of multiparametric platforms for the syndromic diagnosis. In parallel, we outline the consolidation of viral genome quantification practice in different clinical settings. Expert commentary: More rapid, accurate and affordable molecular technology can be predictable with particular emphasis on emerging techniques (next generation sequencing, digital PCR, point of care testing and syndromic diagnosis) to simplify viral diagnosis in the next future.

[Respiratory viral infections in a cohort of children during the first year of life and their role in the development of wheezing]

Introducción

Las infecciones respiratorias virales que requieren hospitalización parecen conferir riesgo de desarrollar sibilancias recurrentes, pero existen pocos datos publicados en poblaciones no seleccionadas por tener factores de riesgo. Nuestro objetivo principal fue analizar si las infecciones respiratorias virales sintomáticas y asintomáticas, de diferente gravedad, durante el primer año de vida en una cohorte de recién nacidos, suponen un mayor riesgo de sibilancias recurrentes.

Pacientes y métodos

Se incluyeron 302 recién nacidos. Se recogió aspirado nasofaríngeo a los niños cuando presentaron una infección respiratoria y de forma periódica en los controles de salud (2, 4, 6 y 12 meses). Se estudiaron 16 virus respiratorios mediante reacción en cadena de polimerasa (PCR).

Resultados

Se analizaron 1.293 muestras (1.005 controles de salud y 288 infecciones respiratorias). El 30,8% de las muestras tomadas en los controles de salud fueron positivas, frente a un 77,8% en las infecciones respiratorias, p < 0,001 (OR: 3, IC 95%: 2,4-3,8). Un total de 239 (79%) lactantes tuvieron al menos una detección viral positiva durante el primer año de vida. El virus más frecuentemente identificado (71%) fue el rinovirus (RV). En 27 lactantes (11%) se detectaron sibilancias recurrentes durante su primer año de vida (2,9 DE: 1,2 episodios). El 58,3% de los lactantes cuya primera infección respiratoria requirió hospitalización desarrollaron sibilancias de repetición, frente al 8,6% de los niños cuya primera infección fue leve o asintomática, p < 0,001 (OR: 2,18; lC 95%: 1,05-4,5).

Conclusiones

En nuestra serie, las infecciones respiratorias virales graves en los primeros meses de vida supusieron un factor de riesgo para desarrollar sibilancias recurrentes. No ocurrió lo mismo con las infecciones respiratorias leves.

Association of Higher MERS-CoV Virus Load with Severe Disease and Death, Saudi Arabia, 2014

More data are needed to determine whether modulation of virus load by therapeutic agents affects clinical outcomes.

Middle East respiratory syndrome coronavirus (MERS-CoV) causes a spectrum of illness. We evaluated whether cycle threshold (C_t) values (which are inversely related to virus load) were associated with clinical severity in patients from Saudi Arabia whose nasopharyngeal specimens tested positive for this virus by real-time reverse transcription PCR. Among 102 patients, median C_t of 31.0 for the upstream of the E gene target for 41 (40%) patients who died was significantly lower than the median of 33.0 for 61 survivors (p = 0.0087). In multivariable regression analyses, risk factors for death were age >60 years), underlying illness, and decreasing C_t for each 1-point decrease in C_t). Results were similar for a composite severe outcome (death and/or intensive care unit admission). More data are needed to determine whether modulation of virus load by therapeutic agents affects clinical outcomes.

Postnatal Infections and Immunology Affecting Chronic Lung Disease of Prematurity

Premature infants suffer significant respiratory morbidity during infancy with long-term negative consequences on health, quality of life, and health care costs. Enhanced susceptibility to a variety of infections and inflammation play a large role in early and prolonged lung disease following premature birth, although the mechanisms of susceptibility and immune dysregulation are active areas of research. This article reviews aspects of host-pathogen interactions and immune responses that are altered by preterm birth and that impact chronic respiratory morbidity in these children.

Analytical performance of the automated multianalyte point-of-care mariPOC® for the detection of respiratory viruses

The analytical performance of mariPOC® respi test (ArcDia® Laboratories, Turku, Finland) was evaluated using nucleic acid amplification techniques (NAATs) as the gold standard. The mariPOC assay allows automated detection of antigens from 8 respiratory viruses: influenza A and B viruses, respiratory syncytial virus, adenovirus, human metapneumovirus, and parainfluenza viruses 1-3. Positive results from samples with high viral load are available in 20min. Nasopharyngeal aspirates (n=192) from patients with acute respiratory infection and from previously positive samples were analyzed by mariPOC and NAATs (Simplexa(TM) FluA/FluB & RSV kit [n=118] and Luminex® Respiratory virus panel xTAG® RVP FAST [n=74]). Sensitivity, specificity, positive predictive value, and negative predictive value of mariPOC were 85.4%, 99.2%, 95.9%, and 97%, respectively, and 84.6% of positive results were reported in 20min. The good analytical performance and extended portfolio of mariPOC show this rapid assay as a good alternative for the etiological diagnosis of acute respiratory infection in laboratories that are not equipped with molecular assays.

Factors associated with real-time RT-PCR cycle threshold values among medically attended influenza episodes

We evaluated the cycle threshold (CT) values of 1,160 influenza A positive and 806 influenza B positive specimens from two seasons of the US Flu VE Network to identify factors associated with CT values. Low CT values (high genomic load) were associated with shorter intervals between illness onset and specimen collection, young age (ages 3-8 years old), and self-rated illness severity for both influenza A and B. Low CT values were also associated with reported fever/feverishness and age ≥65 years for influenza A.

Challenges and opportunities in developing respiratory syncytial virus therapeutics

Two meetings, one sponsored by the Wellcome Trust in 2012 and the other by the Global Virology Foundation in 2013, assembled academic, public health and pharmaceutical industry experts to assess the challenges and opportunities for developing antivirals for the treatment of respiratory syncytial virus (RSV) infections. The practicalities of clinical trials and establishing reliable outcome measures in different target groups were discussed in the context of the regulatory pathways that could accelerate the translation of promising compounds into licensed agents. RSV drug development is hampered by the perceptions of a relatively small and fragmented market that may discourage major pharmaceutical company investment. Conversely, the public health need is far too large for RSV to be designated an orphan or neglected disease. Recent advances in understanding RSV epidemiology, improved point-of-care diagnostics, and identification of candidate antiviral drugs argue that the major obstacles to drug development can and will be overcome. Further progress will depend on studies of disease pathogenesis and knowledge provided from controlled clinical trials of these new therapeutic agents. The use of combinations of inhibitors that have different mechanisms of action may be necessary to increase antiviral potency and reduce the risk of resistance emergence.

[Application of molecular assay for adenovirus detection among different pediatric patients]

OBJECTIVE:

Adenoviruses play an important role in the etiology of severe acute lower respiratory infection, especially in young children. The aim of the present study was to evaluate the Human Adenovirus (HAdV) detection by different methods (Direct Fluorescence Assay DFA and Nested Polymerase Chain Reaction nested PCR), among samples collected from different groups of pediatric patients.

METHODS:

Collection of samples was made in children with congenital heart disease (CHD 123 nasal aspirates collected in the years of 2005, 2007 and 2008) and in community children (CC 165 nasal aspirates collected in 2008). Children were eligible if they presented acute respiratory infection (ARI) of probable viral etiology, within up to 7 days of symptoms' onset. All studied samples were evaluated by DFA and nested PCR assay.

RESULTS:

Of the 290 samples included during the study period, 43 (14.8%) were positive on at least one test: 17/165 (10.3%) of the CC and 26/125 (20.8%) of the CHD children. The nested PCR detection rates in the community children were 15/165 (9.1%), and for children with CHD, 24/125 (19.2%). Molecular method showed higher detection rates when compared to the DFA test (p<0.001). Univariate analysis showed that children with congenital heart disease presented a significantly higher chance for acquiring the HAdV (Odds Ratio 2.3; 95% CI: 1.18-4.43).

CONCLUSIONS:

Based on data obtained in the present evaluation, we suggest that a routine surveillance should be performed in high risk patients by molecular methods, thus improving diagnostic flow and efficiency.

Short- and long-term efficacy of prednisolone for first acute rhinovirus-induced wheezing episode

Background

Rhinovirus-induced wheezing is an important risk factor for recurrent wheezing. There are no randomized controlled trials on the effect of systemic corticosteroids in patients with this disease.

Objective

We sought to study the short- and long-term effects of prednisolone treatment of the first acute, moderate-to-severe, rhinovirus-induced wheezing episode in young children.

Methods

After confirming rhinovirus from nasopharyngeal aspirate by using PCR, 79 children with a first wheezing episode at age 3 to 23 months were randomized to receive oral prednisolone (first dose of 2 mg/kg, followed by 2 mg/kg/d in 2 divided doses for 3 days) or placebo. The trial was double blind throughout the 12-month follow-up. The primary outcomes were long term: new physician-confirmed wheezing episode within 2 months, number of physician-confirmed wheezing episodes within 12 months, and initiation of regular controller medication for asthma symptoms within 12 months. The primary interaction analysis examined rhinovirus load.

Results

Seventy-four patients completed the study (mean age, 13 months; 28% atopic). Long-term outcomes did not differ between groups (all P ≥ .30). For short-term outcomes, the prednisolone group had less cough, rhinitis, noisy breathing, severe breathing difficulties, and nocturnal respiratory symptoms at home within 2 weeks (all P < .05). The 25 children with greater than 7000 rhinovirus copies/mL (most sensitive cutoff) benefitted from prednisolone in terms of less risk of physician-confirmed recurrence within 2 and 12 months compared with placebo (both P < .05).

Conclusions

Prednisolone cannot be routinely recommended for all young children experiencing their first acute, moderate-to-severe, rhinovirus-induced wheezing episode. Prednisolone might be beneficial in a subgroup of children with high viral loads.

Emerging respiratory viruses other than influenza

Non-influenza respiratory virus infections are common worldwide and contribute to morbidity and mortality in all age groups. The recently identified Middle East respiratory syndrome coronavirus has been associated with rapidly progressive pneumonia and high mortality rate. Adenovirus 14 has been increasingly recognized in severe acute respiratory illness in both military and civilian individuals. Rhinovirus C and human bocavirus type 1 have been commonly detected in infants and young children with respiratory tract infection and studies have shown a positive correlation between respiratory illness and high viral loads, mono-infection, viremia, and/or serologically-confirmed primary infection.

Attenuation of respiratory syncytial virus-induced and RIG-I-dependent type I IFN responses in human neonates and very young children

Newborn infants, including those born at term without congenital disorders, are at high risk of severe disease from respiratory syncytial virus (RSV) infection. Indeed, our current local surveillance data demonstrate that approximately half of children hospitalized with RSV were ≤3 mo old, and 74% were born at term. Informed by this clinical epidemiology, we investigated antiviral innate immune responses in early life, with the goal of identifying immunological factors underlying the susceptibility of infants and young children to severe viral lower respiratory tract infections. We compared RSV-induced innate cytokine production in blood mononuclear cells from neonates, young children aged 12-59 mo, and healthy adults. RSV-induced IFN-α production was primarily mediated by plasmacytoid dendritic cells (pDCs), and was significantly lower in term infants and young children < 5 y of age than in adults (p < 0.01). RSV-induced IFN-α production in human pDCs proceeded independently of endosomal TLRs, and human pDCs from healthy adult donors produced IFN-α in a retinoic acid-inducible gene I protein (RIG-I)-dependent manner. Of interest, young age and premature birth were independently associated with attenuated RIG-I-dependent IFN-α responses (p < 0.01). In contrast to IFN-α production, proinflammatory IL-6 responses to RSV were mediated by monocytes, appeared less dependent on RIG-I, and were significantly impaired only among preterm infants, not in term infants and young children. Our results suggest that human pDCs are less functional in early life, which may contribute to the increased susceptibility of infants and young children to severe RSV disease.

Respiratory viral detection and small airway inflammation in lung tissue of patients with stable, mild COPD

BACKGROUND

Viral respiratory tract infections are implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). In lung tissue specimens from patients with stable, mild COPD and from control smokers without airflow obstruction, we determined the prevalence and load of nucleic acid from common respiratory viruses and concomitant inflammation of small airways measuring less than 2-mm in diameter.

METHODS

Frozen lung tissue obtained from patients with stable, mild COPD (n = 20) and control subjects (n = 20) underwent real-time quantitative PCR (qPCR) for 13 respiratory viruses, and quantitative histology for inflammation of small airways. The two groups were compared for viral prevalence and load, and airway inflammation. The relationship between viral load and airway inflammatory cells was also analyzed.

RESULTS

Viral nucleic acid were detected in lung tissue of 18/40 (45.0%) of the individuals studied and included seven co-infections that were characterized by a "dominant virus" contributing to most of the total measured viral load. Lung tissue of COPD patients had a significantly higher prevalence of viral nucleic acid (particularly influenza A virus), and increased inflammation of small airways by macrophages and neutrophils versus controls. In qPCR-positive individuals, linear regression analysis showed a direct correlation between viral load and airway neutrophils, and between influenza A virus load and airway macrophages.

CONCLUSION

The lung tissue of patients with stable, mild COPD has a higher prevalence and load of respiratory viruses versus non-obstructed control subjects, and increased inflammation of small airways. Respiratory viruses may represent potential targets in COPD patient management.

Association of the CT values of real-time PCR of viral upper respiratory tract infection with clinical severity, Kenya

Quantitative real-time polymerase chain reaction (qRT-PCR) assay of the upper respiratory tract is used increasingly to diagnose lower respiratory tract infections. The cycle threshold (CT ) values of qRT-PCR are continuous, semi-quantitative measurements of viral load, although interpretation of diagnostic qRT-PCR results are often categorized as positive, indeterminate, or negative, obscuring potentially useful clinical interpretation of CT values. From 2008 to 2010, naso/oropharyngeal swabs were collected from outpatients with influenza-like illness, inpatients with severe respiratory illness, and asymptomatic controls in rural Kenya. CT values of positive specimens (i.e., CT values < 40.0) were compared by clinical severity category for five viruses using Mann-Whitney U-test and logistic regression. Among children <5 years old we tested with respiratory syncytial virus (RSV), inpatients had lower median CT values (27.2) than controls (35.8, P = 0.008) and outpatients (34.7, P < 0.001). Among children and older patients infected with influenza virus, outpatients had the lowest median CT values (29.8 and 24.1, respectively) compared with controls (P = 0.193 for children, P < 0.001 for older participants) and inpatients (P = 0.009 for children, P < 0.001 for older participants). All differences remained significant in logistic regression when controlling for age, days since onset, and coinfection. CT values were similar for adenovirus, human metapneumovirus, and parainfluenza virus in all severity groups. In conclusion, the CT values from the qRT-PCR of upper respiratory tract specimens were associated with clinical severity for some respiratory viruses.

The significance of rhinovirus detection in hospitalized children: clinical, epidemiological and virological features

Recent developments in molecular diagnostic tools have led to the easy and rapid detection of a large number of rhinovirus (HRV) strains. However, the lack of clinical and epidemiological data hampers the interpretation of these diagnostic findings. From October 2009 to January 2011, we conducted a prospective study in hospitalized children from whom samples were taken for the detection of respiratory viruses. Clinical, epidemiological and microbiological data from 644 patients with 904 disease episodes were collected. When HRV tested positive, strains were further characterized by sequencing the VP4/VP2 region of the HRV genome. HRV was the single respiratory virus detected in 254 disease episodes (28%). Overall, 99 different serotypes were detected (47% HRV‐A, 12% HRV‐B, 39% HRV‐C). Patients with HRV had more underlying pulmonary illness compared with patients with no virus (p 0.01), or patients with another respiratory virus besides HRV (p 0.007). Furthermore, cough, shortness of breath and a need for oxygen were significantly more present in patients with HRV infection. Particularly, patients with HRV‐B required extra oxygen. No respiratory symptom, except for oxygen need, was predictive of the presence of HRV. In 22% of HRV‐positive disease episodes, HRV infection was hospital acquired. Phylogenetic analysis revealed several clusters of HRV; in more than 25% of these clusters epidemiological information was suggestive of transmission within specific wards. In conclusion, the detection of HRV may help in explaining respiratory illness, particular in patients with pulmonary co‐morbidities. Identifying HRV provides opportunities for timely implementation of infection control measures to prevent intra‐hospital transmission.

New molecular virus detection methods and their clinical value in lower respiratory tract infections in children

During the past decade, several new respiratory viruses and their subgroups have been discovered. All these new viruses, as well as previously known respiratory viruses, can be detected by sensitive PCR methods, which have become popular in the diagnostic workup of respiratory viral infections. Currently, respiratory viruses can be detected in up to 95% of children with lower respiratory tract illness. On the other hand, virus detection rates in asymptomatic children are also high (up to 68%), as are coinfection rates in symptomatic children (up to 43%) and justified concerns of causality have been raised. Imposing progress has been made in developing multiplex quantitative PCR assays; here, several primer sets are run within a single PCR mixture. These PCR assays give a better understanding of the dominant viral infection, of viral infections that may be incipient and of any waning infections than does a single-target PCR. Multiplex PCR assays are also gaining popularity due to their cost-effectiveness and short throughput time compared to multiple single-target PCRs. Our understanding of the indications of virus PCRs and our ability to interpret the results from a clinical point of view have improved. This paper reviews the progress in PCR assays and discusses their role in the diagnosis of lower respiratory tract infections in children.

Epidemiology of multiple respiratory viruses in childcare attendees

Background. The identification of multiple viruses during respiratory illness is increasing with advances in rapid molecular testing; however, the epidemiology of respiratory viral coinfections is not well known.

Methods. In total, 225 childcare attendees were prospectively followed for up to 2 years. Nasal swabs were collected at respiratory illness onset and every 7–10 days until illness resolution. Swabs were tested by polymerase chain reaction for 15 respiratory viruses and subtypes.

Results. At least 1 virus was detected in 382 (84%) of 455 new-onset illnesses with multiple viruses identified in 212 (46%). The proportion of subject swabs with multiple viruses detected changed as respiratory illnesses progressed from week to week, as did the prevalence of individual viruses. Children with multiple viruses detected at the time of illness onset had less frequent fever (odds ratio [OR], 0.56; 95% confidence interval [CI], 0.35, 0.90), however, these children more often had illness symptoms lasting over 7 days (OR, 1.94; 95% CI, 1.20, 3.14).

Conclusions. A high proportion of daycare attendees had multiple viruses detected during respiratory illnesses. Delay between onset of illness and viral detection varied by virus, indicating that some viruses may be underrepresented in studies of virus epidemiology that rely on only a single test at symptom onset.

George K, Walsh TJ. Human rhinoviruses

Human rhinoviruses (HRVs), first discovered in the 1950s, are responsible for more than one-half of cold-like illnesses and cost billions of dollars annually in medical visits and missed days of work. Advances in molecular methods have enhanced our understanding of the genomic structure of HRV and have led to the characterization of three genetically distinct HRV groups, designated groups A, B, and C, within the genus Enterovirus and the family Picornaviridae. HRVs are traditionally associated with upper respiratory tract infection, otitis media, and sinusitis. In recent years, the increasing implementation of PCR assays for respiratory virus detection in clinical laboratories has facilitated the recognition of HRV as a lower respiratory tract pathogen, particularly in patients with asthma, infants, elderly patients, and immunocompromised hosts. Cultured isolates of HRV remain important for studies of viral characteristics and disease pathogenesis. Indeed, whether the clinical manifestations of HRV are related directly to viral pathogenicity or secondary to the host immune response is the subject of ongoing research. There are currently no approved antiviral therapies for HRVs, and treatment remains primarily supportive. This review provides a comprehensive, up-to-date assessment of the basic virology, pathogenesis, clinical epidemiology, and laboratory features of and treatment and prevention strategies for HRVs.

Laboratory detection of respiratory viruses by automated techniques

Advances in clinical virology for detecting respiratory viruses have been focused on nucleic acids amplification techniques, which have converted in the reference method for the diagnosis of acute respiratory infections of viral aetiology. Improvements of current commercial molecular assays to reduce hands-on-time rely on two strategies, a stepwise automation (semi-automation) and the complete automation of the whole procedure. Contributions to the former strategy have been the use of automated nucleic acids extractors, multiplex PCR, real-time PCR and/or DNA arrays for detection of amplicons. Commercial fully-automated molecular systems are now available for the detection of respiratory viruses. Some of them could convert in point-of-care methods substituting antigen tests for detection of respiratory syncytial virus and influenza A and B viruses. This article describes laboratory methods for detection of respiratory viruses. A cost-effective and rational diagnostic algorithm is proposed, considering technical aspects of the available assays, infrastructure possibilities of each laboratory and clinic-epidemiologic factors of the infection.

Human parainfluenza virus serotypes differ in their kinetics of replication and cytokine secretion in human tracheobronchial airway epithelium

Human parainfluenza viruses (PIVs) cause acute respiratory illness in children, the elderly, and immunocompromised patients. PIV3 is a common cause of bronchiolitis and pneumonia, whereas PIV1 and 2 are frequent causes of upper respiratory tract illness and croup. To assess how PIV1, 2, and 3 differ with regard to replication and induction of type I interferons, interleukin-6, and relevant chemokines, we infected primary human airway epithelium (HAE) cultures from the same tissue donors and examined replication kinetics and cytokine secretion. PIV1 replicated to high titer yet did not induce cytokine secretion until late in infection, while PIV2 replicated less efficiently but induced an early cytokine peak. PIV3 replicated to high titer but induced a slower rise in cytokine secretion. The T cell chemoattractants CXCL10 and CXCL11 were the most abundant chemokines induced. Differences in replication and cytokine secretion might explain some of the differences in PIV serotype-specific pathogenesis and epidemiology.

Use of an improved quantitative polymerase chain reaction assay to determine differences in human rhinovirus viral loads in different populations

Human rhinoviruses (HRV) frequently cause acute respiratory infections and chronic respiratory disease exacerbations. However, testing is not generally offered. We developed a modified HRV quantitative polymerase chain reaction (qPCR) assay to assess viral loads in the community and hospital patients. The assay had a lower limit of detection of 2 log(10) viral copies/mL and displayed linearity over 5 log(10) viral copies, with a lower limit of quantitation of 4 log(10) viral copies/mL. Mean viral loads (95% confidence interval) for hospitalized children, university students, and institutionalized elderly, were 7.08 log(10) viral copies/mL (6.7-7.5), 6.87 log(10) viral copies/mL (6.5-7.2), and 7.09 log(10) viral copies/mL (6.9-7.3), respectively (P = 0.67). Serial specimens of 14 university students showed a decrease of mean viral loads from 6.36 log(10) viral copies/mL on day 1 to 2.32 log(10) viral copies/mL 7 days past symptom onset (P < 0.001). Using an HRV qPCR, we showed that viral loads did not differ between the community and hospitalized populations and significantly decreased following symptoms onset in healthy individuals.

Lessons learned from a double-blind randomised placebo-controlled study with a iota-carrageenan nasal spray as medical device in children with acute symptoms of common cold

Background

Common cold is caused by a variety of respiratory viruses. The prevalence in children is high, and it potentially contributes to significant morbidity. Iota-carragenan, a polymer derived from red seaweed, has reduced viral load in nasal secretions and alleviated symptoms in adults with common cold.

Methods

We have assessed the antiviral and therapeutic activity of a nasal spray containing iota-carrageenan in children with acute symptoms of common cold. A cohort of 153 children between 1–18 years (mean age 5 years), displaying acute symptoms of common cold were randomly assigned to treatment with a nasal spray containing iota-carrageenan (0.12%) as verum or 0.9% sodium chloride solution as placebo for seven days. Symptoms of common cold were recorded and the viral load of respiratory viruses in nasal secretions was determined at two consecutive visits.

Results

The results of the present study showed no significant difference between the iota carrageenan and the placebo group on the mean of TSS between study days 2–7. Secondary endpoints, such as reduced time to clearance of disease (7.6 vs 9.4 days; p = 0.038), reduction of viral load (p = 0.026), and lower incidence of secondary infections with other respiratory viruses (p = 0.046) indicated beneficial effects of iota-carrageenan in this population. The treatment was safe and well tolerated, with less side effects observed in the verum group compared to placebo.

Conclusion

In this study iota-carrageenan did not alleviate symptoms in children with acute symptoms of common cold, but significantly reduced viral load in nasal secretions that may have important implications for future studies.

Trial registration

ISRCTN52519535, http://www.controlled-trials.com/ISRCTN52519535/

Identifying targets in the hunt for effective respiratory syncytial virus interventions

Respiratory syncytial virus (RSV) is a major cause of human infections worldwide. There is currently no effective vaccine or antiviral therapy available for widespread clinical use; prophylaxis with anti-RSV antibodies is used in only a small percentage of potential recipients. New targets for effective RSV interventions are needed. Previous anti-RSV intervention strategies have focused on targeting aspects of the virus, an approach that can lead to the emergence of resistant RSV strains. Increased understanding of the biology of RSV-host interactions provides an alternative approach for identifying novel targets for RSV interventions that focus on host factors, and exploiting them with the aim to limit the incidence and severity of RSV infections.

Viral load and acute otitis media development after human metapneumovirus upper respiratory tract infection

The role of human metapneumovirus (hMPV) in acute otitis media complicating upper respiratory tract infection (URI) was studied. Nasopharyngeal specimens from 700 URI episodes in 200 children were evaluated; 47 (7%) were positive for hMPV, 25 (3.6%) with hMPV as the only virus. Overall, 24% of URI episodes with hMPV only were complicated by acute otitis media, which was the lowest rate compared with other respiratory viruses. hMPV viral load was significantly higher in children with fever, but there was no difference in viral load in children with hMPV-positive URI with or without acute otitis media complication.

Critical analysis of rhinovirus RNA load quantification by real-time reverse transcription-PCR

Rhinoviruses are the most frequent cause of human respiratory infections, and quantitative rhinovirus diagnostic tools are needed for clinical investigations. Although results obtained by real-time reverse-transcription PCR (RT-PCR) assays are frequently converted to viral RNA loads, this presents several limitations regarding accurate virus RNA quantification, particularly given the need to reliably quantify all known rhinovirus genotypes with a single assay. Using an internal extraction control and serial dilutions of an in vitro-transcribed rhinovirus RNA reference standard, we validated a quantitative one-step real-time PCR assay. We then used chimeric rhinovirus genomes with 5'-untranslated regions (5'UTRs) originating from the three rhinovirus species and from one enterovirus to estimate the impact of the 5'UTR diversity. Respiratory specimens from infected patients were then also analyzed. The assay quantification ability ranged from 4.10 to 9.10 log RNA copies/ml, with an estimated error margin of ±10%. This variation was mainly linked to target variability and interassay variability. Taken together, our results indicate that our assay can reliably estimate rhinovirus RNA load, provided that the appropriate error margin is used. In contrast, due to the lack of a universal rhinovirus RNA standard and the variability related to sample collection procedures, accurate absolute rhinovirus RNA quantification in respiratory specimens is currently hardly feasible.

Viral load at diagnosis and influenza A H1N1 (2009) disease severity in children

To assess viral load at diagnosis (VLAD) as a biomarker of novel influenza disease severity, epidemiologic and clinical data of admitted patients <18 years old with Influenza A H1N1 (2009) infection and respiratory symptoms were prospectively collected in a single pediatric tertiary hospital, from weeks 30-51 of 2009. Seventy patients were included. VLAD in children who had symptoms for ≥ 5 days was an accurate parameter distinguishing the patients who required mechanical ventilation (MV) from those who did not required it (area under the ROC curve: 0.73; P=0.03). Having <4.5 log10 copies/ml with ≥ 5 days of symptoms was associated with a lower risk of requiring MV.

Pathogenesis of acute respiratory illness caused by human parainfluenza viruses

Human parainfluenza viruses (HPIVs) are a common cause of acute respiratory illness throughout life. Infants, children, and the immunocompromised are the most likely to develop severe disease. HPIV1 and HPIV2 are best known to cause croup while HPIV3 is a common cause of bronchiolitis and pneumonia. HPIVs replicate productively in respiratory epithelial cells and do not spread systemically unless the host is severely immunocompromised. Molecular studies have delineated how HPIVs evade and block cellular innate immune responses to permit efficient replication, local spread, and host-to-host transmission. Studies using ex vivo human airway epithelium have focused on virus tropism, cellular pathology and the epithelial inflammatory response, elucidating how events early in infection shape the adaptive immune response and disease outcome.

Timely diagnosis of respiratory tract infections: evaluation of the performance of the Respifinder assay compared to the xTAG respiratory viral panel assay

Background

Respiratory tract infections are the most common cause of hospitalization in infants and young children and are typically caused by viral or, less commonly, bacterial pathogens.

Existing non-molecular diagnostic methods have several drawbacks such as limited sensitivity, long turn-a-round time and limited number of pathogens that can be detected.

Objectives

Nucleic acid amplification methods can increase sensitivity and enable the initiation of appropriate interventions without delay.

Broad-spectrum detection and identification circumvent the use of individual diagnostic DNA or RNA based assays. At present, several commercial assays are available for broad-spectrum detection.

Study design

We compared the performance of the xTAG Respiratory Viral Panel (RVP) (Luminex Molecular Diagnostics, Toronto, Canada) with that of the Respifinder (Pathofinder, Maastricht, Netherlands) for 9 external quality assurance (EQA) panels (QCMD, Scotland) consisting of a total of 106 EQA samples.

Results

Both the RVP and the Respifinder assay have an excellent specificity. Sensitivity was 33% and 78% for the RVP and the Respifinder assay, respectively. For both assays, sensitivity was low for weak positive samples.

Discussion

The results of our study seem to indicate a better sensitivity for the Respifinder. Analysis of patient samples is necessary to evaluate the clinical performance.

PCR for detection of respiratory viruses: seasonal variations of virus infections

Real-time PCR and related methods have revolutionized the laboratory diagnosis of viral respiratory infections because of their high detection sensitivity, rapidness and potential for simultaneous detection of 15 or more respiratory agents. Results from studies with this diagnostic modality have significantly expanded our knowledge about the seasonality of viral respiratory diseases, pinpointed the difficulties to make a reliable etiologic diagnosis without the aid of an unbiased multiplex molecular assay for respiratory viruses, and revealed previously unknown details as to possible infections with multiple agents as aggravating factors. The scope of this article is to review and discuss this new knowledge and its implications for diagnostic strategies and other measures essential for the clinical management of respiratory viral infections and for epidemiological surveillance of seasonal respiratory infections.

Comparison of two multiplex methods for detection of respiratory viruses: FilmArray RP and xTAG RVP

We compared the FilmArray RP (Idaho Technology, Inc., Salt Lake City, UT) and the xTAG RVP (Luminex Corporation, Toronto, Canada) multiplex respiratory virus PCR methods for the detection of respiratory viruses in a set of 200 patient specimens frozen at -70 °C after standard viral culture and antigen detection methods were done. Both systems detected between 40 to 50% more viruses than traditional methods, primarily rhinoviruses and human metapneumovirus. The FilmArray RP detected significantly more total viruses either alone or as part of mixed infections than the xTAG RVP, as well as an additional 21.6% more respiratory syncytial viruses. The xTAG RVP requires 5 to 6 h with 2.5 to 3 h of hands-on time, while the FilmArray RP takes about an hour with 3 to 5 min of hands-on time, making it much easier to perform.