Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP-based multiplex-PCR assay

Laboratory markers among children with respiratory tract infection using a multiplex PCR test

BACKGROUND

Evidence on the comparative impact of laboratory markers on multiple respiratory viruses is scarce. This study aimed to evaluate the comparative impact of multiple respiratory viruses among symptomatic children on laboratory markers, including C-reactive protein (CRP) levels.

METHODS

This was a retrospective observational study between April 2018 and August 2024 for children aged 15 years or younger who received a blood and multiplex polymerase chain reaction (PCR) tests from a nasopharyngeal swab. Children with fever or respiratory symptoms underwent multiplex PCR, irrespective of symptom severity. A generalized linear regression model was used to evaluate the impact of the variables on each inflammatory marker.

RESULTS

Overall, 3,893 multiplex PCR tests were included in the analysis. Pathogen co-detection was not significant for any laboratory marker (e.g., for CRP: Coefficient 0.03 [95 % confidence interval -0.21, 0.28] and p=0.778). Adenoviruses were positively associated with CRP levels (coefficient 0.28 [0.07, 0.50]; p=0.010). SARS-CoV-2 was negatively associated with CRP level (coefficient -0.56 [0.79, -0.32] and p<0.001). Negative multiplex PCR results were associated with higher CRP levels (coefficient, 0.20 [0.00, 0.40]; p=0.046).

CONCLUSION

Our study showed a positive association between adenovirus and negative multiplex PCR test results and a negative association between SARS-CoV-2 and CRP levels. Our study may support a better interpretation of laboratory results and the clinical management of children with respiratory tract infection.

Epidemiological trends and pathogen analysis of pediatric acute respiratory infections in Hanzhong Hospital, China: insights from 2023 to 2024

Background

Acute respiratory infections (ARIs) are a leading cause of morbidity in children. Understanding the distribution of respiratory pathogens is crucial for effective prevention and treatment. This study analyzed the prevalence and epidemiological characteristics of ARIs in children from 2023 to 2024.

Methodology

This study included 9,294 children aged 0-18 years with ARI symptoms who were treated between July 2023 and August 2024. Respiratory samples were tested using polymerase chain reaction (PCR) for eight common viruses. Data were analyzed by age and gender to assess pathogen distribution and demographic patterns.

Results

A total of 14,722 samples were enrolled, with 2,888 (19.62%) testing positive for at least one pathogen. Among these, single-pathogen infections were predominant (97.66%, 2,756/2,822), while co-infections were less frequent (2.34%, 66/2,822). The three most common pathogens were adenovirus (ADV, 33.24%), Mycoplasma pneumoniae (MP, 25.07%), and whooping cough (WC, 22.78%). No significant gender differences were observed in the overall positive rate or pathogen distribution (p > 0.05). Pathogen detection rates varied significantly by age group (χ 2 = 110.03, p < 0.001), with WC and MP being most prevalent in school-age children (χ 2 = 104.58, p < 0.001; χ 2 = 11.546, p = 0.009, respectively) and Flu A more frequent in preschool children (χ 2 = 38.738, p < 0.001). MP, WC, ADV, human rhinovirus, and human metapneumovirus were detected throughout the year.

Discussion

The findings highlight that ARIs in children are primarily caused by single respiratory pathogens, with significant age-related differences in pathogen prevalence. These results emphasize the need for age-specific prevention strategies, such as targeted vaccination programs and public health interventions, particularly for school-age children during peak transmission periods.

Seasonality and Co-Detection of Respiratory Viral Infections Among Hospitalised Patients Admitted With Acute Respiratory Illness-Valencia Region, Spain, 2010-2021

BACKGROUND

Respiratory viruses are known to represent a high burden in winter, yet the seasonality of many viruses remains poorly understood. Better knowledge of co-circulation and interaction between viruses is critical to prevention and management. We use > 10-year active surveillance in the Valencia Region to assess seasonality and co-circulation.

METHODS

Over 2010-2021, samples from patients hospitalised for acute respiratory illness were analysed using multiplex real-time PCR to test for 9 viruses: influenza, respiratory syncytial virus (RSV), parainfluenza virus (PIV), rhino/enteroviruses (HRV/ENV), metapneumovirus (MPV), bocavirus, adenovirus, SARS-CoV-2 and non-SARS coronaviruses (HCoV). Winter seasonal patterns of incidence were examined. Instances of co-detection of multiple viruses in a sample were analysed and compared with expected values under a crude model of independent circulation.

RESULTS

Most viruses exhibited consistent patterns between years. Specifically, RSV and influenza seasons were clearly defined, peaking in December-February, as did HCoV and SARS-CoV-2. MPV, PIV and HRV/ENV showed less clear seasonality, with circulation outside the observed period. All viruses circulated in January, suggesting any pair had opportunity for co-infection. Multiple viruses were found in 4% of patients, with more common co-detection in children under 5 (9%) than older ages. Influenza co-detection was generally observed infrequently relative to expectation, while RSV co-detections were more common, particularly among young children.

CONCLUSIONS

We identify characteristic patterns of viruses associated with acute respiratory hospitalisation during winter. Simultaneous circulation permits extensive co-detection of viruses, particularly in young children. However, virus combinations appear to differ in their rates of co-detection, meriting further study.

The Characteristics of Respiratory Bocavirus Infection in Acutely Sick Children Admitted to a Tertiary Hospital in Jordan

OBJECTIVE

The clinical manifestations of human bocavirus infections are diverse, ranging from mild common cold to severe lower respiratory tract infections. Bocaviruses have frequently been codetected with other respiratory viruses. We aimed to estimate the burden of bocavirus and multiple viral infections and to investigate the risk factors associated with these infections.

METHODS

This study was a retrospective chart review of admitted patients. The medical records of the included children were searched, and data on demographics, clinical presentation, imaging, laboratory and nasopharyngeal swab results were collected.

RESULTS

A total of 157 patients were included. Most of the patients were males (62.1%) and under 6 months of age (52%). The 3 most common symptoms presented in the patients were cough (81.8%), rhinorrhea (58.6%) and fever (55.8%). Bocavirus DNA was detected in 12.66% of the patients, while 22.30% had multiple viruses. Age distribution was significantly different between bocavirus and nonbocavirus groups, with a lower proportion of bocavirus infection in all age groups ( P = 0.032). The radiograph patterns significantly differed between the 2 study groups, with a lower number of patients in the bocavirus group having normal radiographs ( P = 0.007). Patients infected with multiple viruses had more severe respiratory distress symptoms and diarrhea than those infected with only 1 virus.

CONCLUSIONS

The prevalence of multiple viruses and bocavirus respiratory infections is significant. This study can guide physicians toward the clinical presentation and characteristics of children with respiratory bocavirus and multiple viral infections and propose future studies conducted in this regard.

Epidemiology and clinical characteristics of severe acute respiratory infections among hospitalized children under 5 years of age in a tertiary care center in Bangkok, Thailand, 2019-2020

BACKGROUND

Acute respiratory infections (ARIs) are common in children and can range in severity from mild self-limiting illnesses to more severe conditions such as pneumonia and respiratory failure. Data on the epidemiology of viral and bacterial pathogens causing ARIs in children are scarce in this region. This study aimed to investigate the epidemiology and clinical manifestations of pathogens in children aged ≤5 years presenting with severe acute respiratory infection (SARI) in Bangkok, Thailand. The impact of rapid multiplex PCR-based testing on clinical management is also explored.

METHODS

This cross-sectional study enrolled consecutive children aged ≤5 years presenting with SARI at a tertiary care centre in Bangkok, Thailand, between 2019 and 2020. Nasopharyngeal swabs were collected once at admission, and viral and bacterial pathogens were tested using the QIAstat-Dx respiratory panel.

RESULTS

A total of 169 children were enrolled in this study. At least one pathogenic virus was detected in 91.7 % of participants. Based on the final diagnoses made upon discharge, 30.2 % had upper respiratory tract infection, whereas 66.3 % had lower respiratory tract infection. Pneumonia was the most common diagnosis (59.2 %). The most common pathogen identified was rhino/enterovirus (45.2 %), followed by respiratory syncytial virus (31.6 %) and parainfluenza virus (14.2 %). Co-infection was found in 15.4 % and was not associated with increased disease severity.

CONCLUSIONS

This study provides additional insights into the pathogen profiles, clinical diagnosis, and co-infection combinations of ARIs in hospitalized children. This information is useful for diagnosis and treatment of ARIs, as well as implementation of appropriate infection control measures and guidance for future vaccine policy development.

A multicenter study on molecular epidemiology of rhinovirus isolated from children with community acquired pneumonia in China during 2017-2019

Rhinoviruses (RVs) are a major pathogen of community acquired pneumonia in children. To investigate the prevalence and genetic characteristics of RVs in China, we performed a molecular epidemiological study during 2017-2019 in community acquired pneumonia (CAP) in pediatric patients. In this multicenter study, 109 RV-A, 20 RV-B and 80 RV-C were identified. Among them, RV-A12, RV-A101, RV-A78, RV-A49, RV-A22, RV-B52, RV-C2, RV-C53 and RV-C5 were the common genotypes in the study. A total of 23 complete genome of RVs including 4 RV-A, 1 RV-B and 18 RV-C were obtained. Furthermore, in the RV-C isolates, one RV-C5 and five RV-C53 genotypes were found, which have a limited number in the GenBank. Phylogenetic analysis of the complete genome showed that most of the RVs isolated in the study have high nucleotide sequence identities (>95%) compared with the corresponding reference sequence in the GenBank. In RV-A9, RV-A28, RV-A61 and RV-B52, amino acid mutations were found in the potential neutralizing immunogenic (Nim) sites (Nim-1a and Nim-1b) of the VP1. In RV-B52, one of RV-C2 and RV-C5 isolates, amino acid mutations were found in the P1a peptide of the VP1. However, no recombination events were found in the study. In conclusion, RV-A was the predominant specie of RVs followed by RV-C in the study. The complete genomes of one RV-C5 and five RV-C53 genotypes were obtained which have a limited number sequence in the GenBank. High nucleotide sequence identities (>95%) were found among the complete genome obtained in the study and the corresponding reference sequence in the GenBank. Amino acid mutations were found in the potential Nim-1a, Nim-1b sites and P1a peptide region of the VP1 in parts of RVs.

Monoterpene-Containing Substituted Coumarins as Inhibitors of Respiratory Syncytial Virus (RSV) Replication

Respiratory syncytial virus (RSV) is a critical cause of infant mortality. However, there are no vaccines and adequate drugs for its treatment. We showed, for the first time, that O-linked coumarin-monoterpene conjugates are effective RSV inhibitors. The most potent compounds are active against both RSV serotypes, A and B. According to the results of the time-of-addition experiment, the conjugates act at the early stages of virus cycle. Based on molecular modelling data, RSV F protein may be considered as a possible target.

Burden of influenza disease in children under 2 years of age hospitalized between 2011 and 2020 in France

BACKGROUND

Although influenza viruses cause significant morbidity and mortality worldwide, the impact of these infections on children in France and in other European countries has not been extensively characterized. The primary objective of the present study was to describe the burden of influenza disease on hospitalized children under 2 years of age in France, using data from the national hospital discharge summary database (Programme de Médicalisation des Systèmes d'Information, PMSI).

METHODS

In a retrospective study of hospital admissions for influenza among children under the age of 2 in France, we extracted and analyzed hospital administrative data from the PMSI database (from January 1, 2011, to December 31, 2020).

RESULTS

From 2011 to 2020, 28,507 children under the age of 2 were admitted to hospital with a primary or secondary diagnosis of influenza infection. The hospital admission rate was 205 per 100,000 for children under the age of 2, 276 per 100,000 for children under the age of 12 months, and 135 per 100,000 for children aged between 12 and 23 months. Children under 6 months of age were the most affected (45.4%). An underlying condition was identified for 9.4% of the children, and 2.2% of the children were admitted to the intensive care unit. The death rate was 0.12 per 100,000 for children under 2, 0.11 per 100,000 for children under 12 months, and 0.16 per 100,000 for children aged between 12 and 23 months.

CONCLUSIONS

In France, the burden of influenza disease is significant in children under the age of 2.

Development of a multiplex assay to determine the expression of mitochondrial genes in human skeletal muscle

NEW FINDINGS

What is the central question of this study? Can a custom-designed multiplex gene expression assay be used to quantify expression levels of a targeted group of mitochondrial genes in human skeletal muscle? What is the main finding and its importance? A custom-designed GeXP multiplex assay was developed, and the ability to accurately quantify expression of a targeted set of mitochondrial genes in human skeletal muscle was demonstrated. It holds distinct methodological and practical advantages over other commonly used quantification methods.

ABSTRACT

Skeletal muscle is an important endocrine tissue demonstrating plasticity in response to external stimuli, including exercise and nutrition. Mitochondrial biogenesis is a common hallmark of adaptations to aerobic exercise training. Furthermore, altered expression of several genes implicated in the regulation of mitochondrial biogenesis, substrate oxidation and nicotinamide adenine dinucleotide (NAD⁺ ) biosynthesis following acute exercise underpins longer-term muscle metabolic adaptations. Gene expression is typically measured using real-time quantitative PCR platforms. However, interest has developed in the design of multiplex gene expression assays (GeXP) using the GenomeLab GeXP™ genetic analysis system, which can simultaneously quantify gene expression of multiple targets, holding distinct advantages in terms of throughput, limiting technical error, cost effectiveness, and quantifying gene co-expression. This study describes the development of a custom-designed GeXP assay incorporating the measurement of proposed regulators of mitochondrial biogenesis, substrate oxidation, and NAD⁺ biosynthetic capacity in human skeletal muscle and characterises the resting gene expression (overnight fasted and non-exercised) signature within a group of young, healthy, recreationally active males. The design of GeXP-based assays provides the capacity to more accurately characterise the regulation of a targeted group of genes with specific regulatory functions, a potentially advantageous development for future investigations of the regulation of muscle metabolism by exercise and/or nutrition.

The Epidemiology of Admission-Requiring Pediatric Respiratory Infections in a Japanese Community Hospital Using Multiplex PCR

Respiratory tract infections (RTIs) are the most common diseases globally among children. This study aimed to assess the epidemiology of admission-requiring pediatric RTI cases and evaluate the effect of the pathogen type on the length of hospital stay (LOS) using the FilmArray^® respiratory panel, a multiplex PCR test. The age-specific distribution and seasonality of viruses were investigated between March 26, 2018 and April 12, 2019. Multivariable linear regression analyses were performed to evaluate the effect of pathogen type and coinfection on LOS. Among 153 hospitalized RTI patients, respiratory syncytial virus was the leading cause of hospitalization in infants < 12 months of age (27.7%). Human metapneumovirus and parainfluenza virus were also major causes of hospitalization in patients aged 2-3 years (22.6% and 22.6%, respectively). In the multivariable linear regression model excluding rhinovirus/enterovirus, there was a significant association between viral coinfection and longer LOS (p = 0.012), while single viral infection of any type was not positively correlated with LOS. This study revealed the epidemiology of admission-requiring pediatric RTIs.

Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP-based multiplex-PCR assay

Background

The information regarding viral epidemiology and clinical characteristics in hospitalized children with acute respiratory tract infection (ARTI) in central Fujian is limited. In this study, we aimed at analyzing the viral epidemiology and clinical characteristics of ARTI in hospitalized children admitted to The First Affiliated Hospital of Fujian Medical University.

Methods

Cohort of 386 hospitalized children (31 days to 15 years) diagnosed with ARTI admitted to the Department of Pediatrics from January 1, 2018, to December 31, 2018, was enrolled in this study. Nasopharyngeal swab or sputum samples on the day of hospitalization were tested for 11 viruses via a GeXP‐based multiplex‐PCR assay. The viral profiles and clinical characteristics were analyzed.

Results

The overall positive rate of the samples was 43.26% (167/386). Among the 167 positive samples, 134 (80.24%, 134/167) had a single virus and 33 (19.76%, 33/167) had multiple viruses. There was a significant difference in the frequency of single vs mixed infections among positive samples (80.24% vs 19.76%; χ² = 122.168, P = .000) as well as among the total examined samples (34.72% vs 8.55%; χ² = 77.945, P = .000). Human rhinovirus was the most prevalent virus (17.36%, 67/386), followed by influenza A (5.96%, 23/386) and human adenovirus (5.70%, 22/386). There was no significant difference in the etiological distribution of viral pathogens between males and females (χ² = 0.480, P = .489). Viral infections were more likely to occur in the winter‐spring months than in the summer‐autumn months (52.51% vs 33.53%, χ² = 13.830, P = .000).

Conclusions

The GeXP‐based multiplex PCR is an accurate and high‐throughput assay allows us to quickly detect multiple respiratory viruses simultaneously in pediatric patients. Our study provides information on the viral profiles and clinical characteristics in hospitalized children with ARTI, which would help better effective prevention strategies.