Respiratory viral coinfection and disease severity in children: A systematic review and meta-analysis

Viral Codetection and Clinical Outcomes of Infants Hospitalized With Bronchiolitis: A Multicenter Cohort Study

BACKGROUND

The simultaneous identification of multiple respiratory viruses is common in infants hospitalized with respiratory tract infections. Respiratory syncytial virus (RSV) is one of the main pathogens in bronchiolitis, although codetection of rhinovirus, influenza and other respiratory viruses may occur in about one-third of cases. The relevance of viral codetection on disease severity is still controversial. This multicenter cohort study aimed to assess the clinical outcomes of infants under 24 months hospitalized with bronchiolitis, comparing those testing positive for RSV alone, RSV plus another virus and ≥2 viruses distinct from RSV.

METHODS

Data were collected across 13 hospitals in Lombardy, Italy, both in the prepandemic and pandemic years. Random effect regression models were also employed to test the association between 3 groups (infants testing positive for RSV alone, RSV plus another respiratory virus and no RSV but ≥2 respiratory viruses other than RSV) and course of bronchiolitis, adjusted for potential confounders.

RESULTS

Among 1788 infants, 86.7% tested positive for RSV alone, 6.9% for RSV plus another virus and 6.3% for ≥2 other viruses. Significant differences were found in clinical outcomes: infants with multiple non-RSV viruses had shorter oxygen supplementation, intensive care and hospital stay compared with those with RSV alone. Notably, codetection of RSV and another virus was associated with a higher risk of radiologically confirmed pneumonia, whereas detection of ≥2 non-RSV viruses was inversely associated with pneumonia.

CONCLUSIONS

These findings point out that codetection of viruses other than RSV is associated with milder disease courses than detection of RSV alone in infants with bronchiolitis. On the other hand, patients with RSV and another virus are at higher risk of pneumonia than infants affected by RSV alone. Further research is required to understand the underlying mechanisms and optimize management strategies in infants with bronchiolitis testing positive for multiple viruses.

Systematic Review and Meta-Analysis of the Association Between Clinical Severity and Co-Infection of Human Adenovirus With Other Respiratory Pathogens in Children

The correlation between the co-infection of human respiratory adenovirus (HAdV) and clinical severity has not been firmly established yet. We carried out a systematic review and meta-analysis. We scoured six databases for studies published up to 16 May 2024. A total of 66 cohort studies, which involved 16 251 participants, were incorporated. When compared with patients suffering from HAdV single infection, those with co-infection of viruses (risk ratios [RRs] = 1.40, 95% confidence interval [CI]: 1.05-1.86), bacteria (RR = 1.50, 95% CI: 1.05-2.16), or fungi (RR = 2.86, 95% CI: 2.17-3.76) were more prone to experience severe clinical outcomes. Co-infection with Mycoplasma pneumoniae had a tendency to elevate the risk of common pneumonia (RR = 1.81, 95% CI: 1.66-1.97), and bacterial co-infection was likely to extend the hospital stay (mean differences = 2.23 days, 95% CI: 0.44-4.03). In summary, the co-infection of HAdV with other viral, bacterial, fungal respiratory pathogens or Mycoplasma pneumoniae heightened the risk of severe clinical outcomes in pediatric patients, leading to an increased utilization of medical resources. This implied that the ecological and biological mechanisms underlying the potential interactions between HAdV and other microorganisms merited further investigation.

Exploring TMPRSS2 Drug Target to Combat Influenza and Coronavirus Infection

Respiratory viral infections, including influenza and coronaviruses, present significant health risks worldwide. The recent COVID-19 pandemic highlights the urgent need for novel and effective antiviral agents. The host cell protease, transmembrane serine protease 2 (TMPRSS2), facilitates viral pathogenesis by playing a critical role in viral invasion and disease progression. This protease is coexpressed with the viral receptors of angiotensin-converting enzyme 2 (ACE2) for SARS-CoV-2 in the human respiratory tract and plays a significant role in activating viral proteins and spreading. TMPRSS2 activates the coronavirus spike (S) protein and permits membrane fusion and viral entry by cleaving the virus surface glycoproteins. It also activates the hemagglutinin (HA) protein, an enzyme necessary for the spread of influenza virus. TMPRSS2 inhibitors can reduce viral propagation and morbidity by blocking viral entry into respiratory cells and reducing viral spread, inflammation, and disease severity. This review examines the role of TMPRSS2 in viral replication and pathogenicity. It also offers potential avenues to develop targeted antivirals to inhibit TMPRSS2 function, suggesting a possible focus on targeted antiviral development. Ultimately, the review seeks to contribute to improving public health outcomes related to these viral infections.

Epidemiological and molecular characteristics of human parainfluenza virus in southern China during 2016-2020

Human parainfluenza viruses (HPIV) are common viral pathogens in acute respiratory infection (ARI). We aimed to describe the epidemiological and molecular characteristics of HPIV from ARI patients. This cross-sectional study was conducted using respiratory samples from 9,696 ARI patients between 2016 and 2020 in southern China. All samples were analyzed by quantitative real-time polymerase chain reaction to determine the presence of HPIV and other common respiratory viruses. Descriptive statistics were performed to determine the temporal and population distribution of HPIV. The full-length hemagglutinin-neuraminidase (HN) gene of HPIV3-positive samples was sequenced for phylogenetic analysis. A total of 577 (6.0%) patients tested positive for HPIV, with HPIV3 being the predominant serotype, accounting for 46.8% of cases. Notably, 66.0% of these HPIV-positive cases were children aged 0-2 years. The prevalence of HPIV infections showed a decreased trend and altered peak during 2016-2020. Cough, fever, sputum production, and rhinorrhea were common respiratory symptoms in HPIV-positive patients. The majority of cases had pneumonia (63.4%). Human rhinovirus (HRV) and human coronavirus (HCoV) were the most common coinfection viruses in HPIV-positive cases, with proportions of 20.1% and 14.4%, respectively. Phylogenetic analysis revealed that the predominant lineage of HPIV3 was C3f (86.0%), followed by lineage C3a (8.0%), C3d (4.0%), and C3b (2.0%). These findings help to better understand the epidemiology of HPIV, and improve public health strategies to prevent and control HPIV infections in southern China.

Rethinking Paediatric Respiratory Infections: The Role of Mixed Pathogen Infections

Acute respiratory infections (ARIs) stand as a significant cause of morbidity and mortality among children worldwide, contributing substantially to paediatric hospitalisation rates. ARIs stem from various pathogens, including bacteria, viruses, among others. With the advent of novel diagnostic techniques like molecular detection methods, the identification rate of multiple pathogens in paediatric ARIs is steadily rising. However, there is currently no consensus on the impact of mixed infections on the severity of respiratory infections in children. This narrative review summarises existing research indicating that the co-detection rate of multiple viruses among paediatric patients with ARIs ranged from 0.07% to 55%. Multi-virus coinfections did not appear to increase the severity of the disease in children because of viral interference, immune modulation, etc. Conversely, mixed infection of virus and bacteria may exacerbate disease severity through many mechanisms, such as synergistic activation of inflammation, diminished repair efficiency, increased transmission and release and so on. The insights provide aim to improve diagnostic precision and treatment strategies for paediatric ARIs, ultimately reducing complications and mortality rates associated with ARIs in children.

Multiple Respiratory Virus Detection in Acute Respiratory Infection Patients in Mie Prefecture, Japan, 2021-2023

The Coronavirus disease 2019 (COVID-19) pandemic significantly impacted the circulation patterns of respiratory viruses worldwide. To better understand viral circulation patterns during the transition from pandemic to endemic phase, we conducted comprehensive respiratory virus surveillance in Mie Prefecture, Japan, during 2021-2023, coinciding with the Delta-to-Omicron transition of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). We collected respiratory specimens from acute respiratory infection patients in medical institutions, detecting 19 respiratory viruses using real-time PCR in 1573 valid samples out of 1605 specimens. Demographic and clinical data were available for some specimens. SARS-CoV-2 Omicron strains showed a peak positivity of 15-25% during the epidemic, while respiratory syncytial virus and human rhinovirus/enterovirus exhibited one to two annual epidemic peaks up to 57%, and human adenovirus maintained a positivity rate of 5-20% throughout the year. Age-dependent analysis revealed the significant detection of multiple viruses, particularly in children under 2 years, with up to six viruses detected simultaneously in those under 5 years. Our findings demonstrate varied respiratory virus prevalence patterns, with some viruses remaining active during the Omicron epidemic, suggesting its limited impact on other viruses. This comprehensive approach should enhance the understanding of respiratory virus epidemic dynamics and inform public health strategies.

Etiological Spectrum of Acute Respiratory Infections in Bulgaria During the 2023-2024 Season and Genetic Diversity of Circulating Influenza Viruses

Influenza poses a serious threat to both individual and public health. This study aimed to investigate the virological and epidemiological characteristics of influenza infections and to explore the genetic diversity of the circulating influenza viruses. In total, 1886 nasopharyngeal specimens from patients with acute respiratory illnesses were tested against 13 respiratory viruses using a multiplex real-time PCR. Whole-genome sequencing, phylogenetic, and amino acid analyses of representative influenza strains were performed. At least one respiratory virus was detected in 869 (46.1%) patients; 87 (4.6%) were co-infected with two or three viruses. Influenza A(H1N1)pdm09 was the most prevalent virus (16.1%), followed by rhinoviruses (8.1%) and RSV (6.7%). Hemagglutinin (HA) genes of the 74 influenza A(H1N1)pdm09 viruses were categorized in subclades C.1.8, C.1.9, and C.1 within clade 5a.2a and D1, D.2, and D.3 within clade 5a.2a.1. The A(H3N2) viruses analyzed belonged to clade 2a.3a.1, subclades J.2 and J.1. The sequenced B/Victoria lineage viruses fell into clade V1A.3a.2, subclades C.5.6 and C.5.7. Amino acid substitutions in most viral proteins were identified compared with the vaccine strains, including in the HA antigenic sites. This study demonstrated the dominant distribution of the influenza A(H1N1)pdm09 virus among the respiratory viruses studied and the genetic diversity of the circulating influenza viruses.

Harnessing Epigenetics: Innovative Approaches in Diagnosing and Combating Viral Acute Respiratory Infections

Acute respiratory infections (ARIs) caused by viruses such as SARS-CoV-2, influenza viruses, and respiratory syncytial virus (RSV), pose significant global health challenges, particularly for the elderly and immunocompromised individuals. Substantial evidence indicates that acute viral infections can manipulate the host's epigenome through mechanisms like DNA methylation and histone modifications as part of the immune response. These epigenetic alterations can persist beyond the acute phase, influencing long-term immunity and susceptibility to subsequent infections. Post-infection modulation of the host epigenome may help distinguish infected from uninfected individuals and predict disease severity. Understanding these interactions is crucial for developing effective treatments and preventive strategies for viral ARIs. This review highlights the critical role of epigenetic modifications following viral ARIs in regulating the host's innate immune defense mechanisms. We discuss the implications of these modifications for diagnosing, preventing, and treating viral infections, contributing to the advancement of precision medicine. Recent studies have identified specific epigenetic changes, such as hypermethylation of interferon-stimulated genes in severe COVID-19 cases, which could serve as biomarkers for early detection and disease progression. Additionally, epigenetic therapies, including inhibitors of DNA methyltransferases and histone deacetylases, show promise in modulating the immune response and improving patient outcomes. Overall, this review provides valuable insights into the epigenetic landscape of viral ARIs, extending beyond traditional genetic perspectives. These insights are essential for advancing diagnostic techniques and developing innovative treatments to address the growing threat of emerging viruses causing ARIs globally.

Pediatric COVID-19 severity by SARS-CoV-2 lineage and vaccine status in Canada: an IMPACT study

BACKGROUND

Interpretations of pediatric COVID-19 severity are complicated by novel lineages and COVID-19 vaccine introduction. We estimated the risk of severe COVID-19 by SARS-CoV-2 lineage and vaccination status among hospitalized Canadian children.

METHODS

Data were collected through the Canadian Paediatric Surveillance Program (April 2020-May 2021) and Canadian Immunization Monitoring Program, ACTive (June 2021-December 2022). Patients <17 years hospitalized for COVID-19 (excluding incidental SARS-CoV-2) at 13 pediatric hospitals were included. Lineages were defined via genetic sequencing or dominant lineage upon hospitalization. Severe disease included intensive care, ventilatory/hemodynamic requirements, systemic complications, and/or death.

RESULTS

We analyzed 3218 COVID-19 hospitalizations, including 81.4% admitted during Omicron predominance. Median age was highest among Delta cases (2.9 years, interquartile range [IQR] 0.2-10.9) and lowest among Omicron BQ.1 cases (0.6 years, IQR 0.2-1.8). Severe COVID-19 remained common in Omicron vs. ancestral cases (27.2% vs. 23.2%). The proportion of hospitalized cases aged 5-16 years declined following the introduction of age-specific COVID-19 vaccines. Vaccination reduced the risk of in-hospital severe disease for ages 12-16 years (two vs. zero doses; adjusted risk ratio 0.49, 95% confidence interval 0.32-0.77).

CONCLUSION

More children were hospitalized with Omicron lineages than all prior lineages. COVID-19 vaccination was associated with a lower burden of severe disease among ages 5-16 years.

IMPACT STATEMENT

This study estimates the effect of SARS-CoV-2 lineage, Omicron sub-lineage, and vaccination on COVID-19 disease severity, using data from two Canadian national surveillance programs. Few national studies describe the clinical presentation and severity of Omicron sub-lineages among hospitalized children. In Canada, Omicron lineages were associated with substantially more pediatric COVID-19 hospitalizations than all prior lineages combined, though risk of severe COVID-19 was highest during the Delta period. COVID-19 vaccines were associated with reductions in hospitalization (ages 5-16 years) and severe disease (ages 12-16 years) across Omicron sub-lineages.

Pathogenesis of influenza and SARS-CoV-2 co-infection at the extremes of age: decipher the ominous tales of immune vulnerability

The co-circulation of influenza and SARS-CoV-2 has led to co-infection events, primarily affecting children and older adults, who are at higher risk for severe disease. Although co-infection prevalence is relatively low, it is associated with worse outcomes compared to mono-infections. Previous studies have shown that the outcomes of co-infection depend on multiple factors, including viral interference, virus-host interaction and host response. Children and the elderly exhibit distinct patterns of antiviral response, which involve airway epithelium, mucociliary clearance, innate and adaptive immune cells, and inflammatory mediators. This review explores the pathogeneses of SARS-CoV-2 and influenza co-infection, focusing on the antiviral responses in children and the elderly. By comparing immature immunity in children and immune senescence in older adults, we aim to provide insights for the clinical management of severe co-infection cases.

Insights from respiratory virus co-infections

Respiratory viral co-infections present significant challenges in clinical settings due to their impact on disease severity and patient outcomes. Current diagnostic methods often miss these co-infections, complicating the epidemiology and management of these cases. Research, primarily conducted in vitro and in vivo, suggests that co-infections can lead to more severe illnesses, increased hospitalization rates, and greater healthcare utilization, especially in high-risk groups such as children, the elderly, and immunocompromised individuals. Common co-infection patterns, risk factors, and their impact on disease dynamics highlight the need for advanced diagnostic techniques and tailored therapeutic strategies. Understanding the virological interactions and immune response modulation during co-infections is crucial for developing effective public health interventions and improving patient outcomes. Future research should focus on the molecular mechanisms of co-infection and the development of specific therapies to mitigate the adverse effects of these complex infections.

Epidemiological impact of human adenovirus as causative agent of respiratory infections: An Italian multicentre retrospective study, 2022-2023

Human adenoviruses are the causative agents of 5-7% of viral respiratory infections, mainly caused by species B and C. They can infect all age groups, but children are usually at high risk of infections. Adenovirus epidemiology is well documented in East-Asian countries but little is known about adenovirus circulation in Europe in recent years. This multicentre retrospective study aimed to investigate the circulation and molecular epidemiology of hAdVs. This surveillance collected a total of 54463 respiratory specimens between January 1, 2022 and June 20, 2023 were tested for the presence of respiratory viruses. Our results showed that adenovirus was detected in 6.6 % of all cases of acute respiratory infection included in the study and the median age of positive patients was 3 years, with male children in 1-2 years age group being the most affected. 43.5 % of adenovirus cases were co-infected with at least one other respiratory virus, and rhinovirus was co-detected in 54 % of cases. Genotyping of adenovirus allowed the identification of 6 different genotypes circulating in Italy, among which type B3 was the most frequently detected.

Respiratory syncytial virus disease burden in children and adults from Latin America: a systematic review and meta-analysis

Background

Respiratory Syncytial Virus (RSV) is a common cause of lower respiratory tract infections (LRTI) and hospitalization worldwide. The impact of RSV in Latin America and the Caribbean (LAC) including expensive treatment options, such as palivizumab, have been extensively discussed. However, publications on the impact of RSV disease burden in the region are scarce. This systematic review aimed to determine the incidence and prevalence of RSV in LAC by age and RSV subtype.

Methods

We conducted a systematic review following Cochrane methods to evaluate the disease burden of RSV in LAC countries. We searched studies from January 2012 to January 2023 in literature databases and grey literature without language restrictions. We included guidelines, observational, economic, and surveillance studies from LAC countries. Pairs of reviewers independently selected, and extracted data from included studies. The risk of bias was assessed using the Study Quality Assessment Tools (NHLBI) and AGREE-II. We performed proportion meta-analyses using methods to stabilize the variance. The protocol was registered in PROSPERO (CRD42023393731).

Results

We included 156 studies, mainly from Brazil (25%), Colombia (14.5%), and Argentina (13.8%), as well as four clinical practice guidelines. Most studies were cross-sectional (76.9%) and were classified as low risk of bias (52.6%). The majority included inpatients (85.6%), pediatric (73.7%), and normal-risk patients (67.1%). The highest pooled prevalence was estimated in patients <1 year old (58%), with type A and B prevalence of 52 and 34%, respectively. The RSV-LRTI incidence was 15/100 symptomatic infants aged <2 years old, and the ICU admission was 42%. The RSV-LRTI lethality was 0.6, 3% in patients aged <2 and 0-5 years old, respectively, and 23% among >65 years old high-risk patients. The identified guidelines lack methodological rigor and have limitations in their applicability. The seasonality was more evident in South America than in Central America and The Caribbean, with a clear gap during the pandemic.

Conclusion

This is the most exhaustive and updated body of evidence describing a significant burden of RSV in LAC, particularly at the extremes of life, and its seasonality patterns. Our findings could contribute could contribute facilitating effective prevention and treatment strategies for this significant public health problem.

Systematic review registration

PROSPERO CRD UK (registration number: CRD42023393731).

Characterization of Respiratory Viruses in Patients with Acute Respiratory Infection in the City of Barranquilla during the SARS-CoV-2/COVID-19 Pandemic

Introduction: Severe acute respiratory infection (SARI) is mainly caused by viral pathogens, with a high prevalence in high-risk populations such as infants and older adults. Coinfections by different viruses are frequent and, in some cases, associated with severe disease outcomes. Purpose: The main purpose of this study was to identify respiratory viruses circulating in Barranquilla during the peaks of the COVID-19 pandemic and estimate the prevalence of viral coinfections in samples from individuals with different degrees of respiratory infection. Methods: We received 5083 samples between epidemiological weeks 33-42 of 2021 submitted by the District Health Laboratory of Barranquilla and four local healthcare institutions during COVID-19 surveillance. Among them, we analyzed 101 samples from individuals presenting with influenza-like illness (ILI). Eighteen respiratory viruses, including SARS-CoV-2, were evaluated via qRT-PCR using nasal swabs or nasopharyngeal aspirate samples. Results: Of the 101 study individuals, 56 were male and 45 were female (55.5% and 44.5%, respectively); 25.7% of individuals were infected with at least one of the evaluated viruses. Respiratory syncytial virus (RSV) and human rhinovirus (HRV) were the two most frequently detected viruses (30.7% and 15.4% of total positives, respectively). Coinfections with two or more respiratory viruses accounted for 42% of the total positive cases. Discussion: Our findings indicate the presence of different respiratory viruses in swab or nasopharyngeal aspirate samples from individuals with ILI, including coinfections. These results reveal the circulation of several respiratory viruses in the city of Barranquilla, confirming their importance as potential causes of SARI in Colombia and the need for their active surveillance.

A complex remodeling of cellular homeostasis distinguishes RSV/SARS-CoV-2 co-infected A549-hACE2 expressing cell lines

Concurrent infections with two or more pathogens with analogous tropism, such as RSV and SARS-CoV-2, may antagonize or facilitate each other, modulating disease outcome. Clinically, discrepancies in the severity of symptoms have been reported in children with RSV/SARS-CoV-2 co-infection. Herein, we propose an in vitro co-infection model to assess how RSV/SARS-CoV-2 co-infection alters cellular homeostasis. To this end, A549-hACE2 expressing cells were either infected with RSV or SARS-CoV-2 alone or co-infected with both viruses. Viral replication was assessed at 72 hours post infection by droplet digital PCR, immunofluorescence, and transmission electron microscopy. Anti-viral/receptor/autophagy gene expression was evaluated by RT-qPCR and confirmed by secretome analyses and intracellular protein production. RSV/SARS-CoV-2 co-infection in A549-hACE2 cells was characterized by: 1) an increase in the replication rate of RSV compared to single infection; 2) an increase in one of the RSV host receptors, ICAM1; 3) an upregulation in the expression/secretion of pro-inflammatory genes; 4) a rise in the number and length of cellular conduits; and 5) augmented autophagosomes formation and/or alteration of the autophagy pathway. These findings suggest that RSV/SARS-CoV-2 co-infection model displays a unique and specific viral and molecular fingerprint and shed light on the viral dynamics during viral infection pathogenesis. This in vitro co-infection model may represent a potential attractive cost-effective approach to mimic both viral dynamics and host cellular responses, providing in future readily measurable targets predictive of co-infection progression.

Risk factors of severe Chlamydia trachomatis pneumonia in children: a retrospective case-control study

This study explored the clinical characteristics of Chlamydia trachomatis (C. trachomatis) pneumonia in children and the risk factors for severe C. trachomatis pneumonia. This retrospective case-control study included children with C. trachomatis pneumonia who were admitted to the Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University (Xiamen, China) between January 2018 and December 2021. Among 117 children, 33 (28.2%) had severe C. trachomatis pneumonia and 84 children had mild-to-moderate C. trachomatis pneumonia. According to the results of the binary logistic regression analysis, congenital heart disease [odds ratio (OR) = 0.09, 95% confidence interval (CI): 0.01-0.74, P-value = .024], mixed infection (OR = 0.17, 95%CI: 0.05-0.51, P-value = .002), white blood cell count greater than 15 000 cells/dl (OR = 1.20, 95%CI: 1.03-1.40, P-value = .022), and partial pressure of carbon dioxide (PaCO2) (OR = 1.14, 95%CI: 1.02-1.26, P-value = .016) were found as independent predictive factors for severe C. trachomatis pneumonia in children. This study explored key risk factors for severe C. trachomatis pneumonia, a condition underreported in tropical regions where pediatric respiratory infections are a leading cause of morbidity and mortality. By identifying risk factors, such as congenital heart disease, mixed infections, and elevated PaCO2, this research may guide early intervention strategies in resource-limited settings, potentially reducing pediatric pneumonia deaths.

Prevalence of Co-Infections and Pathogens in Hospitalized Children with Acute Respiratory Infections: A Comparative Analysis Between SARS-CoV-2 and Non-SARS-CoV-2 Cases

Objectives. We aimed to compare the prevalence of co-infections, pathogens, and factors associated with SARS-CoV-2 acute respiratory infection (ARI) and non-SARS-CoV-2 ARI, among hospitalized children. Methods. We conducted an observational cross-sectional study of hospitalized children <15 years with ARI, and lasting respiratory symptoms <14 days, using polymerase chain reaction on nasopharyngeal specimens. Results. Of the 184 children with ARI analyzed, 122 were infected with SARS-CoV-2 and 62 were not. SARS-CoV-2 ARI had a significantly lower rate of co-infection than non-SARS-CoV-2 ARI (2.5% vs14.5%, P = .003). SARS-CoV-2 ARI children were significantly associated with a less empirical antibiotics (aOR = 0.09, CI = 0.03-0.21; P = .000), more pneumonia (aOR = 5.15, CI = 1.77-14.95; P = .003), and more abnormal chest X-ray (aOR = 2.81, CI = 1.38-5.71; P = .004). Conclusions. Although SARS-CoV-2 ARI in hospitalized children was associated with pneumonia and abnormal chest x-rays, empirical antibiotics may not be necessary for treating mild to moderate cases.

Whole genome molecular analysis of respiratory syncytial virus pre and during the COVID-19 pandemic in Free State province, South Africa

Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The Coronavirus disease 2019 (COVID-19) pandemic and resulting nonpharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed. Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.

Epidemiology of Human Parainfluenza Virus Infections among Pediatric Patients in Hainan Island, China, 2021-2023

Human parainfluenza viruses (HPIVs) are the leading causes of acute respiratory tract infections (ARTIs), particularly in children. During the COVID-19 pandemic, non-pharmaceutical interventions (NPIs) significantly influenced the epidemiology of respiratory viruses. This study analyzed 19,339 respiratory specimens from pediatric patients with ARTIs to detect HPIVs using PCR or tNGS, focusing on the period from 2021 to 2023. HPIVs were identified in 1395 patients (7.21%, 1395/19,339), with annual detection rates of 6.86% (303/4419) in 2021, 6.38% (331/5188) in 2022, and 7.82% (761/9732) in 2023. Notably, both the total number of tests and HPIV-positive cases increased in 2023 compared to 2021 and 2022. Seasonal analysis revealed a shift in HPIV prevalence from winter and spring in 2021-2022 to spring and summer in 2023. Most HPIV-positive cases were in children aged 0-7 years, with fewer infections among those aged 7-18 years. Since June 2022, HPIV-3 has been the most prevalent serotype (59.55%, 524/880), whereas HPIV-2 had the lowest proportion (0.80%, 7/880). The proportions of HPIV-1 (24.89%, 219/880) and HPIV-4 (15.45%, 136/880) were similar. Additionally, the incidence of co-infections with other common respiratory pathogens has increased since 2021. This study highlights rising HPIV detection rates post-COVID-19 and underscores the need for continuous surveillance of HPIVs to inform public health strategies for future epidemic seasons.

An end-point multiplex RT-PCR for SARS-CoV-2, Influenza A and B detection, including simultaneous RNAse P amplification: a timely tool for more accessible differential diagnosis

The multiplex molecular diagnostic assays described for severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), influenza A (IAV) and B (IBV) viruses have been mainly based on real-time reaction, which limits their access to many laboratories or diagnostic institutions. To contribute to available strategies and expand access to differential diagnosis, we describe an end-point multiplex RT-PCR targeting SARS-CoV-2, IAV and IBV with simultaneous endogenous control amplification. Initially, we looked for well-established primers sets for SARS-CoV-2, IAV, IBV and RNAse P whose amplicons could be distinguished on agarose gel. The multiplex assay was then standardized by optimizing the reaction mix and cycle conditions. The limit of detection (LoD) was determined using titrated viruses (for SARS-CoV-2 and IAV) and by dilution from a pool of IBV-positive samples. The diagnostic performance of the multiplex was evaluated by testing samples with different RNAse P and viral loads, previously identified as positive or negative for the target viruses. The amplicons of IAV (146 bp), SARS-CoV-2 (113 bp), IBV (103 bp) and RNAse P (65 bp) were adequately distinguished in our multiplex. The LoD for SARS-CoV-2, IAV and IBV was 0.02 TCID50/ml, 0.07 TCID50/ml and 10-3 from a pool of positive samples, respectively. All samples positive for SARS-CoV-2 (n=70, Ct 17.2-36.9), IAV (n=53, Ct 14-34.9) and IBV (n=12, Ct 23.9-31.9) remained positive in our multiplex assay. RNAse P from negative samples (n=40, Ct 25.2-30.2) was also amplified in the multiplex. Overall, our assay is a timely and alternative tool for detecting SARS-CoV-2 and influenza viruses in laboratories with limited access to supplies/equipment.

Ten-year retrospective data analysis reveals frequent respiratory co-infections in hospitalized patients in Augsburg

Clinical data on the types of respiratory pathogens which are most frequently engaged in respiratory co-infections of children and adults are lacking. We analyzed 10 years of data on a total of over 15,000 tests for 16 viral and bacterial pathogens detected in clinical samples at the University Hospital of Augsburg, Germany. Co-infection frequencies and their seasonal patterns were examined using a proportional distribution model. Co-infections were detected in 7.3% of samples, with a higher incidence in children and males. The incidence of interbacterial and interviral co-infections was higher than expected, whereas bacterial-viral co-infections were less frequent. H. influenzae, S. pneumoniae, rhinovirus, and respiratory syncytial virus (RSV) were most frequently involved. Most co-infections occurred in winter, but distinct summer peaks were also observed, which occurred even in children, albeit less pronounced than in adults. Seasonality of respiratory (co-)infections decreased with age. Our results suggest to adjust existing testing strategies during high-incidence periods.

Clinical relevance of viral codetection in infants with respiratory syncytial virus bronchiolitis

INTRODUCTION

Respiratory syncytial virus (RSV) is the main cause of severe bronchiolitis, especially in infants. The aim of this study is to assess whether codetection of RSV and other respiratory viruses could affect the severity of this infection comparing with unique RSV detection.

METHODS

A prospective study from 2016 to 2019 including children under 2 years who were admitted in the Emergency Service of the Hospital Universitari Arnau de Vilanova de Lleida (Spain) was performed. Nasopharyngeal samples from all patients were sent to the laboratory for RSV real-time PCR detection (GeneXpert®). A multiplex PCR that detects other respiratory viruses was done in all RSV-positive samples. Patients'medical records were checked to collect clinical data (hospital length of stay, BROSJOD score, ICU admission, need for ventilatory support or transfer to a reference hospital). Patients were divided in two groups: infants with unique RSV detection and infants with viral codetection. Bivariant analyses were performed to analyze the data obtained.

RESULTS

During the period of study 437 RSV bronchiolitis were diagnosed. In 199 of them (177/437; 45,5%) another respiratory virus was detected concomitantly. Bivariant analyses do not show statistically significant differences between both groups.

CONCLUSIONS

Viral codetection in infants with RSV bronchiolitis is frequent. However, it does not seems to affect the severity of this infection.

Presence and Significance of Multiple Respiratory Viral Infections in Children Admitted to a Tertiary Pediatric Hospital in Italy

Viral co-infections are frequently observed among children, but whether specific viral interactions enhance or diminish the severity of respiratory disease is still controversial. This study aimed to investigate the type of viral mono- and co-infections by also evaluating viral correlations in 3525 respiratory samples from 3525 pediatric in/outpatients screened by the Allplex Respiratory Panel Assays and with a Severe Acute Respiratory Syndrome-COronaVirus 2 (SARS-CoV-2) test available. Overall, viral co-infections were detected in 37.8% of patients and were more frequently observed in specimens from children with lower respiratory tract infections compared to those with upper respiratory tract infections (47.1% vs. 36.0%, p = 0.003). SARS-CoV-2 and influenza A were more commonly detected in mono-infections, whereas human bocavirus showed the highest co-infection rate (87.8% in co-infection). After analyzing viral pairings using Spearman's correlation test, it was noted that SARS-CoV-2 was negatively associated with all other respiratory viruses, whereas a markedly significant positive correlation (p < 0.001) was observed for five viral pairings (involving adenovirus/human bocavirus/human enterovirus/metapneumoviruses/rhinovirus). The correlation between co-infection and clinical outcome may be linked to the type of virus(es) involved in the co-infection rather than simple co-presence. Further studies dedicated to this important point are needed, since it has obvious implications from a diagnostic and clinical point of view.

Respiratory Viral Coinfections: Insights into Epidemiology, Immune Response, Pathology, and Clinical Outcomes

Respiratory viral coinfections are a global public health threat that poses an economic burden on individuals, families, and healthcare infrastructure. Viruses may coinfect and interact synergistically or antagonistically, or their coinfection may not affect their replication rate. These interactions are specific to different virus combinations, which underlines the importance of understanding the mechanisms behind these differential viral interactions and the need for novel diagnostic methods to accurately identify multiple viruses causing a disease in a patient to avoid misdiagnosis. This review examines epidemiological patterns, pathology manifestations, and the immune response modulation of different respiratory viral combinations that occur during coinfections using different experimental models to better understand the dynamics respiratory viral coinfection takes in driving disease outcomes and severity, which is crucial to guide the development of prevention and treatment strategies.

The impact of non-pharmaceutical interventions on community non-SARS-CoV-2 respiratory infections in preschool children

BACKGROUND

Effects of non-pharmaceutical interventions during the pandemic were mainly studied for severe outcomes. Among children, most of the burden of respiratory infections is related to infections which are not medically attended. The perspective on infections in the community setting is necessary to understand the effects of the pandemic on non-pharmaceutical interventions.

METHODS

In the unique prospective LoewenKIDS cohort study, we compared the true monthly incidence of self-reported acute respiratory infections (ARI) in about 350 participants (aged 3-4 years old) between October 2019 to March 2020 (pre-pandemic period) and October 2020 to March 2021 (pandemic period). Parents reported children's symptoms using a diary. Parents were asked to take a nasal swab of their child during all respiratory symptoms. We analysed 718 swabs using Multiplex PCR for 25 common respiratory viruses and bacteria.

RESULTS

During the pre-pandemic period, on average 44.6% (95% CI: 39.5-49.8%) of children acquired at least one ARI per month compared to 19.9% (95% CI: 11.1-28.7%) during the pandemic period (Incidence Rate Ratio = 0.47; 95% CI: 0.41-0.54). The detection of influenza virus decreased absolute by 96%, respiratory syncytial virus by 65%, metapneumovirus by 95%, parainfluenza virus by 100%, human enterovirus by 96% and human bocavirus by 70% when comparing the pre-pandemic to the pandemic period. However, rhinoviruses were nearly unaffected by NPI. Co-detection (detection of more than one virus in a single symptomatic swab) was common in the pre-pandemic period (222 of 390 samples with viral detection; 56.9%) and substantially less common during the pandemic period (46 of 216 samples; 21.3%).

CONCLUSION

Non-pharmaceutical interventions strongly reduced the incidence of all respiratory infections in preschool children but did not affect rhinovirus.

Epidemiological Characterization of Respiratory Pathogens Using the Multiplex PCR FilmArray™ Respiratory Panel

Various pathogens can cause upper respiratory tract infections, presenting challenges in accurate diagnosis due to similar symptomatology. Therefore, rapid and precise diagnostic tests are crucial for effective treatment planning. Traditional culture-based methods for diagnosis are limited by their reliance on skilled personnel and lengthy processing times. In contrast, multiplex polymerase chain reaction (PCR) techniques offer enhanced accuracy and speed in identifying respiratory pathogens. In this study, we aimed to assess the efficacy of the FilmArray™ Respiratory Panel (RP), a multiplex PCR test capable of simultaneously screening 20 pathogens. This retrospective analysis was conducted at Dankook University Hospital, South Korea, between January 2018 and December 2022. Samples from patients with upper respiratory tract infections were analyzed. Results revealed adenovirus as the most prevalent pathogen (18.9%), followed by influenza virus A (16.5%), among others. Notably, a 22.5% co-infection rate was observed. The FilmArray™ RP method successfully identified 20 pathogens within 2 h, facilitating prompt treatment decisions and mitigating unnecessary antibiotic prescriptions. This study underscores the utility of multiplex PCR in respiratory pathogen identification, offering valuable insights for epidemiological surveillance and diagnosis.

Co-infections and immune-evading viral hybrids: A perspective

Background and Aims

Co-infections occur when two or more different types of pathogens infect the same host at the same time. Initially, it may develop via a primary infection and then later segue into a superinfection. Although some research suggests that coinfections do not affect the effect of disease outcomes, alternate evidence says otherwise. While the disease outcomes are frequently influenced by the interactions between many viruses, how these viruses interact during coinfections is poorly understood. This article aims to shed light on the interaction between viruses at a cellular and subcellular level, and the clinical implications for the same.

Methods

The articles were sought by conducting a thorough literature search on Google Scholar, ScienceDirect, PubMed, PubMed Central, Dimensions, and EBSCO Host, using keywords such as coinfections, virus, viral hybrids, and superinfection. The articles pertinent to the concept were then included.

Results

There is a growing body of evidence that suggests the formation of hybrid viral particles (HVPs) which conjugate at the cellular and subcellular level. While the formation of HVPs is bizarre, it may potentially have a profound effect on the clinical manifestations.

Conclusion

While there has been evidence of the formation of HVPs between a couple of viruses, researchers fear the existence of several other combinations, including zoonotic viruses. While this could be detrimental to the human race both at an individual-as well as a community-level, an in-depth understanding of the same may help in better management of the clinical manifestations of the disease.

Etiology of Acute Lower Respiratory Illness Hospitalizations Among Infants in 4 Countries

Background

Recent studies explored which pathogens drive the global burden of pneumonia hospitalizations among young children. However, the etiology of broader acute lower respiratory tract infections (ALRIs) remains unclear.

Methods

Using a multicountry study (Albania, Jordan, Nicaragua, and the Philippines) of hospitalized infants and non-ill community controls between 2015 and 2017, we assessed the prevalence and severity of viral infections and coinfections. We also estimated the proportion of ALRI hospitalizations caused by 21 respiratory pathogens identified via multiplex real-time reverse transcription polymerase chain reaction with bayesian nested partially latent class models.

Results

An overall 3632 hospitalized infants and 1068 non-ill community controls participated in the study and had specimens tested. Among hospitalized infants, 1743 (48.0%) met the ALRI case definition for the etiology analysis. After accounting for the prevalence in non-ill controls, respiratory syncytial virus (RSV) was responsible for the largest proportion of ALRI hospitalizations, although the magnitude varied across sites-ranging from 65.2% (95% credible interval, 46.3%-79.6%) in Albania to 34.9% (95% credible interval, 20.0%-49.0%) in the Philippines. While the fraction of ALRI hospitalizations caused by RSV decreased as age increased, it remained the greatest driver. After RSV, rhinovirus/enterovirus (range, 13.4%-27.1%) and human metapneumovirus (range, 6.3%-12.0%) were the next-highest contributors to ALRI hospitalizations.

Conclusions

We observed substantial numbers of ALRI hospitalizations, with RSV as the largest source, particularly in infants aged <3 months. This underscores the potential for vaccines and long-lasting monoclonal antibodies on the horizon to reduce the burden of ALRI in infants worldwide.

Ketoprofen lysine salt treatment in adolescents with acute upper respiratory infections: a primary-care experience

BACKGROUND

Acute upper respiratory infections (AURI) are widespread in adolescents. Infections are associated with inflammation which in turn is responsible for symptoms and fever occurrence. Ketoprofen lysine salt (KLS) has a potent anti-inflammatory activity associated with effective analgesic and antipyretic effects and has a valuable safety profile. In this regard, KLS could be advantageous in adolescents with AURI.

METHODS

A group of primary-care pediatricians retrospectively collected data from adolescents with AURI treated with KLS for three days. Fever and symptom perception were assessed by a visual analog scale and were monitored daily for five days. Adolescents (or parents) sent their data to doctors using a phone application (WhatsApp; Meta Platforms, Inc., Menlo Park, CA, USA).

RESULTS

This retrospective analysis included sixty-one adolescents (mean age 13.4 years, females and males). KLS treatment markedly and quickly reduced fever and symptoms severity. In addition, the treatment was very well tolerated by all adolescents.

CONCLUSIONS

Adolescents present peculiar psychological characteristics that may determine some difficulties in prompt management of AURI treatment, while an adolescent with a respiratory infection requires a prompt and adequate cure. KLS, thanks to its pharmacologic profile, could be favorably used in this context. In addition, the treatment was safe, and the acceptability was high.

Not all respiratory infections were SARS-CoV-2 during the pandemic, analysis in a clinic on the Colombian Caribbean coast

INTRODUCTION

Acute Respiratory Infections (ARIs) are considered one of the leading causes of morbidity and mortality worldwide. Children under five and older adults are most likely to die from this cause.

OBJECTIVE

To describe the behavior of infection by respiratory viruses other than SARS-CoV-2 during the pandemic in a clinic in the Colombian Caribbean.

METHODS

This descriptive and retrospective study evaluates the characteristics, associated comorbidities, and requirements of hospitalization or Intensive Care Unit in patients diagnosed with respiratory viral infections treated at IMAT Oncomedica clinic from July 2020 to August 2022.

RESULTS

This study evaluated 351 patients with respiratory symptoms, observing an exponential increase in cases of respiratory infection as of April 2022, with a high proportion of syncytial virus infections mainly in children under 18 years of age (22.1%) and Human Rhinovirus/Enterovirus in patients with solid tumors and hematological disorders (48.8%), the latter was associated with a higher rate of hospitalization and ICU requirement in the individuals evaluated.

CONCLUSIONS

Respiratory viruses other than SARS-CoV-2, such as Rhino/Enterovirus, RSV, and adenovirus, are circulating in the population at a clinic on the Colombian Caribbean coast. The findings should motivate public health authorities to conduct more thorough surveillance in the rest of the state.

Influenza A and Respiratory Syncytial Virus Trigger a Cellular Response That Blocks Severe Acute Respiratory Syndrome Virus 2 Infection in the Respiratory Tract

BACKGROUND

Multiple viruses cocirculate and contribute to the burden of respiratory disease. Virus-virus interactions can decrease susceptibility to infection and this interference can have an epidemiological impact. As humans are normally exposed to a community of cocirculating respiratory viruses, experimental coinfection studies are necessary to understand the disease mechanisms of multipathogen systems. We aimed to characterize interactions within the respiratory tract between severe acute respiratory syndrome virus 2 (SARS-CoV-2) and 2 major respiratory viruses: influenza A virus (IAV), and respiratory syncytial virus (RSV).

METHODS

We performed single infections and coinfections with SARS-CoV-2 combined with IAV or RSV in cultures of human bronchial epithelial cells. We combined microscopy with quantification of viral replication in the presence or absence of an innate immune inhibitor to determine changes in virus-induced pathology, virus spread, and virus replication.

RESULTS

SARS-CoV-2 replication is inhibited by both IAV and RSV. This inhibition is dependent on a functional antiviral response and the level of inhibition is proportional to the timing of secondary viral infection.

CONCLUSIONS

Infections with other respiratory viruses might provide transient resistance to SARS-CoV-2. It would therefore be expected that the incidence of coronavirus disease 2019 (COVID-19) may decrease during periods of high circulation of IAV and RSV.

Co-Infection Rates between SARS-CoV-2 and RSV in Oropharyngeal, Nasopharyngeal Aspirate and Saliva Samples of COVID-19 Patients, Shiraz, South of Iran

Statement of the Problem

Determining the prevalence of respiratory viruses' coinfection with coronavirus disease 2019 (COVID-19) is essential to defining its true clinical influence.

Purpose

This study aimed to evaluate co-infection rates between severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and respiratory syncytial virus (RSV) in infected patients in Shiraz, south of Iran.

Materials and Method

In a cross-sectional descriptive study, oropharyngeal, nasopharyngeal aspirate (NPA), and saliva samples of 50 COVID-19 patients who were referred to Ali-Asghar hospital (Shiraz, Iran) from March to August 2020, were collected. A control group consisted of age and sex-matched healthy participants. The nasopharyngeal and oropharyngeal aspirates were collected by sterile swabs. All cases were hospitalized, and all SARS-CoV-2 patients had a fever and respiratory symptoms. The samples were packed in a vial with 1 mL of transport medium and transported to the Valfagre specialty laboratory, where they were tested for RSV using a real-time polymerase chain reaction (PCR).

Results

100 nasopharyngeal/oropharyngeal aspirates and saliva samples including 50 healthy controls (24 females, 26 males) and 50 COVID-19 patients' samples (27 males and 23 females) were studied. There was no significant difference regarding age as well as gender between both groups (p> 0.05). None of the healthy subjects was infected with RSV; however, 5(10%) patients from COVID-19 group were infected with the RSV virus. Chi-square test did not show a significant difference between RSV infection in COVID-19 patients and healthy subjects.

Conclusion

The outcome of present research showed that concurrent RSV with COVID 19 infection might be seen in hospitalized patients in Shiraz Southwest of Iran. For more reliable findings, further research on bigger populations, including more pathogens in several places around the country, and considering the severity of symptoms is required.

How Interactions during Viral-Viral Coinfection Can Shape Infection Kinetics

Respiratory viral infections are a leading global cause of disease with multiple viruses detected in 20-30% of cases, and several viruses simultaneously circulating. Some infections with unique viral copathogens result in reduced pathogenicity, while other viral pairings can worsen disease. The mechanisms driving these dichotomous outcomes are likely variable and have only begun to be examined in the laboratory and clinic. To better understand viral-viral coinfections and predict potential mechanisms that result in distinct disease outcomes, we first systematically fit mathematical models to viral load data from ferrets infected with respiratory syncytial virus (RSV), followed by influenza A virus (IAV) after 3 days. The results suggest that IAV reduced the rate of RSV production, while RSV reduced the rate of IAV infected cell clearance. We then explored the realm of possible dynamics for scenarios that had not been examined experimentally, including a different infection order, coinfection timing, interaction mechanisms, and viral pairings. IAV coinfection with rhinovirus (RV) or SARS-CoV-2 (CoV2) was examined by using human viral load data from single infections together with murine weight-loss data from IAV-RV, RV-IAV, and IAV-CoV2 coinfections to guide the interpretation of the model results. Similar to the results with RSV-IAV coinfection, this analysis shows that the increased disease severity observed during murine IAV-RV or IAV-CoV2 coinfection was likely due to the slower clearance of IAV-infected cells by the other viruses. The improved outcome when IAV followed RV, on the other hand, could be replicated when the rate of RV infected cell clearance was reduced by IAV. Simulating viral-viral coinfections in this way provides new insights about how viral-viral interactions can regulate disease severity during coinfection and yields testable hypotheses ripe for experimental evaluation.

How Interactions During Viral-Viral Coinfection Can Shape Infection Kinetics

Respiratory virus infections are a leading cause of disease worldwide with multiple viruses detected in 20-30% of cases and several viruses simultaneously circulating. Some infections with viral copathogens have been shown to result in reduced pathogenicity while other virus pairings can worsen disease. The mechanisms driving these dichotomous outcomes are likely variable and have only begun to be examined in the laboratory and clinic. To better understand viral-viral coinfections and predict potential mechanisms that result in distinct disease outcomes, we first systematically fit mathematical models to viral load data from ferrets infected with respiratory syncytial virus (RSV) followed by influenza A virus (IAV) after 3 days. The results suggested that IAV reduced the rate of RSV production while RSV reduced the rate of IAV infected cell clearance. We then explored the realm of possible dynamics for scenarios not examined experimentally, including different infection order, coinfection timing, interaction mechanisms, and viral pairings. IAV coinfection with rhinovirus (RV) or SARS-CoV-2 (CoV2) was examined by using human viral load data from single infections together with murine weight loss data from IAV-RV, RV-IAV, and IAV-CoV2 coinfections to guide the interpretation of the model results. Similar to the results with RSV-IAV coinfection, this analysis showed that the increased disease severity observed during murine IAV-RV or IAV-CoV2 coinfection was likely due to slower clearance of IAV infected cells by the other viruses. On the contrary, the improved outcome when IAV followed RV could be replicated when the rate of RV infected cell clearance was reduced by IAV. Simulating viral-viral coinfections in this way provides new insights about how viral-viral interactions can regulate disease severity during coinfection and yields testable hypotheses ripe for experimental evaluation.

Clinical characteristics and outcomes of children with single or co-detected rhinovirus-associated acute respiratory infection in Middle Tennessee

BACKGROUND

Rhinovirus (RV) is one of the most common etiologic agents of acute respiratory infection (ARI), which is a leading cause of morbidity and mortality in young children. The clinical significance of RV co-detection with other respiratory viruses, including respiratory syncytial virus (RSV), remains unclear. We aimed to compare the clinical characteristics and outcomes of children with ARI-associated RV-only detection and those with RV co-detection-with an emphasis on RV/RSV co-detection.

METHODS

We conducted a prospective viral surveillance study (11/2015-7/2016) in Nashville, Tennessee. Children < 18 years old who presented to the emergency department (ED) or were hospitalized with fever and/or respiratory symptoms of < 14 days duration were eligible if they resided in one of nine counties in Middle Tennessee. Demographics and clinical characteristics were collected by parental interviews and medical chart abstractions. Nasal and/or throat specimens were collected and tested for RV, RSV, metapneumovirus, adenovirus, parainfluenza 1-4, and influenza A-C using reverse transcription quantitative polymerase chain reaction assays. We compared the clinical characteristics and outcomes of children with RV-only detection and those with RV co-detection using Pearson's χ² test for categorical variables and the two-sample t-test with unequal variances for continuous variables.

RESULTS

Of 1250 children, 904 (72.3%) were virus-positive. RV was the most common virus (n = 406; 44.9%), followed by RSV (n = 207; 19.3%). Of 406 children with RV, 289 (71.2%) had RV-only detection, and 117 (28.8%) had RV co-detection. The most common virus co-detected with RV was RSV (n = 43; 36.8%). Children with RV co-detection were less likely than those with RV-only detection to be diagnosed with asthma or reactive airway disease both in the ED and in-hospital. We did not identify differences in hospitalization, intensive care unit admission, supplemental oxygen use, or length of stay between children with RV-only detection and those with RV co-detection.

CONCLUSION

We found no evidence that RV co-detection was associated with poorer outcomes. However, the clinical significance of RV co-detection is heterogeneous and varies by virus pair and age group. Future studies of RV co-detection should incorporate analyses of RV/non-RV pairs and include age as a key covariate of RV contribution to clinical manifestations and infection outcomes.

Severe COVID-19 outcomes in pediatrics: An observational cohort analysis comparing Alpha, Delta, and Omicron variants

Objective

COVID-19 can rarely lead to severe illness in pediatric patients. The aim of this study was to determine if severe outcomes in pediatric COVID-19 have changed over the course of the pandemic.

Methods

This was a multicenter, observational cohort analysis from a large regional healthcare system in metro Detroit using electronic health record data to evaluate emergency visits, hospitalization, and severe COVID-19 disease in pediatric patients. Consecutive pediatric patients presenting to the emergency department with a primary diagnosis of COVID-19 were included. Outcomes data was gathered from three distinct time intervals that coincided with Alpha, Delta, and Omicron variant predominance (Time interval 1 (T1) 1/1/2021-6/30/2021: Alpha, T2 7/1/2021-12/31/2021: Delta, T3 1/1/2022-6/16/2022): Omicron. The primary outcome was severe disease inclusive of composite intensive care unit admission, mechanical ventilation, multisystem inflammatory syndrome in children (MIS-C), myocarditis, or death. Secondary outcomes included severe outcomes considering viral coinfection and vaccination status.

Results

Between 1/1/2021 and 6/16/2022, there were 4517 emergency COVID-19 visits, of which 12.5% (566) of children were hospitalized. 24.4% (138), 31.6% (179), and 44.0% (249) of admissions occurred during T1, T2 and T3 respectively. Most patients were male (55.1%) and 59.9% identified as Caucasian. The median age was 5.0 (interquartile range 1.0, 13.0) with infants comprising 22.8% (129), toddlers 25.1% (142), children 23.0% (130), and teenagers 29.2% (165). Over the course of the pandemic, the proportion of infants in hospitalization increased from 16.7% in T1 to 19.6% in T2 to 28.5% in T3 (p < 0.01) while the proportion of teenagers in hospitalization decreased from 39.1% in T1 to 31.3% in T2 to 22.1% in T3 (p < 0.001). Oxygen therapy was required in a minority (29.9%) of cases with supplemental oxygen utilized the least in T3 (16.5%) and most in T2 (30.2%). Composite severe disease decreased throughout the pandemic occurring in 36.2% in T1, 27.4% in T2, and 18.9% in T3. A multivariable logistic regression analysis revealed the odds of composite severe disease was significantly lower in T3 compared to T1 (adjusted odds ratio [aOR] 0.35, 95% Confidence Interval 0.21-0.60, p < 0.001). Fully vaccinated or fully vaccinated and boosted admission rates remained low throughout all periods with 4.4% in T1, 4.5% in T2 and 8.4% in T3. Viral coinfection was most common during T2 (16.8%) followed by T3 (12.5%) and least common in T1 (5.1%) (p = 0.006). Coinfection occurred more commonly in younger children with a median age of 1.2 (0.0, 4.5) compared to those with mono-infection with a median age of 6 (1.0, 14.0) (p < 0.001). Severe outcomes occurred in 45.6% of coinfection cases compared to 22.1% without coinfection (p < 0.001).

Conclusions

While Omicron cases had the highest admission frequency, severe illness was lower than Delta and Alpha variants. Coinfection with respiratory viruses increased the risk of severe outcomes and impacted infants more than older children.

Funding

None.

Viral Coinfections

In nature, viral coinfection is as widespread as viral infection alone. Viral coinfections often cause altered viral pathogenicity, disrupted host defense, and mixed-up clinical symptoms, all of which result in more difficult diagnosis and treatment of a disease. There are three major virus-virus interactions in coinfection cases: viral interference, viral synergy, and viral noninterference. We analyzed virus-virus interactions in both aspects of viruses and hosts and elucidated their possible mechanisms. Finally, we summarized the protocol of viral coinfection studies and key points in the process of virus separation and purification.

Respiratory Syncytial Virus Protects Bystander Cells against Influenza A Virus Infection by Triggering Secretion of Type I and Type III Interferons

Influenza A virus (IAV) and respiratory syncytial virus (RSV) are common recurrent respiratory infectants that show a relatively high coincidence. We demonstrated that preinfection with RSV partitions the cell population into a subpopulation susceptible to subsequent infection with IAV and an IAV-proof subpopulation.

Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence

Though instances of arthropod-borne (arbo)virus co-infection have been documented clinically, the overall incidence of arbovirus co-infection and its drivers are not well understood. Now that dengue, Zika and chikungunya viruses are all in circulation across tropical and subtropical regions of the Americas, it is important to understand the environmental and biological conditions that make co-infections more likely to occur. To understand this, we developed a mathematical model of co-circulation of two arboviruses, with transmission parameters approximating dengue, Zika and/or chikungunya viruses, and co-infection possible in both humans and mosquitoes. We examined the influence of seasonal timing of arbovirus co-circulation on the extent of co-infection. By undertaking a sensitivity analysis of this model, we examined how biological factors interact with seasonality to determine arbovirus co-infection transmission and prevalence. We found that temporal synchrony of the co-infecting viruses and average temperature were the most influential drivers of co-infection incidence. Our model highlights the synergistic effect of co-transmission from mosquitoes, which leads to more than double the number of co-infections than would be expected in a scenario without co-transmission. Our results suggest that appreciable numbers of co-infections are unlikely to occur except in tropical climates when the viruses co-occur in time and space.

SARS-CoV-2: The Impact of Co-Infections with Particular Reference to Mycoplasma pneumonia-A Clinical Review

Background: After its 2019 outbreak in Wuhan, scientists worldwide have been studying the epidemiology and clinical characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in children. Evidence indicates that children with SARS-CoV-2 infection are more likely to develop upper and lower respiratory tract infections in association with other infectious agents, such as Mycoplasma pneumoniae. Here, we conducted a systematic review of SARS-CoV-2 and Mycoplasma pneumoniae co-infection and their clinical course in children. Methods: We evaluated the published literature on SARS-CoV-2 by using the medical databases PubMed, Embase, Cochrane Library, Scopus, and Web of Science. In the searches, the Medical Subject Heading (MeSH) terms "SARS-CoV-2 and Mycoplasma pneumoniae" AND "co-infection SARS-CoV-2" were used. Studies describing co-infection with SARS-CoV-2 and Mycoplasma pneumoniae in children were included in the review. The study was conducted and reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results: According to the PRISMA guidelines, of the 38 identified studies, 14 were conducted in children (children/adolescents 0-18 years), 6 of which were included in this review. In total, 5867 children under the age of 17 years were diagnosed with SARS-CoV-2 infection through real-time polymerase chain reaction analysis of nasopharyngeal swabs to detect viral RNA. Elevated serum IgM levels specific to Mycoplasma pneumoniae were observed in 534 children and were associated with a Kawasaki-like illness in one child. To date, all of the children are alive. Conclusion: This study underlines the importance of considering, depending on the clinical context, a possible co-infection between SARS-CoV-2 and atypical bacteria, such as Mycoplasma pneumoniae. Co-infections with other respiratory pathogens during the pandemic and hospital stay can cause mistakes in clinical diagnostic and drug treatment. Physicians should perform early differential diagnosis of SARS-CoV-2 in association with other infectious agents. Further studies are needed to have a real incidence of these co-infections and their impact on symptoms, course, and outcome of patients with SARS-CoV-2.

Precautions against COVID-19 reduce respiratory virus infections among children in Southwest China

Acute respiratory tract infections pose a serious threat to the health of children worldwide, with viral infections representing a major etiology of this type of disease. Protective measures such as mask-wearing, social distancing, and hand hygiene can be effective in curbing the spread of severe acute respiratory syndrome coronavirus 2. These precautions may also have an impact on the spread of other respiratory viruses. In this study, we retrospectively compared the respiratory virus infections of children in Southwest China before and after the outbreak of COVID-19. Nasopharyngeal swabs were collected from 1578 patients under 14 years old with acute respiratory tract infection symptoms before and after COVID-19 pandemic. Nine common respiratory viruses including human bocavirus, human rhinoviruses, human coronaviruses, human adenoviruses, human metapneumovirus, respiratory syncytial virus, influenza A virus, influenza B virus, and parainfluenza virus were measured by advanced fragment analysis. The respiratory virus infection rates among children of all ages and genders in Southwest China under the precautions against COVID-19 pandemic were significantly lower than that of the same period before the pandemic. Our findings indicate that public health measures implemented during the COVID-19 pandemic, including strict mask-wearing, social distancing, and hand hygiene, may be effective in preventing the transmission of other respiratory viruses in children, thereby controlling the spread of infections.

Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa

Severe acute respiratory infections (SARI) contribute to mortality in children ≤5 years. Their microbiological aetiologies are often unknown and may be exacerbated in light of coronavirus disease 19 (COVID-19). This study reports on respiratory pathogens in children ≤5 years (n = 84) admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Nasopharyngeal/oropharyngeal swabs collected were subjected to viral detection using QIAstat-Dx^® Respiratory SARS-CoV-2 Panel. The results revealed viral positivity and negativity detection rates of 88% (74/84) and 12% (10/84), respectively. Of the 21 targeted pathogens, human rhinovirus/enterovirus (30%), respiratory syncytial virus (RSV; 26%), and severe acute respiratory syndrome coronavirus 2 (24%) were mostly detected, with other viruses being 20% and a co-infection rate of 64.2% (54/84). Generally, RSV-positive samples had lower Ct values, and fewer viruses were detected during the third wave. Changes in the circulation patterns of respiratory viruses with total absence of influenza virus could be attributed to measures against COVID-19 transmission, which may result in waned immunity, thereby increasing susceptibility to severe infections in the following season. High viral co-infection rate, as detected, may complicate diagnosis. Nonetheless, accurate identification of the pathogens may guide treatment decisions and infection control.

Viral etiology among children hospitalized for acute respiratory tract infections and its association with meteorological factors and air pollutants: a time-series study (2014-2017) in Macao

Background

The associations between viral etiology of acute respiratory infections (ARI) with meteorological factors and air pollutants among children is not fully understood. This study aimed to explore the viral etiology among children hospitalized for ARI and the association of meteorological factors and air pollutants with children hospitalization due to viral ARI.

Methods

Electronic health record data about children (aged between 1 month and 14 years) admitted for ARI at Kiang Wu Hospital in Macao between 2014 and 2017 was analyzed retrospectively. xMAP multiplex assays were used to detect viruses in the nasopharyngeal swab and distributed-lag nonlinear model (DLNM) was used to evaluate associations.

Results

Among the 4880 cases of children hospitalization due to ARI, 3767 (77.2%) were tested positive for at least one virus and 676 (18%) exhibited multiple infections. Enterovirus (EV)/rhinovirus (HRV), adenovirus (ADV), respiratory syncytial virus (RSV) and influenza virus (IFV) were the most common viral pathogens associated with ARI and human bocavirus (hBOV) exhibited the highest multiple infection rates. Meteorological factors and air pollutants (PM₁₀, PM_2.5 and NO₂) were associated with the risk of viral ARI hospitalization. The relative risk of viral infection increased with daily mean temperature but plateaued when temperature exceeded 23 °C, and increased when the relative humidity was < 70% and peaked at 50%. The effect of solar radiation was insignificant. Air pollutants (including PM₁₀, PM_2.5, NO₂ and O₃) showed strong and immediate effect on the incidence of viral infection.

Conclusions

The effects of mean temperature, relative humidity and air pollutants should be taken into account when considering management of ARI among children.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07585-y.

Impact of rhinovirus on hospitalization during the COVID-19 pandemic: a prospective cohort study

Background

Although the clinical course of the COVID-19 in adults has been extensively described, the impact of the co-detection of SARS-CoV-2 and rhinovirus on severity outcomes is not understood.

Objectives

This study aimed to compare the risk of hospitalization of outpatients with COVID-19 with and without the co-detection of rhinovirus in southern Brazil. Secondarily, such risk was also compared between all individuals with COVID-19 and those with single rhinovirus infection.

Study design

Outpatients (>18 years) with acute signs of cough, fever, or sore throat were prospectively enrolled at two emergency departments from May to September 2020. Sample collection was performed to detect SARS-CoV-2 and other 20 respiratory pathogens. Participants were followed for 28 days through telephone interviews.

Results

1,047 participants were screened and 1,044 were included. Of these, 4.9% were lost during follow-up, and 993/1,044 (95.1%) were included in severity-related analysis. Rhinovirus was the most prevalent pathogen (25.0%, 248/993), followed by SARS-CoV-2 (22.6%, 224/993), with coinfection of these two viruses occurring in 91/993 (9.2%) participants. The risk of COVID-19-related hospitalizations were not different between individuals with and without co-detection of rhinovirus (9.9% vs. 7.6%, respectively, P = 0.655). Conversely, subjects with COVID-19 had a higher hospitalization risk than single rhinovirus infection (8.3 vs 0.4%, respectively, P < 0.001).

Conclusions

The co-detection of SARS-CoV-2 and rhinovirus did not change the risk of hospitalizations in adults. Furthermore, COVID-19 was more severe than single rhinovirus infection.

Analysis of severe human adenovirus infection outbreak in Guangdong Province, southern China in 2019

During 2018-2019, a severe human adenovirus (HAdV) infection outbreak occurred in southern China. Here, we screened 18 respiratory pathogens in 1704 children (≤ 14 years old) hospitalized with acute respiratory illness in Guangzhou, China, in 2019. In total, 151 patients had positive HAdV test results; 34.4% (52/151) of them exhibited severe illness. HAdV infection occurred throughout the year, with a peak in summer. The median patient age was 3.0 (interquartile range: 1.1-5.0) years. Patients with severe HAdV infection exhibited increases in 12 clinical indexes (P ​≤ ​0.019) and decreases in four indexes (P ​≤ ​0.007), compared with patients exhibiting non-severe infection. No significant differences were found in age or sex distribution according to HAdV infection severity (P ​> ​0.05); however, the distributions of comorbid disease and HAdV co-infection differed according to HAdV infection severity (P ​< ​0.05). The main epidemic types were HAdV-3 (47.0%, 71/151) and HAdV-7 (46.4%, 70/151). However, the severe illness rate was significantly higher in patients with HAdV-7 (51.4%) than in patients with HAdV-3 (19.7%) and other types of HAdV (20%) (P ​< ​0.001). Sequencing analysis of genomes/capsid genes of 13 HAdV-7 isolates revealed high similarity to previous Chinese isolates. A representative HAdV-7 isolate exhibited a similar proliferation curve to the curve described for the epidemic HAdV-3 strain Guangzhou01 (accession no. DQ099432) (P ​> ​0.05); the HAdV-7 isolate exhibited stronger virulence and infectivity, compared with HAdV-3 (P ​< ​0.001). Overall, comorbid disease, HAdV co-infection, and high virulence and infectivity of HAdV-7 were critical risk factors for severe HAdV infection; these data can facilitate treatment, control, and prevention of HAdV infection.

Clinical manifestations and outcome of viral acute lower respiratory infection in hospitalised children in Myanmar

BACKGROUND

Acute lower respiratory infection (ALRI) remains the leading cause of death in children worldwide, and viruses have been the major cause of ALRI. In Myanmar, ALRI is associated with high morbidity and mortality in children, and detailed information on ALRI is currently lacking.

METHODS

This prospective study investigated the viral aetiologies, clinical manifestations, and outcomes of ALRI in hospitalised children aged 1 month to 12 years at the Yankin Children Hospital, Yangon, Myanmar from May 2017 to April 2019. The sample size was set to 300 patients for each year. Two nasopharyngeal swabs were obtained for the patients with suspected viral ALRI; one for rapid tests for influenza and respiratory syncytial virus (RSV), and the other for real-time PCR for the 16 ALRI-causing viruses. Pneumococcal colonization rates were also investigated using real-time PCR. Clinical information was extracted from the medical records, and enrolled patients were categorised by age and severity for comparison.

RESULTS

Among the 5463 patients admitted with a diagnosis of ALRI, 570 (10.4%) were enrolled in this study. The median age of the patients was 8 months (interquartile range, 4-15 months). The most common symptoms were cough (93%) and difficulty in breathing (73%), while the most common signs of ALRI were tachypnoea (78%) and chest indrawing (67%). A total of 16 viruses were detected in 502 of 570 patients' samples (88%), with RSV B (36%) and rhinovirus (28%) being the most commonly detected. Multiple viruses were detected in 221 of 570 samples (37%) collected from 570 patients. Severe ALRI was diagnosed in 107 of 570 patients (19%), and RSV B and human rhinovirus were commonly detected. The mortality rate was 5%; influenza virus A (29%) and RSV B (21%) were commonly detected, and stunting and lack of immunization were frequently observed in such cases. Additionally, 45% (259/570) of the patients had pneumococcal colonization.

CONCLUSIONS

Viral ALRI in hospitalised children with a median of 8 months has significant morbidity and mortality rates in Myanmar. RSV and rhinovirus were the most commonly detected from nasopharyngeal swabs, while influenza virus and RSV were the most frequently associated with fatal cases.

Novel factors to predict respiratory viral disease progression in allogeneic hematopoietic cell transplant recipients

We assessed novel factors and the immunodeficiency scoring index (ISI) to predict progression to lower respiratory tract infection (LRTI) among hematopoietic cell transplant (HCT) recipients presenting with upper respiratory tract infection (URTI) with 12 viruses in the PCR era. We retrospectively analyzed the first respiratory virus detected by multiplex PCR in allogeneic HCT recipients (4/2008-9/2018). We used Cox proportional hazards models to examine factors for progression to LRTI within 90 days among patients presenting with URTI. A total of 1027 patients (216 children and 811 adults) presented with URTI only. Among these, 189 (18%) progressed to LRTI (median: 12 days). Multivariable models demonstrated a history of  >1 transplant, age  ≥40 years, time post-HCT (≤30 days), systemic steroids, hypoalbuminemia, hyperglycemia, cytopenia, and high ISI (scores 7-12) were associated with an increased risk of progression to LRTI. Respiratory syncytial virus and human metapneumovirus showed the highest progression risk. Patients with ≥3 independent risk factors or high ISI scores were highly likely to progress to LRTI. We identified novel risk factors for progression to LRTI, including history of multiple transplants and hyperglycemia, suggesting an intervention opportunity with glycemic control. ISI and number of risk factors appear to predict disease progression across several viruses.

A COVID-19 primer for primary care clinicians

COVID-19 has challenged primary care clinicians to rapidly learn new information and adapt clinical practice in response to the continuous evolution of prevention, diagnosis, and management measures. The introduction of COVID-19 vaccination for age-eligible children has afforded increased opportunities for disease prevention, and the pandemic has highlighted the need for primary care clinicians to serve as advocates for their young patients and their communities.