Epidemiology of viral respiratory infections in a tertiary care centre in the era of molecular diagnosis, Geneva, Switzerland, 2011-2012

Detection of Human Coronavirus-OC43 in Nasopharyngeal Swab Specimens Via Immunofluorescence Staining Using Human Serum and an Anti-human Antibody

Immunofluorescence methods using cell lines to detect seasonal human coronavirus (HCoV)-OC43 in nasopharyngeal swab specimens have not yet been established. A human rectal adenocarcinoma cell line (HRT-18) was exposed to the specimens obtained from patients with upper respiratory tract infections. Immunofluorescence staining was conducted using a combination of human serum containing an HCoV-OC43 anti-spike protein antibody and a fluorescence-labeled anti-human antibody. Positive staining in HRT-18 cells was detected after exposure to specimens obtained from nine of eleven patients in whom HCoV-OC43 RNA was detected using the FilmArray method. Increased viral RNA levels in the supernatant were also detected in HRT-18 cells exposed to specimens obtained from four of five patients. In contrast, positive staining was not detected in HRT-18 cells exposed to six patient specimens that tested negative for RNA from 17 types and subtypes of respiratory viruses, including HCoV-OC43. Cells inoculated with the established strain HCoV-OC43 (ATCC VR-759) also showed positive staining. These findings suggest that replication-competent HCoV-OC43 in the specimens can be detected via immunofluorescence staining of HRT-18 cells with human serum. Using this method, positive staining for viruses other than HCoV-OC43 may be obtained.

Interplay between respiratory viruses and cilia in the airways

The airway epithelium is the first point of contact for inhaled pathogens. The role of epithelial cells in clearance, infection and colonisation of bacteria is established. The interactions of respiratory viruses and cilia is less understood, but viruses are known to target ciliated epithelial cells for entry, replication and dissemination. Furthermore, some respiratory viruses impair and/or enhance ciliary activity. This review examines what is known about the interactions between cilia and viral infection and how respiratory viruses effect cilia function with subsequent consequences for human health. We discuss the models which can be used to investigate the relationship between respiratory viruses and the host airway.

The role of human rhinovirus in COPD exacerbations in Abu Dhabi: molecular epidemiology and clinical significance

This study aimed to describe the molecular epidemiology and seasonality of human rhinovirus (HRV) in chronic obstructive pulmonary disease (COPD) and its association with COPD exacerbations in Abu Dhabi, the United Arab Emirates (UAE). Sputum specimens were collected for analysis from all COPD patients who visited a medical center from November 2021 to October 2022. The real-time quantitative polymerase chain reaction (qPCR) test was used to detect HRV. Of the 78 COPD patients included in the study, 58 (74%) patients presented with one or more exacerbation episodes. The incidence of COPD exacerbation peaked over the winter and substantially decreased during the summer. HRV positivity in patients during exacerbation (E1) was 11/58 (19%) and 15/58 (26%) two weeks after the exacerbation episode (E2). There was no significant difference in the HRV load in these patients. No statistically significant difference was observed in the detection of HRV during exacerbation compared to patients with stable COPD. This is the first study to assess the association between HRV detection by qPCR and COPD exacerbations in the UAE. The high sensitivity of the detection technology helped collect reliable epidemiologic data. Few studies have provided similar Middle East data. This study's pattern of COPD exacerbations and HRV detection parallels that of temperate countries. This information can help with future, more extensive surveillance of respiratory viruses in the UAE and the Middle East and their association with COPD exacerbations.

Viral co-detection of influenza virus and other respiratory viruses in hospitalized Brazilian patients during the first three years of the coronavirus disease (COVID)-19 pandemic: an epidemiological profile

Introduction

In Brazil, few studies were performed regarding the co-detection of respiratory viruses in hospitalized patients. In this way, the study aimed to describe the epidemiological profile of hospitalized patients due to influenza virus infection that presented co-detection with another respiratory virus.

Methods

The epidemiological analysis was made by collecting data from Open-Data-SUS. The study comprised patients infected by the influenza A or B virus with positive co-detection of another respiratory virus, such as adenovirus, bocavirus, metapneumovirus, parainfluenza virus (types 1, 2, 3, and 4), rhinovirus, and respiratory syncytial virus (RSV). The markers [gender, age, clinical signs and symptoms, comorbidities, need for intensive care unit (ICU) treatment, and need for ventilatory support] were associated with the chance of death. The data was collected during the first three years of the coronavirus disease (COVID)-19 pandemic-from December 19, 2019, to April 06, 2023.

Results

A total of 477 patients were included, among them, the influenza A virus was detected in 400 (83.9%) cases. The co-detection occurred, respectively, for RSV (53.0%), rhinovirus (14.0%), adenovirus (13.4%), parainfluenza virus type 1 (10.7%), parainfluenza virus type 3 (5.2%), metapneumovirus (3.8%), parainfluenza virus type 2 (3.6%), bocavirus (3.4%), and parainfluenza virus type 4 (1.5%). The co-detection rate was higher in the male sex (50.7%), age between 0-12 years of age (65.8%), and white individuals (61.8%). The most common clinical symptoms were cough (90.6%), dyspnea (78.8%), and fever (78.6%). A total of 167 (35.0%) people had at least one comorbidity, mainly cardiopathy (14.3%), asthma (8.4%), and diabetes mellitus (7.3%). The need for ICU treatment occurred in 147 (30.8%) cases, with most of them needing ventilatory support (66.8%), mainly non-invasive ones (57.2%). A total of 33 (6.9%) patients died and the main predictors of death were bocavirus infection (OR = 14.78 [95%CI = 2.84-76.98]), metapneumovirus infection (OR = 8.50 [95%CI = 1.86-38.78]), race (other races vs. white people) (OR = 3.67 [95%CI = 1.39-9.74]), cardiopathy (OR = 3.48 [95%CI = 1.13-10.71]), and need for ICU treatment (OR = 7.64 [95%CI = 2.44-23.92]).

Conclusion

Co-detection between the influenza virus and other respiratory viruses occurred, mainly with RSV, rhinovirus, and adenovirus being more common in men, white people, and in the juvenile phase. Co-detection of influenza virus with bocavirus and metapneumovirus was associated with an increased chance of death. Other factors such as race, cardiopathy, and the need for an ICU were also associated with a higher chance of death.

Respiratory viral infections before the COVID-19 in Portugal: A single center study

Objectives

We aimed to describe the respiratory viruses (RV) found in respiratory samples from patients admitted to Hospital de São Bernardo, Setúbal, Portugal, between October 2019 and March 2020, and to correlate these with clinical features.

Design

This retrospective study explored 948 fresh frozen naso/oropharyngeal swabs, tested by reverse transcription-polymerase chain reaction.

Results

Rhinovirus/enterovirus, influenza, and respiratory syncytial virus (hRSV) were the most prevalent RV. Half of the patients fulfilled the acute respiratory infection (ARI) and/or influenza-like illness (ILI) criteria, with increasing age significantly reducing the risk of ARI and/or ILI. Hospital admission was more frequently observed in symptomatic patients, but the length of stay and mortality were significantly lower. Most (96.5 %) patients had a main respiratory diagnosis. In adults, the most prevalent was pneumonia, which particularly affected older patients, while in children, the most common was bronchiolitis. The number of hospital admissions was high. Sudden onset, shortness of breath, older age, and hRSV detection significantly increased the risk of hospital admission overall. In bronchiolitis, female gender significantly increased the risk of hospital admission, while older age significantly reduced this risk. Twenty patients died within the first month of sampling, and all were older adults. Older age and male gender significantly increased the risk of death.

Conclusions

Respiratory viral infections can have a significant clinical impact, particularly in young infants with bronchiolitis and older adults with pneumonia. This study provides the first snapshot of the respiratory viral infections just before the outbreak of SARS-CoV-2 in Portugal, providing relevant clinical insights.

Global prevalence of infections in newborns with respiratory complications: systematic review and meta-analysis

Background and Objectives

Newborns as a vulnerable population are exposed to congenital and acquired infections during and after birth. There are several reports of the isolation and reporting of infectious agents (IAs) in early life of newborns with respiratory manifestations, and the present comprehensive study provides a snapshot of the current global situation of the prevalence of IAs in newborns with respiratory symptoms.

Materials and Methods

A systematic search was conducted in main databases, including PubMed, Scopus, Web of science, and Google scholar. The pooled prevalence of infectious agents (IAs) in newborns was estimated using comprehensive meta-analysis software based on random effects model.

Results

Out of 44 inclusive studies (50 datasets) for IAs in newborns, the pooled prevalence was estimated to be 12.2% (95% CI: 6.40-22.0%) and the highest and lowest prevalence of IAs was related to the Brazil (78.2%, 95% CI: 31.0-96.6%), and UK (0.01%, 95% CI 0.01-0.01%) respectively.

Conclusion

The high prevalence of IAs in newborns emphasizes considers the necessary measures to prevent respiratory infections.

Positive and negative viral associations in patients with acute respiratory tract infections in primary care: the ECOVIR study

Introduction

Acute respiratory infections (ARIs) are the most common viral infections encountered in primary care settings. The identification of causal viruses is still not available in routine practice. Although new strategies of prevention are being identified, knowledge of the relationships between respiratory viruses remains limited.

Materials and methods

ECOVIR was a multicentric prospective study in primary care, which took place during two pre-pandemic seasons (2018-2019 and 2019-2020). Patients presenting to their General practitioner (GP) with ARIs were included, without selecting for age or clinical conditions. Viruses were detected on nasal swab samples using a multiplex Polymerase Chain Reaction test focused on 17 viruses [Respiratory Syncytial Virus-A (RSV-A), RSV-B, Rhinovirus/Enterovirus (HRV), human Metapneumovirus (hMPV), Adenovirus (ADV), Coronaviruses (CoV) HKU1, NL63, 229E, OC43, Influenza virus (H1 and H3 subtypes), Influenza virus B, Para-Influenza viruses (PIVs) 1-4, and Bocavirus (BoV)].

Results

Among the 668 analyzed samples, 66% were positive for at least one virus, of which 7.9% were viral codetections. The viral detection was negatively associated with the age of patients. BoV, ADV, and HRV occurred more significantly in younger patients than the other viruses (p < 0.05). Codetections were significantly associated with RSV, HRV, BoV, hMPV, and ADV and not associated with influenza viruses, CoV, and PIVs. HRV and influenza viruses were negatively associated with all the viruses. Conversely, a positive association was found between ADV and BoV and between PIVs and BoV.

Conclusion

Our study provides additional information on the relationships between respiratory viruses, which remains limited in primary care.

Contribution of the FilmArray BioFire® Technology in the Diagnosis of Viral Respiratory Infections during the COVID-19 Pandemic at Ibn Sina University Hospital Center in Rabat: Epidemiological Study about 503 Cases

Respiratory viruses are the most involved pathogens in acute respiratory infections. During the COVID-19 pandemic, new elements have been brought to this topic, especially at the diagnostic and therapeutic level. The objective of this work is to describe the epidemiology of respiratory viruses in patients admitted to the Ibn Sina University Hospital of Rabat during a period characterized by the emergence and spread of SARS-CoV-2. We conducted a retrospective study from January 1 to December 31. We included all patients treated for acute respiratory infection and for whom a multiplex respiratory panel PCR was requested. Virus detection was performed using a FilmArray RP 2.1 plus BioFire multiplex respiratory panel. The study population was relatively adults with a mean age of 39 years. The sex ratio M/F was 1.20. The survey revealed a high prevalence of 42.3% of patients hospitalized in the adult intensive care unit whose respiratory distress was the most common reason for hospitalization (58%). The positivity rate was 48.1%. This rate was higher in the pediatric population 83.13% compared to adults 29.7%. Monoinfection was found in 36.4% of cases, and codetection in 11.7% of cases. This survey revealed that a total of 322 viruses were detected, HRV being the most incriminated virus (48.7%), followed by RSV in 13.8% of patients. Considering the five most detected viruses in our study (HRV, RSV, PIV3, ADV, and hMPV), we found that the incidence was significantly higher in the pediatric population. SARS-CoV-2 was detected only in adult's population. In our study, we found that influenza A and B viruses, PIV2, MERS, and all bacteria were not detected by this kit during the study period. Regarding the seasonal distribution, RSV and hMPV showed a significantly high incidence during autumn and summer and SARS-CoV-2 and CoV OC43 showed a high peak during winter. In this study, we found a lack of detection of influenza virus and a shift in the usual winter peak of RSV to the summer, while the detection of ADV and HRV was less affected. This difference in detection could be due on the one hand to the difference in stability between enveloped and nonenveloped viruses and on the other hand to the escape of certain viruses to the different sanitary measures introduced after the declaration of the COVID-19 pandemic. These same measures were effective against enveloped viruses such as RSV and influenza viruses. The emergence of SARS-CoV-2 has modified the epidemiology of other respiratory viruses, either directly by viral interference or indirectly by the preventive measures taken.

Anti-inflammatory effects of medications used for viral infection-induced respiratory diseases

Respiratory viruses like rhinovirus, influenza virus, respiratory syncytial virus, and coronavirus cause several respiratory diseases, such as bronchitis, pneumonia, pulmonary fibrosis, and coronavirus disease 2019, and exacerbate bronchial asthma, chronic obstructive pulmonary disease, bronchiectasis, and diffuse panbronchiolitis. The production of inflammatory mediators and mucin and the accumulation of inflammatory cells have been reported in patients with viral infection-induced respiratory diseases. Interleukin (IL)-1β, IL-6, IL-8, tumor necrosis factor-α, granulocyte-macrophage colony-stimulating factor, and regulated on activation normal T-cell expressed and secreted are produced in the cells, including human airway and alveolar epithelial cells, partly through the activation of toll-like receptors, nuclear factor kappa B and p44/42 mitogen-activated protein kinase. These mediators are associated with the development of viral infection-induced respiratory diseases through the induction of inflammation and injury in the airway and lung, airway remodeling and hyperresponsiveness, and mucus secretion. Medications used to treat respiratory diseases, including corticosteroids, long-acting β2-agonists, long-acting muscarinic antagonists, mucolytic agents, antiviral drugs for severe acute respiratory syndrome coronavirus 2 and influenza virus, macrolides, and Kampo medicines, reduce the production of viral infection-induced mediators, including cytokines and mucin, as determined in clinical, in vivo, or in vitro studies. These results suggest that the anti-inflammatory effects of these medications on viral infection-induced respiratory diseases may be associated with clinical benefits, such as improvements in symptoms, quality of life, and mortality rate, and can prevent hospitalization and the exacerbation of chronic obstructive pulmonary disease, bronchial asthma, bronchiectasis, and diffuse panbronchiolitis.

Altered cell function and increased replication of rhinoviruses and EV-D68 in airway epithelia of asthma patients

Introduction

Rhinovirus (RV) infections constitute one of the main triggers of asthma exacerbations and an important burden in pediatric yard. However, the mechanisms underlying this association remain poorly understood.

Methods

In the present study, we compared infections of in vitro reconstituted airway epithelia originating from asthmatic versus healthy donors with representative strains of RV-A major group and minor groups, RV-C, RV-B, and the respiratory enterovirus EV-D68.

Results

We found that viral replication was higher in tissues derived from asthmatic donors for all tested viruses. Viral receptor expression was comparable in non-infected tissues from both groups. After infection, ICAM1 and LDLR were upregulated, while CDHR3 was downregulated. Overall, these variations were related to viral replication levels. The presence of the CDHR3 asthma susceptibility allele (rs6967330) was not associated with increased RV-C replication. Regarding the tissue response, a significantly higher interferon (IFN) induction was demonstrated in infected tissues derived from asthmatic donors, which excludes a defect in IFN-response. Unbiased transcriptomic comparison of asthmatic versus control tissues revealed significant modifications, such as alterations of cilia structure and motility, in both infected and non-infected tissues. These observations were supported by a reduced mucociliary clearance and increased mucus secretion in non-infected tissues from asthmatic donors.

Discussion

Altogether, we demonstrated an increased permissiveness and susceptibility to RV and respiratory EV infections in HAE derived from asthmatic patients, which was associated with a global alteration in epithelial cell functions. These results unveil the mechanisms underlying the pathogenesis of asthma exacerbation and suggest interesting therapeutic targets.

Cardiovascular Complications of Viral Respiratory Infections and COVID-19

Viral respiratory infections (VRI) are the most prevalent type of infectious diseases and constitute one of the most common causes of contact with medical care. Regarding the pathophysiology of the cardiovascular system, VRI can not only exacerbate already existing chronic cardiovascular disease (such as coronary artery disease or heart failure) but also trigger new adverse events or complications (e.g., venous thromboembolism), the latter particularly in subjects with multimorbidity or disease-related immobilization. In the current paper, we provide a narrative review of diverse cardiovascular complications of VRI as well as summarize available data on the pathology of the circulatory system in the course of coronavirus disease 2019 (COVID-19).

An anti-influenza combined therapy assessed by single cell RNA-sequencing

Influenza makes millions of people ill every year, placing a large burden on the healthcare system and the economy. To develop a treatment against influenza, we combined virucidal sialylated cyclodextrins with interferon lambda and demonstrated, in human airway epithelia, that the two compounds inhibit the replication of a clinical H1N1 strain more efficiently when administered together rather than alone. We investigated the mechanism of action of the combined treatment by single cell RNA-sequencing analysis and found that both the single and combined treatments impair viral replication to different extents across distinct epithelial cell types. We showed that each cell type comprises multiple sub-types, whose proportions are altered by H1N1 infection, and assessed the ability of the treatments to restore them. To the best of our knowledge this is the first study investigating the effectiveness of an antiviral therapy against influenza virus by single cell transcriptomic studies.

When combined with interferon lambda, virucidal sialylated cyclodextrins inhibit the replication of a clinical H1N1 influenza strain in ex vivo human airway epithelia more efficiently than when delivered alone.

Coronavirus seasonality, respiratory infections and weather

Background

The survival of coronaviruses are influenced by weather conditions and seasonal coronaviruses are more common in winter months. We examine the seasonality of respiratory infections in England and Wales and the associations between weather parameters and seasonal coronavirus cases.

Methods

Respiratory virus disease data for England and Wales between 1989 and 2019 was extracted from the Second-Generation Surveillance System (SGSS) database used for routine surveillance. Seasonal coronaviruses from 2012 to 2019 were compared to daily average weather parameters for the period before the patient’s specimen date with a range of lag periods.

Results

The seasonal distribution of 985,524 viral infections in England and Wales (1989–2019) showed coronavirus infections had a similar seasonal distribution to influenza A and bocavirus, with a winter peak between weeks 2 to 8. Ninety percent of infections occurred where the daily mean ambient temperatures were below 10 °C; where daily average global radiation exceeded 500 kJ/m²/h; where sunshine was less than 5 h per day; or where relative humidity was above 80%. Coronavirus infections were significantly more common where daily average global radiation was under 300 kJ/m²/h (OR 4.3; CI 3.9–4.6; p < 0.001); where average relative humidity was over 84% (OR 1.9; CI 3.9–4.6; p < 0.001); where average air temperature was below 10 °C (OR 6.7; CI 6.1–7.3; p < 0.001) or where sunshine was below 4 h (OR 2.4; CI 2.2–2.6; p < 0.001) when compared to the distribution of weather values for the same time period. Seasonal coronavirus infections in children under 3 years old were more frequent at the start of an annual epidemic than at the end, suggesting that the size of the susceptible child population may be important in the annual cycle.

Conclusions

The dynamics of seasonal coronaviruses reflect immunological, weather, social and travel drivers of infection. Evidence from studies on different coronaviruses suggest that low temperature and low radiation/sunlight favour survival. This implies a seasonal increase in SARS-CoV-2 may occur in the UK and countries with a similar climate as a result of an increase in the R₀ associated with reduced temperatures and solar radiation. Increased measures to reduce transmission will need to be introduced in winter months for COVID-19.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06785-2.

Lack of clinical significance for molecular detection of respiratory viruses in bronchoalveolar lavage samples

The clinical significance of molecular detection of respiratory viruses in bronchoalveolar lavage (BAL) samples is poorly defined. We performed an observational retrospective study including all patients who underwent a BAL procedure in our institution, regardless of the reason for bronchoscopy, from January 2015 to December 2018. Respiratory viruses were detected by real-time polymerase chain reaction with a commercial multiplex panel, and a cell culture was performed to detect cytomegalovirus and herpes simplex virus. Positive results were correlated with clinical symptoms and patients' characteristics. Of 540 BAL samples analyzed, 113 (20.9%) were positive for any respiratory virus. Viral detection was significantly associated with respiratory symptoms (83.2% vs. 68.9%, p = .004) and radiological infiltrates (67.3% vs. 52.2%, p = .006). The most frequent viruses detected were rhinovirus (42/113, 37.2%), influenza virus (20/113, 17.7%), and parainfluenza virus (PIV) (16/113, 14.2%). Respiratory pathogens codetections were found in 51/113 (45.1%) BAL samples, including more than one virus (16/51, 31.4%), fungi (8/51, 15.7%), and bacteria (9/51, 17.6%). Viral detection was significantly higher in immunocompromised patients (26.5% vs. 16.9%; p = .022). PIV and human metapneumovirus were mostly observed in lung (50.0%, 8/16) and hemopoietic transplant recipients (25%, 2/8), respectively, with clinical repercussions. Our data underline that molecular diagnosis allows identification of viral agents as the etiology of respiratory infections; however, the high frequency of codetections hinders identification of the agent responsible for the current respiratory symptomatology. Immunocompromised patients are the target population in whom to investigate the presence of respiratory viruses in their BAL samples.

Validation and performance comparison of three SARS-CoV-2 antibody assays

Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of coronavirus disease 2019 (COVID-19), although its clinical and epidemiologic utilities are still debatable. Characterizing these assays provides scientific basis to best use them. The current study assessed one chemiluminescent assay (Abbott COVID-2 IgG) and two lateral flow assays (STANDARD Q [SQ] IgM/IgG Duo and Wondfo total antibody test) using 113 blood samples from 71 PCR-confirmed COVID-19 hospitalized patients, 119 samples with potential cross-reactions, and 1068 negative controls including 942 pre-pandemic samples. SARS-CoV-2 IgM antibodies became detectable 3-4 days post-symptom onset using SQ IgM test and IgG antibodies were first detected 5-6 days post-onset using SQ IgG. Abbott IgG and Wondfo Total were able to detect antibodies 7 to 8 days post-onset. After 14 days post-symptom onset, the SQ IgG, Abbott IgG and Wondfo Total tests were able to detect antibodies from 100% of the PCR-confirmed patients in this series; 87.5% sensitivity for SQ IgM. Overall agreement was 88.5% between SQ IgM/IgG and Wondfo Total and 94.6% between SQ IgG and Abbott IgG. No cross-reaction due to recent sera with three of the endemic coronaviruses was observed. Viral hepatitis and autoimmune samples were the main source of limited cross-reactions. The specificities were 100% for SQ IgG and Wondfo Total, 99.62% for Abbott IgG, and 98.87% for SQ IgM. These findings demonstrated high sensitivity and specificity of appropriately validated SARS-CoV-2 serologic assays with implications for clinical use and epidemiological seroprevalence studies.

Cross-Immunization Against Respiratory Coronaviruses May Protect Children From SARS-CoV2: More Than a Simple Hypothesis?

In January 2020, a new coronavirus was identified as responsible for a pandemic acute respiratory syndrome. The virus demonstrated a high infectious capability and not-neglectable mortality in humans. However, similarly to previous SARS and MERS, the new disease COVID-19 caused by SARS-CoV-2 seemed to relatively spare children and younger adults. Some hypotheses have been proposed to explain the phenomenon, including lower ACE2 expression in children, cross-immunization from measles/rubella/mumps and BCG-vaccination, as well as the integrity of respiratory mucosa. Herein, we hypothesize that an additional mechanism might contribute to children's relative protection from SARS-CoV-2, the cross-immunization conferred by previous exposures to other common respiratory coronaviruses. To support our hypothesis, we show a statistically significant similarity in genomic and protein sequences, including epitopes for B- and T-cell immunity, of SARS-CoV-2 and the other beta coronaviruses. Since these coronaviruses are highly diffused across pediatric populations, cross-reactive immunity might reasonably induce an at least partial protection from SARS-CoV-2 in children.

First contact: the role of respiratory cilia in host-pathogen interactions in the airways

Respiratory cilia are the driving force of the mucociliary escalator, working in conjunction with secreted airway mucus to clear inhaled debris and pathogens from the conducting airways. Respiratory cilia are also one of the first contact points between host and inhaled pathogens. Impaired ciliary function is a common pathological feature in patients with chronic airway diseases, increasing susceptibility to respiratory infections. Common respiratory pathogens, including viruses, bacteria, and fungi, have been shown to target cilia and/or ciliated airway epithelial cells, resulting in a disruption of mucociliary clearance that may facilitate host infection. Despite being an integral component of airway innate immunity, the role of respiratory cilia and their clinical significance during airway infections are still poorly understood. This review examines the expression, structure, and function of respiratory cilia during pathogenic infection of the airways. This review also discusses specific known points of interaction of bacteria, fungi, and viruses with respiratory cilia function. The emerging biological functions of motile cilia relating to intracellular signaling and their potential immunoregulatory roles during infection will also be discussed.

Validation and performance comparison of three SARS-CoV-2 antibody assays

Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of coronavirus disease 2019 (COVID-19), although its clinical and epidemiologic utilities are still debatable. Characterizing these assays provides scientific basis to best use them. The current study assessed one chemiluminescent assay (Abbott COVID-2 IgG) and two lateral flow assays (STANDARD Q [SQ] IgM/IgG Duo and Wondfo total antibody test) using 113 blood samples from 71 PCR-confirmed COVID-19 hospitalized patients, 119 samples with potential cross-reactions, and 1068 negative controls including 942 pre-pandemic samples. SARS-CoV-2 IgM antibodies became detectable 3-4 days post-symptom onset using SQ IgM test and IgG antibodies were first detected 5-6 days post-onset using SQ IgG. Abbott IgG and Wondfo Total were able to detect antibodies 7 to 8 days post-onset. After 14 days post-symptom onset, the SQ IgG, Abbott IgG and Wondfo Total tests were able to detect antibodies from 100% of the PCR-confirmed patients in this series; 87.5% sensitivity for SQ IgM. Overall agreement was 88.5% between SQ IgM/IgG and Wondfo Total and 94.6% between SQ IgG and Abbott IgG. No cross-reaction due to recent sera with three of the endemic coronaviruses was observed. Viral hepatitis and autoimmune samples were the main source of limited cross-reactions. The specificities were 100% for SQ IgG and Wondfo Total, 99.62% for Abbott IgG, and 98.87% for SQ IgM. These findings demonstrated high sensitivity and specificity of appropriately validated SARS-CoV-2 serologic assays with implications for clinical use and epidemiological seroprevalence studies.

Non-influenza respiratory viruses in adult patients admitted with influenza-like illness: a 3-year prospective multicenter study

PURPOSE

To describe the burden, and characteristics, of influenza-like illness (ILI) associated with non-influenza respiratory viruses (NIRV).

METHODS

We performed a prospective, multicenter, observational study of adults admitted with ILI during three influenza seasons (2012-2015). Patients were screened for picornavirus, respiratory syncytial virus (RSV), coronavirus, human metapneumovirus, adenovirus, bocavirus, parainfluenza virus, and influenza, by PCR on nasopharyngeal samples. We excluded patients coinfected with NIRV and influenza.

RESULTS

Among 1421 patients enrolled, influenza virus was detected in 535 (38%), and NIRV in 215 (15%), mostly picornavirus (n = 61), RSV (n = 53), coronavirus 229E (n = 48), and human metapneumovirus (n = 40). In-hospital mortality was 5% (NIRV), 4% (influenza), and 5% (no respiratory virus). As compared to influenza, NIRV were associated with age (median, 73 years vs. 68, P = 0.026), chronic respiratory diseases (53% vs. 45%, P = 0.034), cancer (14% vs. 9%, P = 0.029), and immunosuppressive drugs (21% vs. 14%, P = 0.028), and inversely associated with diabetes (18% vs. 25%, P = 0.038). On multivariable analysis, only chronic respiratory diseases (OR 1.5 [1.1-2.0], P = 0.008), and diabetes (OR 0.5 [0.4-0.8], P = 0.01) were associated with NIRV detection.

CONCLUSIONS

NIRV are common in adults admitted with ILI during influenza seasons. Outcomes are similar in patients with NIRV, influenza, or no respiratory virus.

The dynamics of humoral immune responses following SARS-CoV-2 infection and the potential for reinfection

SARS-CoV-2 is a novel coronavirus that is the causative agent of coronavirus infectious disease 2019 (COVID-19). As of 17 April 2020, it has infected 2 114 269 people, resulting in 145 144 deaths. The timing, magnitude and longevity of humoral immunity is not yet understood for SARS-CoV-2. Nevertheless, understanding this is urgently required to inform the likely future dynamics of the pandemic, to guide strategies to allow relaxation of social distancing measures and to understand how to deploy limiting vaccine doses when they become available to achieve maximum impact. SARS-CoV-2 is the seventh human coronavirus to be described. Four human coronaviruses circulate seasonally and cause common colds. Two other coronaviruses, SARS and MERS, have crossed from animal sources into humans but have not become endemic. Here we review what is known about the human humoral immune response to epidemic SARS CoV and MERS CoV and to the seasonal, endemic coronaviruses. Then we summarize recent, mostly non-peer reviewed, studies into SARS-CoV-2 serology and reinfection in humans and non-human primates and summarize current pressing research needs.

Detection of community-acquired respiratory viruses in allogeneic stem-cell transplant recipients and controls-A prospective cohort study

Background

Community‐acquired respiratory viruses (CARV) cause upper and lower respiratory tract infections (URTI/LRTI) and may be life‐threatening for recipients of an allogeneic stem cell transplantation (allo‐SCT).

Methods

In a prospective study encompassing 4 winter‐seasons, we collected throat gargles (TG) at random time points from allo‐SCT recipients (patients) and controls and followed them up for at least 3 weeks including repetitive sampling and documentation of symptoms. A Multiplex‐PCR system to identify 20 CARV and Mycoplasma pneumoniae was used to detect CARV.

Results

One hundred ninety‐four patients with 426 TG and 273 controls with 549 TG were included. There were more patients with a positive test result (25% vs 11% in the controls), and the patients had a higher number of positive TG (70 = 16%) compared to controls (32 = 6%) (P < .001). Altogether, 115 viruses were detected. Multiple viruses in one TG (11/48, 34%) and prolonged shedding were only observed in patients (13/48, 27%). Patients had more RSV (18/83, 26%) and adenovirus (15/83, 21%) than controls (both viruses 2/32, 6%). Independent risk factors for the detection of CARV included age >40 years (OR 3.38, 95% CI 1.8‐6.4, P < .001) and presence of URTI‐symptoms (OR 3.22, 95% CI 1.9‐5.5, P < .001). No controls developed a LRTI or died whereas 4/48 (8%) patients developed a LRTI (coronavirus in 2, RSV in 1 and influenza A H1N1 in 1 patient). One patient died of CARV (influenza A H1N1).

Conclusion

Allo‐SCT‐recipients have more CARV‐infections, exhibit a different epidemiology, have more cases of co‐infection or prolonged shedding and have a higher rate of LRTI and mortality.

Interferon-Dependent and Respiratory Virus-Specific Interference in Dual Infections of Airway Epithelia

Many respiratory viruses cocirculate in the population and multiple infections are commonly reported. The clinical impact of coinfection is unclear and may vary depending on the viral couples involved. Using three-dimensional reconstituted human airway epithelia and clinical viral strains, we investigated the interaction between influenza virus (Flu), respiratory syncytial virus (RSV) and rhinovirus (RV). We showed that Flu and RSV interfere with RV replication, whereas RV does not interfere with either of these viruses. We then experimentally demonstrated that, when present, the interference is not related to a block of viral entry but rather to type I and type III interferon (IFN), the front-line antiviral defense of the respiratory mucosa. Consistent with this observation, we highlighted the differential sensitivity of each virus to IFNs, with RV being the only virus significantly inhibited by IFN-λ and the most sensitive to IFN-α. Finally, as type III IFN is of therapeutic interest due to its low proinflammatory profile, we also assessed and confirmed an inhibitory effect of IFN-λ in the context of persistent RV infections. The present work provides mechanistic clues concerning innate immunity involvement during respiratory virus interactions and confirms that IFN-λ is a promising candidate in the treatment of RV infections.

Community acquired respiratory virus infections in adult patients undergoing umbilical cord blood transplantation

Characteristics and risk factors (RFs) of community-acquired respiratory virus (CARV) infections after umbilical cord blood transplantation (UCBT) are lacking. We retrospectively analyzed CARV infections in 216 single-unit myeloablative UCBT recipients. One-hundred and fourteen episodes of CARV infections were diagnosed in 62 (29%) patients. Upper respiratory tract disease (URTD) occurred in 61 (54%) whereas lower respiratory tract disease (LRTD) in 53 (46%). The 5-year cumulative incidence of CARV infection was 29%. RFs for developing CARV infections were: prednisone-based graft-versus-host disease (GVHD) prophylaxis and grade II–IV acute GVHD. RFs analysis of CARV progression to LRTD identified 2007–2009 period and absolute lymphocyte count (ALC) < 0.5 × 10⁹/L. ALC < 0.5 × 10⁹/L had a negative impact on day 60 mortality in both overall CARV and those with LRTD, whereas proven LRTD was associated with higher day 60 mortality. CARV infections had a negative effect on non-relapse mortality. Overall survival at day 60 after CARV detection was significantly lower in recipients with LRTD compared with URTD (74% vs. 93%, respectively). In conclusion, CARV infections after UCBT are frequent and may have a negative effect in the outcomes, in particular in the context of lymphocytopenia.

Incidence and seasonality of respiratory viruses causing acute respiratory infections in the Northern United Arab Emirates

Background

The data on the seasonality of respiratory viruses helps to ensure the optimal vaccination period and to monitor the possible outbreaks of variant type.

Objectives

This study was designed to describe the molecular epidemiology and seasonality of acute respiratory infection (ARI)‐related respiratory viruses in the United Arab Emirates (UAE).

Methods

Both upper and lower respiratory specimens were collected for the analysis from all the patients who visited the Sheikh Khalifa Specialty Hospital (SKSH) with ARI for over 2 years. The multiplex real‐time reverse transcription polymerase chain reaction (rRT‐PCR) test was used to detect respiratory viruses, which include human adenovirus, influenza virus (FLU) A and B, respiratory syncytial virus, parainfluenza viruses, human rhinovirus (HRV), human metapneumovirus, human enterovirus, human coronavirus, and human bocavirus.

Results

A total of 1,362 respiratory samples were collected from 733 (53.8%) male and 629 (46.2%) female patients with ARI who visited the SKSH between November 2015 and February 2018. The rRT‐PCR test revealed an overall positivity rate of 37.2% (507/1362). The positive rate increased during winter; it was highest in December and lowest in September. FLU was the most frequently detected virus (273/1362 [20.0%]), followed by human rhinovirus (146/1362 [10.7%]). The FLU positivity rate showed two peaks, which occurred in August and December. The peak‐to‐low ratio for FLU was 2.26 (95% confidence interval: 1.52‐3.35).

Conclusions

The pattern of FLU in the UAE parallels to that of temperate countries. The trend of the small peak of FLU in the summer suggests a possibility of semi‐seasonal pattern in the UAE.

A novel PCR-based point-of-care method facilitates rapid, efficient, and sensitive diagnosis of influenza virus infection

OBJECTIVE

The aim of this single-centre study was the comparative analysis of the GeneXpert (Cepheid Inc.) and the LIAT (Roche) system for the rapid polymerase chain reaction (PCR)-based detection of influenza A (IA) and influenza B (IB) viruses.

PATIENTS AND METHODS

During the 2017-2018 flu season, 651 prospectively collected samples (throat and nasal swabs) of patients with symptoms of influenza-like illness or acute respiratory infection were tested for the presence of IA and IB viruses using the GeneXpert and LIAT systems. To evaluate the usefulness for near-patient testing, a LIAT system was installed at the Department of Emergency Medicine, and sample testing was performed on site. Reference testing of all samples was performed with the Xpert Flu assay and for 313 samples in addition with the Xpert Xpress Flu/RSV (respiratory syncytial virus) assay at the central laboratory. Analysis of all samples was carried out within 24 hr after collection.

RESULTS

Overall, 267 of the 651 samples analysed were positive for influenza viruses in at least one of the three assays investigated (IA, 88; IB, 179). The overall rates of agreement between the LIAT assay and the Xpert Flu assay was 96.0% for the detection of IA and IB viruses. The sensitivity and specificity of the LIAT assay compared to the Xpert Flu assay for the detection of IA was 98.80% (95% confidence interval (CI) 93.47-99.97%) and 99.12% (95% CI, 97.96% to 99.71%) and for the detection of IB 98.76% (95% CI 95.58-99.85%), and 96.33% (95% CI 94.26-97.81%), respectively. The LIAT assay showed a statistically significant higher detection rate of IB virus than the Xpert Flu assay (p <0.01). No significant difference was found between the detection rate of the LIAT assay and the Xpert Xpress Flu/RSV assay. The mean time to the availability of a definite test result was significantly shorter with the on-site LIAT system than the GeneXpert system (mean 59 min saving time; p <0.01).

CONCLUSION

The LIAT system represents a robust and highly sensitive point-of-care device for the rapid PCR-based detection of influenza A and influenza B viruses.

Epidemiology of viral respiratory infections in Australian working-age adults (20–64 years): 2010–2013

Acute respiratory infections cause significant morbidity and mortality accounting for 5.8 million deaths worldwide. In Australia, influenza-like illness (ILI), defined as cough, fever and fatigue is a common presentation in general practice and results in reduced productivity and lost working days. Little is known about the epidemiology of ILI in working-age adults. Using data from the ASPREN influenza surveillance network in Australia (2010–2013) we found that working-age adults made up 45.2% of all ILI notifications with 55% of samples positive for at least one respiratory virus. Viruses most commonly detected in our study included influenza A (20.6%), rhinovirus (18.6%), influenza B (6.2%), human meta-pneumovirus (3.4%), respiratory syncytial virus (3.1%), para-influenza virus (2.6%) and adenovirus (1.3%). We also demonstrated that influenza A is the predominant virus that increases ILI (by 1.2% per month for every positive influenza A case) in working-age adults during autumn–winter months while other viruses are active throughout the year. Understanding the epidemiology of viral respiratory infections through a year will help clinicians make informed decisions about testing, antibiotic and antiviral prescribing and when the beginning of the ‘flu season’ can be more confidently predicted.

Epidemiology of Respiratory Pathogens among Elderly Nursing Home Residents with Acute Respiratory Infections in Corsica, France, 2013-2017

Background

The current study aims to describe the demographical and clinical characteristics of elderly nursing home (NH) residents with acute respiratory infections (ARIs) during four winter seasons (2013/2014–2016/2017), as well as the microbiological etiology of these infections.

Methods

Seventeen NHs with at least one ARI resident in Corsica, France, were included. An ARI resident was defined as a resident developing a sudden onset of any constitutional symptoms in addition to any respiratory signs. Nasopharyngeal swabs from ARI residents were screened for the presence of 21 respiratory agents, including seasonal influenza viruses.

Results

Of the 107 ARI residents enrolled from NHs, 61 (57%) were positive for at least one of the 21 respiratory pathogens. Forty-one (38.3%) of the 107 ARI residents had influenza: 38 (92%) were positive for influenza A (100% A(H3N2)) and three (8%) for influenza B/Victoria. Axillary fever (≥38°C) was significantly more common among patients infected with influenza A(H3N2).

Conclusion

The circulation of seasonal respiratory viruses other than influenza A(H3N2) seems to be sporadic among elderly NH residents. Investigating the circulation of respiratory viruses in nonwinter seasons seems to be important in order to understand better the dynamic of their year-round circulation in NHs.

Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures

Background

The leading cause of acute illnesses, respiratory viruses, typically cause self-limited diseases, although severe complications can occur in fragile patients. Rhinoviruses (RVs), respiratory enteroviruses (EVs), influenza virus, respiratory syncytial viruses (RSVs), and coronaviruses are highly prevalent respiratory pathogens, but because of the lack of reliable animal models, their differential pathogenesis remains poorly characterized.

Objective

We sought to compare infections by respiratory viruses isolated from clinical specimens using reconstituted human airway epithelia.

Methods

Tissues were infected with RV-A55, RV-A49, RV-B48, RV-C8, and RV-C15; respiratory EV-D68; influenza virus H3N2; RSV-B; and human coronavirus (HCoV)–OC43. Replication kinetics, cell tropism, effect on tissue integrity, and cytokine secretion were compared. Viral adaptation and tissue response were assessed through RNA sequencing.

Results

RVs, RSV-B, and HCoV-OC43 infected ciliated cells and caused no major cell death, whereas H3N2 and EV-D68 induced ciliated cell loss and tissue integrity disruption. H3N2 was also detected in rare goblet and basal cells. All viruses, except RV-B48 and HCoV-OC43, altered cilia beating and mucociliary clearance. H3N2 was the strongest cytokine inducer, and HCoV-OC43 was the weakest. Persistent infection was observed in all cases. RNA sequencing highlighted perturbation of tissue metabolism and induction of a transient but important immune response at 4 days after infection. No majority mutations emerged in the viral population.

Conclusion

Our results highlight the differential in vitro pathogenesis of respiratory viruses during the acute infection phase and their ability to persist under immune tolerance. These data help to appreciate the range of disease severity observed in vivo and the occurrence of chronic respiratory tract infections in immunocompromised hosts.

Respiratory virus infection after allogeneic hematopoietic stem cell transplant in a tropical center: Predictive value of the immunodeficiency scoring index

Background

Respiratory virus infection (RVI) is a prevalent infection in patients after allogeneic hematopoietic stem cell transplant (allo‐HSCT) and can result in significant morbidity and mortality. Ability to assess the potential severity of RVI is important in the management of such patients.

Methods

We reviewed the cases of RVI in allo‐HSCT recipients and explored the predictive value of the immunodeficiency scoring index (ISI) established for respiratory syncytial virus (RSV) and its applicability for RVI caused by other respiratory viruses.

Results

RVI occurred year‐round in our tropical transplant center, with peaks in the middle and end of the year. Ninety‐five of the 195 recipients developed a total of 191 episodes of RVI, giving a cumulative incidence of 28% by 6 months and 52% by 24 months for the first episode of RVI. RSV, influenza, rhinovirus, and parainfluenza were the most common viruses. Pneumonia occurred in 63.64%, 42.31%, and 32.42% of adenovirus, influenza, and RSV RVI episodes, respectively, but was also non‐negligible in the more benign viruses, such as coronavirus (31.58%) and rhinovirus (23.68%). Nineteen of the 63 episodes of viral pneumonia required mechanical ventilation and 14 deaths occurred within 6 weeks of the RVI. Receiver operating characteristic analysis showed that an ISI of ≥8 predicted pneumonia with a positive predictive value of >80% for RVI caused by RSV, influenza, adenovirus, and parainfluenza, while it was not predictive for coronavirus and rhinovirus.

Conclusions

The ISI is a useful aid for decision‐making during clinic consultation for patients presenting with symptoms suggestive of an RVI.

Interference Between Respiratory Syncytial Virus and Human Rhinovirus Infection in Infancy

BACKGROUND

Respiratory syncytial virus (RSV) and human rhinovirus (HRV) are the most common viruses associated with acute respiratory tract infections in infancy. Viral interference is important in understanding respiratory viral circulation and the impact of vaccines.

METHODS

To study viral interference, we evaluated cases of RSV and HRV codetection by polymerase chain reaction in 2 prospective birth cohort studies (the Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure [INSPIRE] study and the Tennessee Children's Respiratory Initiative [TCRI]) and a double-blinded, randomized, controlled trial (MAKI), using adjusted multivariable regression analyses.

RESULTS

Among 3263 respiratory tract samples, 24.5% (798) and 37.3% (1216) were RSV and HRV positive, respectively. The odds of HRV infection were significantly lower in RSV-infected infants in all cohorts, with adjusted odds ratios of 0.30 (95% confidence interval [CI], .22-.40 in the INSPIRE study, 0.18 (95% CI, .11-.28) in the TCRI (adjusted for disease severity), and 0.34 (95% CI, .16-.72) in the MAKI trial. HRV infection was significantly more common among infants administered RSV immunoprophylaxis, compared with infants who did not receive immunoprophylaxis (OR, 1.65; 95% CI, 1.65-2.39).

CONCLUSIONS

A negative association of RSV on HRV codetection was consistently observed across populations, seasons, disease severity, and geographical regions. Suppressing RSV infection by RSV immunoprophylaxis might increase the risk of having HRV infection.

Impact of viral multiplex real-time PCR on management of respiratory tract infection: a retrospective cohort study

Background

Significance and clinical utility of multiple virus detection by multiplex real-time polymerase chain reaction (rtPCR) in respiratory tract infection remain unclear.

Methods

This retrospective cohort study analyzed how virus detection affected clinical management. During a 27-month period, clinical and laboratory information was collected from all children and adults in two Swiss tertiary centres whose respiratory samples were tested for respiratory viruses with a 16-plex rtPCR test.

Results

Pathogens were identified in 140 of 254 patients (55%); of those patients, there was ≥1 virus in 91 (65%), ≥ 1 bacterium in 53 (38%), and ≥1 virus and bacterium in 11 (8%). Of 80 patients with viral infection, 59 (74%) received antibiotics. Virus detection was associated with discontinuation of antibiotics in 2 of 20 adults (10%) and 6 of 14 children (43%). Overall 12 adults (34%) and 18 children (67%) were managed correctly without antibiotics after virus detection (p = 0.01). When taking biomarkers, radiologic presentations, and antibiotic pre-treatment into account, the impact of rtPCR and appropriateness of therapy for clinically viral infections increased to 100% in children and 62% in adults.

Conclusions

A substantial reduction of unnecessary antibiotic prescriptions seems possible. Appropriate application of rtPCR results in respiratory tract infections should be encouraged.

Rhinovirus Infections and Associated Respiratory Morbidity in Infants: A Prospective Cohort Study

BACKGROUND

Risk factors promoting rhinovirus (RV) infections are inadequately described in healthy populations, especially infants.

OBJECTIVES

To determine the frequency of symptomatic and asymptomatic RV infections and identify possible risk factors from host and environment among otherwise healthy infants.

METHODS

In a prospective birth cohort, respiratory health was assessed in 41 term-born infants by weekly telephonic interviews during the first year of life, and weekly nasal swabs were collected to determine RV prevalence. In a multilevel logistic regression model, associations between prevalence and respiratory symptoms during RV infections and host/environmental factors were determined.

RESULTS

Twenty-seven percent of nasal swabs in 41 infants tested positive for RVs. Risk factors for RV prevalence were autumn months [odds ratio (OR) = 1.71, P = 0.01, 95% confidence interval (CI): 1.13-2.61], outdoor temperatures between 5 and 10°C (OR = 2.33, P = 0.001, 95% CI: 1.41-3.86), older siblings (OR = 2.60, P = 0.001, 95% CI: 1.50-4.51) and childcare attendance (OR = 1.53, P = 0.07, 95% CI: 0.96-2.44). Fifty-one percent of RV-positive samples were asymptomatic. Respiratory symptoms during RV infections were less likely during the first 3 months of life (OR = 0.34, P = 0.003, 95% CI: 0.17-0.69) and in infants with atopic mothers (OR = 0.44, P = 0.008, 95% CI: 0.24-0.80). Increased tidal volume (OR = 1.67, P = 0.03, 95% CI: 1.04-2.68) and outdoor temperatures between 2 and 5°C (OR = 2.79, P = 0.02, 95% CI: 1.17-6.61) were associated with more symptoms.

CONCLUSIONS

RVs are highly prevalent during the first year of life, and most infections are asymptomatic. Frequency of RV infections is associated with environmental factors, while respiratory symptoms during RV infections are linked to host determinants like infant age, maternal atopy or premorbid lung function.

Molecular viral epidemiology and clinical characterization of acute febrile respiratory infections in hospitalized children in Taiwan

Acute respiratory infection (ARI) is a leading cause of morbidity and hospitalization in children. To profile the viruses causing ARI in children admitted to a community‐based hospital in central Taiwan, a cross‐sectional study was conducted on children under 14 years of age that were hospitalized with febrile ARI. Viral etiology was determined using conventional cell culture and a commercial respiratory virus panel fast assay (xTAG RVP), capable of detecting 19 different respiratory viruses and subtype targets. Demographic, clinical, and laboratory data were recorded and analyzed. The RVP fast assay identified at least one respiratory virus in 130 of the 216 specimens examined (60.2%) and rose to 137 (63.4%) by combining the results of cell culture and RVP fast assay. In order of frequency, the etiological agents identified were, rhinovirus/enterovirus (24.6%), respiratory syncytial virus (13.8%), adenovirus (11.5%), parainfluenza virus (9.2%), influenza B (8.4%), influenza A (5.4%), human metapneumovirus (4.6%), human coronavirus (2%), and human bocavirus (2%). Co‐infection did not result in an increase in clinical severity. The RVP assay detected more positive specimens, but failed to detect 6 viruses identified by culture. The viral detection rate for the RVP assay was affected by how many days after admission the samples were taken (P = 0.03). In conclusion, Rhinovirus/enterovirus, respiratory syncytial virus, and adenovirus were prevalent in this study by adopting RVP assay. The viral detection rate is influenced by sampling time, especially if the tests are performed during the first three days of hospitalization. J. Med. Virol. 87:1860–1866, 2015. © 2015 Wiley Periodicals, Inc.

Effect of Financially Punished Audit and Feedback in a Pediatric Setting in China, within an Antimicrobial Stewardship Program, and as Part of an International Accreditation Process

Background

Prior authorization, audit and feedback, and pay for performance are the three core “active” strategies of antimicrobial stewardship program (ASP), yet little is known about the individual or combined benefits of such programs, particularly in a pediatric setting.

Objectives

The aim of this study was to compare these core ASP strategies and determine the incremental effect of financially punished audit and feedback.

Methods

During the journey to the Joint Commission International accreditation, a tertiary pediatric medical center performed two different hospital-wide stewardship interventions in succession. The first stage without formalized ASPs served as pre-intervention period, January 2011 to April 2011. The ASP used prior authorization alone during the first-intervention period, May 2011 to September 2011. In October 2011, financially punished audit and feedback was introduced, marking the start of the second-intervention period, October 2011 to November 2012. We compared the differences of the change in monthly average use of antibiotics and expenditure on antibiotics before and after the ASP changes by using interrupted time series via dynamic regression. The main end points included the proportions of antibiotic prescriptions and expenditure on antibacterial relative to all medications.

Results

Before the second-intervention period, neither the proportion of antibiotic prescriptions nor the proportion of expenditure on antibiotics declined significantly in both ambulatory and inpatient settings. However, after the introduction of financially punished audit and feedback, the proportion of both antibiotic prescriptions (β = −6.269, P < 0.001, and reduction = 59.4% for outpatients; β = −1.235, P < 0.001, and reduction = 19.8% for inpatients) and expenditure on antibiotics (β = −7.777, P < 0.001, and reduction = 46.7% for outpatients; β = −4.933, P = 0.001, and reduction = 16.3% for inpatients) dropped immediately.

Conclusion

The combination of more than one core strategies (prior authorization, audit and feedback, and pay for performance) will be more effective than one strategy alone.

Vitamin D Supplementation and the Risk of Colds in Patients with Asthma

RATIONALE

Restoration of vitamin D sufficiency may reduce asthma exacerbations, events that are often associated with respiratory tract infections and cold symptoms.

OBJECTIVES

To determine whether vitamin D supplementation reduces cold symptom occurrence and severity in adults with mild to moderate asthma and vitamin D insufficiency.

METHODS

Colds were assessed in the AsthmaNet VIDA (Vitamin D Add-on Therapy Enhances Corticosteroid Responsiveness) trial, in which 408 adult patients were randomized to receive placebo or cholecalciferol (100,000 IU load plus 4,000 IU/d) for 28 weeks as add-on therapy. The primary outcome was cold symptom severity, which was assessed using daily scores on the 21-item Wisconsin Upper Respiratory Symptom Survey.

MEASUREMENTS AND MAIN RESULTS

A total of 203 participants experienced at least one cold. Despite achieving 25-hydroxyvitamin D levels of 41.9 ng/ml (95% confidence interval [CI], 40.1-43.7 ng/ml) by 12 weeks, vitamin D supplementation had no effect on the primary outcome: the average peak WURSS-21 scores (62.0 [95% CI, 55.1-68.9; placebo] and 58.7 [95% CI, 52.4-65.0; vitamin D]; P = 0.39). The rate of colds did not differ between groups (rate ratio [RR], 1.2; 95% CI, 0.9-1.5); however, among African Americans, those receiving vitamin D versus placebo had an increased rate of colds (RR, 1.7; 95% CI, 1.1-2.7; P = 0.02). This was also observed in a responder analysis of all subjects achieving vitamin D sufficiency, regardless of treatment assignment (RR, 1.4; 95% CI, 1.1-1.7; P = 0.009).

CONCLUSIONS

Our findings in patients with mild to moderate asthma undergoing an inhaled corticosteroid dose reduction do not support the use of vitamin D supplementation for the purpose of reducing cold severity or frequency.

Viruses as Sole Causative Agents of Severe Acute Respiratory Tract Infections in Children

Background

Respiratory syncytial virus (RSV) and influenza A viruses are known to cause severe acute respiratory tract infections (SARIs) in children. For other viruses like human rhinoviruses (HRVs) this is less well established. Viral or bacterial co-infections are often considered essential for severe manifestations of these virus infections.

Objective

The study aims at identifying viruses that may cause SARI in children in the absence of viral and bacterial co-infections, at identifying disease characteristics associated with these single virus infections, and at identifying a possible correlation between viral loads and disease severities.

Study Design

Between April 2007 and March 2012, we identified children (<18 year) with or without a medical history, admitted to our paediatric intensive care unit (PICU) with SARI or to the medium care (MC) with an acute respiratory tract infection (ARTI) (controls). Data were extracted from the clinical and laboratory databases of our tertiary care paediatric hospital. Patient specimens were tested for fifteen respiratory viruses with real-time reverse transcriptase PCR assays and we selected patients with a single virus infection only. Typical bacterial co-infections were considered unlikely to have contributed to the PICU or MC admission based on C-reactive protein-levels or bacteriological test results if performed.

Results

We identified 44 patients admitted to PICU with SARI and 40 patients admitted to MC with ARTI. Twelve viruses were associated with SARI, ten of which were also associated with ARTI in the absence of typical bacterial and viral co-infections, with RSV and HRV being the most frequent causes. Viral loads were not different between PICU-SARI patients and MC-ARTI patients.

Conclusion

Both SARI and ARTI may be caused by single viral pathogens in previously healthy children as well as in children with a medical history. No relationship between viral load and disease severity was identified.

Viral Respiratory Tract Infections in Adult Patients Attending Outpatient and Emergency Departments, Taiwan, 2012-2013: A PCR/Electrospray Ionization Mass Spectrometry Study

Viral etiologies of respiratory tract infections (RTIs) have been less studied in adult than in pediatric populations. Furthermore, the ability of PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) to detect enteroviruses and rhinoviruses in respiratory samples has not been well evaluated. We sought to use PCR/ESI-MS to comprehensively investigate the viral epidemiology of adult RTIs, including testing for rhinoviruses and enteroviruses. Nasopharyngeal or throat swabs from 267 adults with acute RTIs (212 upper RTIs and 55 lower RTIs) who visited a local clinic or the outpatient or emergency departments of a medical center in Taiwan between October 2012 and June 2013 were tested for respiratory viruses by both virus isolation and PCR/ESI-MS. Throat swabs from 15 patients with bacterial infections and 27 individuals without active infections were included as control samples. Respiratory viruses were found in 23.6%, 47.2%, and 47.9% of the 267 cases by virus isolation, PCR/ESI-MS, and both methods, respectively. When both methods were used, the influenza A virus (24.3%) and rhinoviruses (9.4%) were the most frequently identified viruses, whereas human coronaviruses, human metapneumovirus (hMPV), enteroviruses, adenoviruses, respiratory syncytial virus, and parainfluenza viruses were identified in small proportions of cases (<5% of cases for each type of virus). Coinfection was observed in 4.1% of cases. In the control group, only 1 (2.4%) sample tested positive for a respiratory virus by PCR/ESI-MS. Patients who were undergoing steroid treatment, had an active malignancy, or suffered from chronic obstructive pulmonary disease (COPD) were at risk for rhinovirus, hMPV, or parainfluenza infections, respectively. Overall, immunocompromised patients, patients with COPD, and patients receiving dialysis were at risk for noninfluenza respiratory virus infection. Rhinoviruses (12.7%), influenza A virus (10.9%), and parainfluenza viruses (7.3%) were the most common viruses involved in the 55 cases of lower RTIs. The factors of parainfluenza infection, old age, and immunosuppression were independently associated with lower RTIs. In conclusion, PCR/ESI-MS improved the diagnostic yield for viral RTIs. Non-influenza respiratory virus infections were associated with patients with comorbidities and with lower RTIs. Additional studies that delineate the clinical need for including non-influenza respiratory viruses in the diagnostic work-up in these populations are warranted.

Transmission and effect of multiple clusters of seasonal influenza in a Swiss geriatric hospital

Objectives

To investigate a nosocomial outbreak of influenza.

Design

Prospective outbreak investigation with active case finding and molecular typing.

Setting

A large academic geriatric hospital in Switzerland.

Participants

Elderly hospitalized adults.

Measurements

Based on syndromic surveillance, a nosocomial influenza outbreak was suspected in February 2012. All suspected cases were screened for respiratory viruses using real‐time reverse transcription polymerase chain reaction of nasopharyngeal swabs. Infection control procedures (droplet precautions with single room isolation whenever possible) were implemented for all suspected or confirmed cases. Specimens positive for influenza viruses were processed and sequenced whenever possible to track transmission dynamics.

Results

Respiratory samples from 155 suspected cases were analyzed during the outbreak period, of which 69 (44%) were positive for influenza virus, 26 (17%) were positive for other respiratory viruses, and 60 (39%) were negative. Three other cases fulfilled clinical criteria for influenza infection but were not sampled, and one individual was admitted with an already positive test, resulting in a total of 73 influenza cases, of which 62 (85%) were classified as nosocomial. Five distinct clusters of nosocomial transmission were identified using viral sequencing, with epidemiologically unexpected in‐hospital transmission dynamics. Seven of 23 patients who experienced influenza complications died. Sixteen healthcare workers experienced an influenza‐like illness (overall vaccination rate, 36%).

Conclusion

Nosocomial influenza transmission caused more secondary cases than repeated community importation during this polyclonal outbreak. Molecular tools revealed complex transmission dynamics. Low healthcare worker vaccination rates and gaps in recommended infection control procedures are likely to have contributed to nosocomial spread of influenza, which remains a potentially life‐threatening disease in elderly adults.

Prevalence of respiratory virus in symptomatic children in private physician office settings in five communities of the state of Veracruz, Mexico

BACKGROUND

Acute respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. Many studies have described the frequency of viruses in hospitalized patients, but studies describing the prevalence of viruses in the community setting are limited, particularly in developing countries, where most of the deaths from serious respiratory diseases occur. The aim of this study was to evaluate the diversity of respiratory viruses in the community setting using molecular diagnostic tools, as well as the clinical characteristics of respiratory viral infections in the general pediatric practice in Mexico.

METHODS

Children with respiratory tract infections attending private pediatric practices during a 10-month period in five cities of the state of Veracruz were included. Nasal swabs were taken and processed by a multiplex detection kit for 15 respiratory viruses.

RESULTS

525 children were included from July 2011 to May 2012; 44% were female, mean age was 45 months. The 3 most frequent clinical diagnosis were: rhinopharyngitis 68%, pharyngitis 18%, and 3.3% influenza-like illness. 71.5% of the samples were positive for virus. The five most frequent pathogens were respiratory syncycitial virus in 18.3% of the children, rhinovirus in 17.5%, influenza A 9.1%, adenovirus 7.2%, and enterovirus 3.4%, although all 15 viruses were detected; there were viral coinfections in 14.1%, and 28.5% of the samples were negative.

CONCLUSIONS

A large proportion of respiratory infections in the community setting in Mexico was associated to viruses. Although testing for common respiratory pathogens in children with acute respiratory tract infections may lead to a better understanding of the role of viral pathogens in, and eventually to improvement in the management of, individual patients, additional prospective studies are required to study the need of routinely using such tests in general pediatric practices in resource-limited countries.

Molecular epidemiology of severe respiratory disease by human rhinoviruses and enteroviruses at a tertiary paediatric hospital in Barcelona, Spain

In order to describe the molecular epidemiology of human rhinovirus (HRV) and enterovirus (EV) infection in severely ill children, we studied all episodes of bronchospasm/bronchopneumonia in 6-month-old to 18-year-old patients from January 2010 to May 2012 who required mechanical ventilation. HRV/EVs were detected in 55 (57.3%) of 96 patients, of which 50 (91%) were HRV (HRV-A, 16; HRV-B, 1; HRV-C, 18) and 5 (9%) were EVs (EV-D68, 3). No significant differences in epidemiologic and clinical characteristics were found between different types. In six of the 13 patients who required invasive mechanical ventilation, HRV was the only pathogen detected.

Role of rhinovirus load in the upper respiratory tract and severity of symptoms in lung transplant recipients

BACKGROUND

Rhinovirus is the most common cause of respiratory viral infections and leads to frequent respiratory symptoms in lung transplant recipients. However, it remains unknown whether the rhinovirus load correlates with the severity of symptoms.

OBJECTIVES

This study aimed to better characterize the pathogenesis of rhinoviral infection and the way in which viral load correlates with symptoms.

STUDY DESIGN

We assessed rhinovirus load in positive upper respiratory specimens of patients enrolled prospectively in a cohort of 116 lung transplant recipients. Rhinovirus load was quantified according to a validated in-house, real-time, reverse transcription polymerase chain reaction in pooled nasopharyngeal and pharyngeal swabs. Symptoms were recorded in a standardised case report form completed at each screening/routine follow-up visit, or during any emergency visit occurring during the 3-year study.

RESULTS

Rhinovirus infections were very frequent, including in asymptomatic patients not seeking a specific medical consultation. Rhinovirus load ranged between 4.1 and 8.3 log copies/ml according to the type of visit and clinical presentation. Patients with highest symptom scores tended to have higher viral loads, particularly those presenting systemic symptoms. When considering symptoms individually, rhinovirus load was significantly higher in the presence of symptoms such as sore throat, fever, sputum production, cough, and fatigue. There was no association between tacrolimus levels and rhinovirus load.

CONCLUSIONS

Rhinovirus infections are very frequent in lung transplant recipients and rhinoviral load in the upper respiratory tract is relatively high even in asymptomatic patients. Patients with the highest symptom scores tend to have a higher rhinovirus load.

Epidemiology of viral respiratory infections in a tertiary care centre in the era of molecular diagnosis, Geneva, Switzerland, 2011-2012

Few studies have examined the epidemiology of respiratory viral infections in large tertiary centres over more than one season in the era of molecular diagnosis. Respiratory clinical specimens received between 1 January 2011 and 31 December 2012 were analysed. Respiratory virus testing was performed using a large panel of real‐time PCR or RT‐PCR. Results were analysed according to sample type (upper versus lower respiratory tract) and age group. In all, 2996 (2469 (82.4%) upper; 527 (17.6%) lower) specimens were analysed. Overall positivity rate was 47.4% and 23.7% for upper and lower respiratory samples, respectively. The highest positivity rate was observed in patients under 18 years old (p <0.001); picornaviruses were the most frequent viruses detected over the year. Influenza virus, respiratory syncytial virus, human metapneumovirus and coronaviruses showed a seasonal peak during the winter season, while picornaviruses and adenoviruses were less frequently detected in these periods. Multiple viral infections were identified in 12% of positive cases and were significantly more frequent in children (p <0.001). In conclusion, we observed significant differences in viral infection rates and virus types among age groups, clinical sample types and seasons. Follow‐up of viral detection over several seasons allows a better understanding of respiratory viral epidemiology.