Respiratory viruses are ubiquitous and cause a large variety of clinical symptoms. Respiratory tract infection (RTI) is undoubtedly common, and the recognition of a causative pathogen contributes to the appropriate management. In addition to the well-known respiratory viruses, such as respiratory syncytial virus (RSV) and influenza virus, human metapneumovirus (MPV) was identified in 2001, followed by the discovery of other respiratory viruses. Currently, the disease burden of respiratory viruses is beyond our knowledge. Respiratory viruses have been detected in more than two-thirds of children with radiographically confirmed community-acquired pneumonia (CAP). Similarly, in the United States, molecular diagnostics revealed viral infection in 43%–67% of pediatric CAP cases. Respiratory viruses also play an important role in adult pneumonia and are detected in 15%–56% of adult CAP cases. Viruses are responsible for the majority of respiratory infectious diseases in both children and adults, causing a massive disease burden. Furthermore, the identification of causative viruses enables the accurate diagnosis of respiratory infections and prescription of specific antiviral agents against certain viruses, such as oseltamivir for influenza viruses, and improves evaluation of the prognosis. Recognizing causative viruses can also provide information on the appropriate infection control measures, which can potentially reduce unnecessary hospital stays and allow discontinuation of unnecessary antibiotics. In summary, respiratory virus infection is common, and testing for respiratory pathogens can improve understanding of the roles of pathogens in respiratory diseases and contribute to their better clinical management.

A timely and accurate diagnosis of viral infection can be challenging. Rapid antigen tests are used to detect influenza virus infection worldwide, but there are some concerns regarding the sensitivity of currently available viral antigen tests. Technological advances have improved the sensitivity, accessibility, and utility of viral diagnostic tools. Molecular assays have been developed and progressively multiplexed to diagnose a large number of respiratory viruses in a single assay with excellent sensitivity and specificity. The importance of molecular-based diagnostic modalities is currently on the rise, and polymerase chain reaction (PCR) technology is being increasingly used in the clinic to rapidly diagnose respiratory infections. This study aims to detect respiratory viruses in children using PCR and to compare the detection power of this technique against that when using traditional antigen tests and virus cultures. The clinical conditions were also investigated.

Viral respiratory tract infections (RTIs) in humans occur throughout the year and represent a major cause of clinical visits worldwide. In the past, the viral causes of RTIs were largely unknown, primarily due to the insensitivity of culture-based methods for the detection of viruses or to the narrow spectrum of viral detection using singleplex nucleic acid tests (NATs). Recently, the development of multiplex respiratory NATs has allowed for the simultaneous, rapid, and sensitive detection of multiple viruses, which facilitates comprehensive studies regarding the epidemiology of viral RTIs. Currently, the viral epidemiology of RTIs has been studied more extensively among pediatric populations compared with adult populations throughout the world.1 Similarly, most studies describing the viral etiology of respiratory illness in Taiwan, a subtropical country in Eastern Asia, were limited to pediatric populations.2–4 Thus, studies among adult patients are lacking, particularly regarding infections due to fastidious or newly identified viruses, such as human metapneumovirus (hMPV) and human coronavirus (hCoV). Overlapping clinical presentations shared by different respiratory viruses make differential diagnoses difficult to perform based solely on the clinical parameters.5 Moreover, effective antiviral agents are currently restricted to influenza virus infections. Hence, a better understanding of the epidemiology of adult viral RTIs would aid the future design of diagnostic strategies, infection control, and patient management.

Among the various multiplex NATs, multilocus polymerase chain reaction coupled with electrospray ionization mass spectrometry (PCR/ESI-MS) can simultaneously identify and subtype multiple respiratory viruses.6–9 Despite the diagnostic potential, the ability of PCR/ESI-MS to detect human enterovirus and rhinovirus in respiratory samples from patients with RTIs has not been well evaluated. Previous PCR/ESI-MS studies in patients with RTIs did not include these 2 viruses in the diagnostic panels.6–9 Here, we expanded upon these previous studies utilizing PCR/ESI-MS for respiratory virus detection. We aimed to comprehensively investigate the epidemiology of adult viral RTIs using PCR/ESI-MS and compare the diagnostic performance between PCR/ESI-MS and conventional culture methods for identifying multiple, clinically relevant, respiratory viruses, including enterovirus and rhinovirus.

Respiratory virus infections have a major impact on health. Acute respiratory illnesses, mostly caused by viruses, are the most common illness experienced by otherwise healthy children and adults worldwide. Upper respiratory tract infections (URIs) such as common cold are exceedingly prevalent in infants and young children and continue to be common in older children and adults. Infants and young children may have 3–8 episodes of cold per year; those who attend daycare centers may have many more episodes per year [1–4]. URI can lead to complications such as acute otitis media, asthma exacerbation, and lower respiratory tract infections (LRIs). While LRIs such as pneumonia, bronchitis, and bronchiolitis occur much less frequently, they cause higher morbidity and some mortality, thus they are associated with high impact and greater healthcare costs. Approximately one third of children develop an LRI in the first year of life; LRI incidence decreases to 5%–10% during early school year, and 5% during preadolescent to healthy adult years [5, 6].

Common respiratory viruses include influenza A and B, respiratory syncytial virus A and B, parainfluenza virus types 1–3, adenovirus, rhinovirus, human metapneumovirus, and coronavirus types OC43 and 229E. Less common respiratory viruses include parainfluenza virus type 4, influenza virus C, and specific types of enteroviruses. The significance of more recently discovered viruses such as human bocavirus, coronavirus NL63, and HKU1 has yet to be elucidated [7, 8].

Clinical presentations of respiratory virus infections overlap among those caused by various viruses. In addition, clinical manifestations may mimic those of diseases caused by bacteria. Therefore, antibiotics are most often used in these infections, most of them unnecessarily. Furthermore, LRIs often require hospitalization for management such as intravenous antibiotics and symptomatic and supportive treatment. Specific antiviral treatment for respiratory virus infections is only available for influenza. Respiratory viral diagnosis is an integral part of patient management. Accurate diagnosis of specific respiratory virus infection not only improves the knowledge of disease the patient has but also can affect patient management and help prevent secondary spread of the infection. Rapid viral diagnosis may result in discontinuation of unnecessary antibiotics, initiation of antiviral drug for influenza, reduction of costs related to reduction of unnecessary investigations, and shortened hospital stay [9–11].

This paper describes up-to-date information on laboratory methods presently available in the diagnostic virology laboratories and those upcoming for detection of respiratory viruses.

In winter 2012/2013, the number of viral respiratory tract infections in Germany was the highest observed during the past decade. Infections with respiratory viruses are a common cause of usually mild respiratory illness in all age groups. Immunosuppressed adults and elderly persons with underlying chronic conditions, however, are at increased risk for a severe course of disease [1–4]. In hematopoietic stem cell recipients, respiratory viruses cause higher rates of lower respiratory tract disease and are associated with a higher mortality rate [5–9]. For patients with hematological disorders presenting with respiratory symptoms, a screening for influenza virus, parainfluenza virus and respiratory syncytial virus (RSV) is recommended [10, 11].

Although a vaccine against seasonal and pandemic influenza is available, vaccines against parainfluenza and RSV are still under development [6, 12]. However, the effect of vaccination in immunosuppressed patients is limited. As the major pathogen causing severe lower respiratory tract disease in immunocompromised adults, RSV is of high priority for vaccine development. RSV infections only partially induce protective immunity, and repeated infections occur in childhood and throughout life. Strain variation in respiratory viruses is thought to contribute to their ability to cause frequent reinfections. The attachment protein of RSV is able to accommodate changes with the emergence of new variants. Sequencing of hypervariable gene regions has been widely used to further subdivide parainfluenza and RSV into genotypes and facilitate differentiation between virus isolates. Influenza viruses are highly variable and characterized by a continuous genetic and antigenic drift. Accumulation of mutations especially in the antigenic sites of the hemagglutinin is the cause of the emergence of new drift variants and the co-circulation of different groups and lineages.

Viral shedding studies provide fundamental information about the natural course of respiratory virus infections, related clinical illness and the implementation of effective prevention strategies. Influenza is generally a self-limiting infection with systemic and respiratory symptoms, usually resolving within 3 to 6 days in most patients. Viral clearance in the respiratory tract usually occurs after 3 to 5 days. However, in immunocompromised patients respiratory viruses tend to persist longer due to a constrained immune response and therefore also spread more easily into the lower respiratory tract. Prolonged influenza and RSV viral shedding has been previously described in immunocompromised patients [16–18] and similar results have been observed for rhinovirus and coronavirus. However, there is only limited information regarding the molecular epidemiology of respiratory viruses in immunocompromised adults combined with the prevalence, duration and clinical impact of viral shedding.

In our study, we retrospectively investigated patients with respiratory tract infection in the hematology and transplant unit of the University Hospital Heidelberg between December 2012 and May 2013. We performed molecular characterization of influenza virus, parainfluenza virus and RSV investigating their genetic diversity and patterns of co-circulating subtypes and genotypes. Furthermore, we assessed the prevalence, duration and clinical impact of prolonged viral shedding in immunocompromised adults.

2017.

Acute respiratory illnesses (ARIs) are common in school‐aged children, with approximately 30‐40% affected during the winter months in the United States.1 Influenza accounts for the majority of the ARIs in this age group,2, 3 but other viruses such as respiratory syncytial virus (RSV), human metapneumovirus, and parainfluenza virus also circulate in the winter. School‐aged children with influenza tend to miss more school than those with respiratory illnesses of other etiologies.4, 5 Few studies have assessed the burden of school absenteeism due to laboratory‐confirmed influenza,5, 6, 7 and only one was conducted after the recommendation for annual influenza vaccination in children in the United States.5 Absenteeism data on the relative contribution of ARIs caused by viruses other than influenza are lacking. Non‐influenza viral illnesses may be less common, but also likely to disrupt usual activities and cause increased school absenteeism. Quantifying school absenteeism due to specific viruses can help target prevention or treatment strategies to reduce burden in school‐aged children.

We utilized data from an observational influenza vaccine effectiveness study to evaluate parental‐reported school absenteeism across three seasons among children with medically attended ARI due to various viruses. Specifically, we aim to estimate the average days absent for specific respiratory viruses in children, identify risk factors for prolonged (>2 days) absence from school due to viral ARIs, and evaluate the association between influenza vaccination and prolonged absence among children with influenza.

Severe acute respiratory infections (SARI) are one of the major causes of illness and death worldwide and are the third most common cause of death among children. Acute respiratory infections (ARI) cause more deaths in children < 5 years with most cases reported from India (43 million), China (21 million), Pakistan (10 million), Bangladesh, Indonesia and Nigeria (56 million). Respiratory infections can be caused by many viruses, both DNA and RNA. These include the Respiratory Syncytial Virus (RSV), human Parainfluenza Virus (HPIV), Influenza A Virus (Flu A), Influenza B Virus (Flu B), human Adenovirus (HAdV), human Coronavirus (HCoV), human Rhinovirus (HRV), human Metapneumovirus (HMPV) and human Bocavirus (HBoV). A new wave of viral diagnosis was established with the development of Polymerase Chain Reaction (PCR) techniques in the 1990s. PCR is more sensitive and rapid than conventional methods for detection of respiratory viruses. Different respiratory viruses present with similar signs and symptoms and can’t be differentiated symptomatically or clinically. Tests capable of rapid simultaneous identification of various viruses at the same time can help expedite initiation of appropriate therapy. Uniplex RT-PCR requires individual amplification of each virus under study which is expensive, time consuming and laborious. To overcome this, multiplex real-time PCRs targeting the detection of multiple pathogens simultaneously have been developed commercially but they are very expensive. There is a need to develop cheaper systems for rapid simultaneous identification of various viruses. The present study compares custom real-time multiplex PCR primers and probes for the simultaneous detection of 18 respiratory viruses with an in-vitro diagnostics (IVD) approved fast track diagnostics (FTD) kit.

Children with SARI, admitted in J. K. Lone Hospital, a pediatric hospital attached to Sawai Man Singh (SMS) Medical College Jaipur were enrolled in the study and tested for respiratory viruses with prior consent of the parent/guardian. Duration of the study was 27 months i.e. between September, 2012 to December, 2014. Children enrolled were ≤ 5 years of age, presenting with fever, cough, sore throat, nasal catarrh, shortness of breath, bronchiolitis, pneumonia, and wheezing.

To conduct a comprehensive epidemiologic study that included patients with and without comorbidity, we enrolled adults (of at least 18 yr of age) with acute RTIs within 7 days of onset who were treated at a local outpatient clinic of YC hospital or the outpatient or emergency departments of National Cheng-Kung University Hospital (NCKUH), a university-affiliated medical center in southern Taiwan, between October 2012 and June 2013. Acute RTI was defined as the simultaneous occurrence of at least 1 respiratory symptom or sign (new or worsening cough, sputum production, sore throat, nasal congestion, rhinorrhea, dyspnea, wheezing, or injected tonsils) and at least 1 of the following symptoms: fever, chills, and cough. Lower RTI (LRTI) was defined as the presence of acute RTI and a new infiltrate on chest radiograph. For patients experiencing more than 1 episode of RTI, the most recent episode was counted as separate only if the patient fully recovered from the previous episode and there was a least a 3-week interval between the onset of the 2 episodes. Clinical, laboratory, and radiological data and the contact history of each patient were retrieved. Comorbidities were assessed in all patients based on the Charlson comorbidity index (CCI).10 Steroid use was defined as the receipt of corticosteroid treatment (10 mg prednisolone or an equivalent daily dosage) for more than 2 weeks. An immunocompromised state was diagnosed if the patients met one of the following conditions: corticosteroid treatment, solid organ or hematopoietic stem cell recipient, or chemotherapy for an underlying malignancy during the past 6 months.

Nasopharyngeal or throat swabs were obtained from all patients and collected in transport medium, as previously described.11 for virus detection and identification by both virus isolation and PCR/ESI-MS. Clinical specimens were stored at 4°C and transported to the study sites within 24 hours of collection. Throat swabs from 42 cases without respiratory infections during the month prior to enrollment were included as control samples for PCR/ESI-MS analysis, including 15 patients with exclusively bacterial infections (documented cases of bacteremia or urinary tract infection) who were admitted to NCKUH and 27 individuals without active infections. These subjects without active infections included 10 patients with stable chronic diseases followed up in NCKUH clinics and 17 healthy individuals whose medical information was collected using a clinical questionnaire.

The study was approved by the Institutional Review Board (B-ER-101-031) of the study hospital, and all patients provided informed consent.

Previous studies have proposed a hypothesis of viral interference between influenza and other respiratory viruses. Experiments have shown that respiratory virus infection can stimulate temporary non-specific innate immunity, thereby protecting the host from secondary infections of other viruses. This finding is further supported by the observation that children who receive trivalent influenza inactivated vaccines have an increased risk of infection of non-influenza viruses. However, other studies have failed to find an association between influenza vaccination and non-influenza infections. Investigations into the age-specific epidemic curves of multiple respiratory viruses across different regions and climates can help resolve the controversy over the potential interference between different viruses. The 2009 H1N1 pandemic was characterized with an offseason surge of infected cases in temperate regions, with an age distribution shift towards children and young adults, which is distinct from seasonal influenza outbreaks. A similar age shift was also observed in the subtropical city of Hong Kong, but the pandemic coincided with the summer epidemic of seasonal influenza. We hypothesize that the emergence of this new influenza virus strain could have interrupted the regular circulation of other respiratory viruses through the viral interference of competing for entry sites and changing the preexisting innate immunity. This viral interference could be reflected by the change of age distribution and seasonal variations of the respiratory viruses other than influenza, such as late (or early) peaks and altered seasonal patterns during and after the pandemic. In this study, we utilized 10 years of age-specific surveillance data on common respiratory viruses of influenza, RSV, adenovirus and parainfluenza in subtropical Hong Kong, with the aim to assess the impact of the 2009 H1N1 pandemic on the age-specific epidemic curves of other respiratory viruses by comparing the periods before, during, and after the pandemic.

Viral respiratory tract infections (VRTIs) are very common in children and their presentations vary from simple colds to life-threatening infections.1–5 The detection of a respiratory virus does not necessarily infer that the child has only a viral infection,6 since outbreaks of VRTIs are being linked to increased incidence of bacterial coinfections.7 The human body is usually capable of eliminating respiratory viral infections with no sequelae; however, in some cases, viruses bypass the immune response of the airways, causing conceivable severe respiratory diseases.8 Robust mechanical and immunosuppressive processes protect the lungs against external infections, but a single respiratory tract infection might change immunity and pathology.9

Health care providers often face a dilemma when encountering a febrile infant or child with respiratory tract infection. The reason expressed by many clinicians is the challenge to confirm whether the fever is caused by a virus or bacterium.10 Acute otitis media (AOM) is a usual bacterial coinfection that occurs in 20%–60% of cases of VRTIs.11–14 In addition, almost 60% of children with VRTI have changes in the maxillary, ethmoidal, and frontal sinuses.11,12 Moreover, in the year 1918, it was estimated that 40–50 million individuals died from the influenza pandemic, many of which were due to secondary bacterial pneumonia with Streptococcus pneumoniae.15

Acute respiratory infections (ARIs) are common and contribute significantly to morbidity and mortality. They are the leading causes of outpatient visits and hospitalizations in all age groups, especially for children under 5 years of age.1 Most ARIs in children and outpatients are caused by nine common respiratory viruses, including respiratory syncytial virus (RSV), influenza virus A, influenza virus B, rhinovirus, adenovirus, parainfluenza virus, coronavirus, human metapneumovirus, and boca virus2, 3 Additionally, atypical pathogens, such as Mycoplasma pneumoniae, are also major causes of ARIs in children. The symptoms caused by these pathogens are largely similar, thus definitive diagnosis requires effective laboratory testing. By using multiplex assay targeting these pathogens, early diagnosis can be made in a timely manner. Consequential antimicrobial or antiviral therapy may thus be administrated promptly and appropriately.4 Most importantly, the early diagnosis of influenza viruses, which are contagious, is beneficial for early isolation of patients, thus reducing the spread of influenza viruses.

The routine clinical laboratory testing for respiratory viruses is largely conducted by direct fluorescent‐antibody assays and rapid antigen tests in China. Given the poor sensitivity and complicated manual operation, these methods have been gradually replaced by nucleic acid amplification tests (NAATs), which are more sensitive and more specific. However, majority of the NAAT kits are based on real‐time polymerase chain reaction (PCR), which can only detect one or two pathogens of ARIs within a single tube, thus are not syndromic testing.5 The clinical and economic impacts of syndromic testing for respiratory pathogens have been evaluated in several studies. Overall, the implementation of syndromic testing can decrease the time of diagnosis,4 decreased healthcare resource utilization,6 decrease inpatient length of stay and time in isolation,7 and improve antiviral use for influenza virus‐positive patients.8

SureX 13 Respiratory Pathogen Multiplex Kit (ResP) is a syndromic multiplex molecular test for simultaneous detection of 13 pathogens in a single tube. The aim of this study was to evaluate the application of the ResP for detection of respiratory pathogens in outpatients with flu‐like manifestations.

To determine viral causes of influenza-like illness in Uganda.

Acute bronchiolitis (AB), which is the most common acute lower respiratory system disease in infants, is often caused by a viral infection. It is especially the leading cause of hospitalization in infants under 6 months of age.1,2 Epidemic peaks of AB are frequently seen during the winter season. Respiratory syncytial virus (RSV) is usually the cause of 50% to 80% of the cases, but other viruses including adenovirus, influenza virus, and parainfluenza virus have also been reported to cause AB as the sole pathogen or as coinfection with or without RSV.3,4 With various polymerase chain reaction (PCR) techniques, possible new agents like rhinovirus, human metapnomovirus, human bocavirus, Bordatella pertussis, and atypical pathogens were also described as the leading causes of AB.5-7 Having a cardiovascular disease, chronic pulmonary disease, immunodeficiency, and premature birth increase the risk of AB-associated respiratory failure, or even death.8 The World Health Organization has reported that RSV is the causative pathogen for over 30 million new acute lower respiratory infection episodes in children under 5 years of age and it gives rise to more than 3.4 million hospital admissions and 160 000 deaths every year.9,10

The diagnosis of AB is made based on typical history with wheezing and characteristic clinical features such as tachypnea, nasal flaring, chest retractions, and wheezing and/or rales followed by a viral upper respiratory infection in infants. The American Academy of Pediatrics (AAP) 2006 Clinical Practice Guidelines for the Diagnosis and Management of Bronchiolitis described AB as the first episode of wheezing in children under 24 months of age who have respiratory findings during the viral infection episode.11 Chest radiographs and laboratory studies may be thought of on clinical suspicion after evaluating the differential diagnosis for secondary or comorbid bacterial infection, complications, or other conditions. Viral diagnosis methods including antigen detection or immunofluorescence of nasal secretion wash or nasal aspiration, rapid antigen tests, and PCR are only suggested for identifying specific viral agents in children with bronchiolitis if the results will determine discontinuation of palivizumab prophylaxis, initiation or continuation/discontinuation of antibiotic therapy.12-15

Majority of studies have recently researched the burden of respiratory viral tract infection agents in AB with larger groups. In these studies, epidemiological, clinical, and risk factors of AB have also been defined. So, it can be said that AB is frequent in infancy and that there is an increase in the number of admissions to hospitals and bronchiolitis-related morbidity.

The purpose of this study was to evaluate the frequency of pathogens and to determine the differences in clinical and microbiological features among patients under 24 months of age, who were hospitalized with AB in Ege University Children’s Hospital.

Acute respiratory tract infections are one of the leading causes of childhood morbidity and mortality worldwide, and it has been estimated that globally, respiratory infections are responsible for about 2 million deaths in children between 0 and 5 years of age (Bryce et al., 2005; Kallander et al., 2008). Approximately 80% of these respiratory infection cases are caused by viral pathogens such as influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza virus types 1–3, adenovirus, rhinovirus, human metapneumovirus (hMPV), and others (Mahony, 2008). The non-specific clinical presentation of respiratory infections poses a considerable challenge to the differential diagnosis of these pathogens. Early and accurate diagnosis of the causative pathogens in respiratory infections is essential to administer appropriate antiviral or antibacterial therapy, initiate effective infection control measures, and reduce the length of hospital stay (Barenfanger et al., 2000; Byington et al., 2002; Akers et al., 2017). In the last decade, there has been a remarkable improvement in the diagnosis of respiratory pathogens with the availability of molecular and point-of-care (POC) testing. Although an increasing number of laboratories are adopting rapid molecular assays, conventional testing methods, such as culture and immunodiagnostics are still used. This review focuses on current laboratory methods for testing for respiratory pathogens, and discusses the advantages and disadvantages of each approach.

The human myxovirus resistance protein 1 (MxA) is an important intermediary of the IFN-induced antiviral response against a variety of viruses. MxA expression is firmly modified by type I and type III IFNs, which also requires signal transducer and activator of transcription 1 signaling. Additionally, MxA has many characteristics similar to the superfamily of large guanosine triphosphatases.78 MxA analysis could be beneficial to differentiate between bacterial and viral infections. Engelmann et al79 conducted a prospective, multicenter cohort study in different pediatric emergency departments in France on the role of MxA in the diagnosis of viral infections. MxA blood values were calculated in infants and children with verified bacterial or viral infections, uninfected controls, and infections of unknown origin. A receiver operating characteristic analysis was used to verify the diagnostic performance of MxA. The study, which included 553 children, showed that MxA was significantly higher in children with viral versus bacterial infections and uninfected controls (P<0.0001). Additionally, MxA levels were significantly higher in children with clinically diagnosed viral infections than in those with clinically diagnosed bacterial infections (P<0.001).79 Other authors have also reported the usefulness of blood MxA testing in patients with viral infections.80,81 The use MxA in diagnosing viral infection is very promising, especially in patients who are at risk of infectious complications. Two separate studies have shown that blood MxA is beneficial in differentiating between viral illness and acute graft-versus-host disease after allogenic stem cell transplantation.82,83

All respiratory viruses may cause symptoms such as nasal congestion, runny nose, wheezing, and cough. We found no significant association between the viruses and a specific symptom.

Electron microscopy (EM) is one of the oldest direct examination methods that has been implemented for both clinical viral diagnosis and study of viral ultrastructure and pathogenesis in developed countries (Roingeard, 2008). Historically, EM has played an instrumental role in identifying novel viral strains in several outbreak situations, such as the coronavirus associated with the severe acute respiratory syndrome (SARS) outbreak (Falsey and Walsh, 2003; Ksiazek et al., 2003). However, despite several advantages, the use of EM has been limited in respiratory viral diagnosis as it is expensive, laborious, time-consuming, and has a greater turnaround time (approximately 3–16 h including specimen preparation), and is often insensitive when compared to other diagnostic methods (Goldsmith and Miller, 2009; Zhang et al., 2013). Additionally, EM requires strict control of experimental conditions, a high concentration of viral particles (> 105 L-1), and considerable technical skill and expertise for accurate analysis.

Children with viral infection in the upper respiratory tract showed symptoms such as runny nose, cough, and hoarseness. Some of them also present lower respiratory tract symptoms such as wheezing, severe cough, breathlessness, and respiratory distress, which may be due to bronchiolitis or pneumonia.

We divided the patients according to three clinical manifestations: pneumonia, bronchiolitis, and bronchitis, and investigated whether the detected viruses were associated with a specific clinical manifestation. Our analysis showed that in most cases, RSV infections induced bronchiolitis (n = 45), followed by pneumonia (n = 22, p=0.004) and bronchitis (n = 6, p=0.0015). EV/Rhi infections more often induced pneumonia or bronchiolitis (n = 19 for both) instead of bronchitis (n = 6, p=0.03) (Figure 2). Other viruses showed a similar prevalence of each clinical manifestation.

Influenza, respiratory syncytial virus (RSV) and other respiratory viruses are the cause of substantial morbidity and mortality, with children under 5 years of age and the elderly disproportionately burdened. Both influenza and RSV display distinct seasonality, however, the exact timing and magnitude of their annual epidemics remain difficult to predict. A better understanding of the epidemiology of these pathogens is useful for the prevention and control of future epidemics and for optimising clinical management of patients. Moreover, this knowledge may inform prediction models used to estimate the timing and magnitude of influenza epidemics.

Interference between respiratory viruses has been well documented. During peaks of influenza epidemics, the spread of other respiratory viruses, particularly RSV, appears to be limited [4–6]. Delays in outbreaks of influenza during the 2009 pandemic in Europe were linked to the annual rhinovirus epidemic associated with the beginning of the school year [7–9]. In turn, the influenza pandemic was observed to interfere with seasonal epidemics of RSV in France and Israel, RSV and metapneumovirus in Germany, seasonal influenza in Hong Kong and all respiratory viruses except rhinovirus in Beijing. Studies investigating viral interference since the pandemic are sparser, though two studies reported that the timing and magnitude of respiratory virus epidemics were affected by the timing of the seasonal influenza A peak [15, 16]. Collectively, these observations suggest interference may prevent respiratory viruses reaching their epidemic peaks concurrently, but also underscore the complexity of these interactions.

The exact nature of interactions between different respiratory viruses remains unclear, although they are proposed to be driven by the innate immune system. Once a viral infection is established, interferon production is believed to confer temporary immunity to neighbouring cells against infection by other respiratory viruses. In vitro, infection with RSV is blocked by competitive infection of influenza A if the host is not infected with the two viruses simultaneously. Similarly, ferret models have shown that influenza A infection may prevent successive infection with RSV and that coinfection with different influenza subtypes is dependent upon the order in which the viruses infect the host.

Despite this apparent interference, viral co-infections do occur, albeit with insufficient frequency to maintain an epidemic-level spread of the co-infecting viruses. A recent study reported infrequent co-detection of rhinovirus with other viruses, despite observations that rhinovirus continues to be shed for several weeks post-resolution of symptoms. Negative associations have also been observed between the detection of influenza A, RSV, parainfluenza virus or coronavirus and co-detection of other respiratory viruses [8, 23, 24], providing further evidence for a refractory period after initial infection during which the host is less likely to be infected by subsequent exposure to another respiratory virus.

We used routine diagnostic testing data of specimens from both the community and hospitals at the Victorian Infectious Diseases Reference Laboratory (VIDRL) between 2002 and 2017 to describe relationships between respiratory viruses, with a focus on influenza A and RSV.

Influenza like-illness (ILI) or acute respiratory infections can be caused by several types of respiratory viruses or bacteria in humans. Influenza viruses, Respiratory Syncytial viruses (RSV) and Parainfluenza viruses are identified as major viruses mostly responsible for ILI and pneumonia in several studies. However practitioners cannot diagnose the infection without a biological test confirmation. Unfortunately, these infections causes are identified in less than 50%.

Réunion Island, a French overseas territory with 850,000 inhabitants, is located in the southern hemisphere between Madagascar and Mauritius in the Indian Ocean (Latitude: 21°05.2920 S Longitude: 55°36.4380 E.). The island benefits from a healthcare system similar to mainland France and epidemiological surveillance has been developed by the regional office of the French Institute for Public Health Surveillance (Cire OI), based on the surveillance system of mainland France. Influenza activity generally increases during austral winter, corresponding to summer in Europe. Since 2011, influenza vaccination campaign in Reunion Island starts in April and the vaccine used corresponds to World Health Organization recommendations for the southern hemisphere.

Since 1996, clinical and biological influenza surveillance has been based on a sentinel practitioner’s network. In 2014, this network was composed of 58 general practitioners (GPs) spread over the island and represented around 7% of all Réunion Island GPs. Nasal swabs are randomly collected all along the year and are tested by RT-PCR for influenza viruses. Among these surveillance samples, 40 to 50% are tested positive for influenza A virus, A(H1N1)pdm09 or B virus by the virological laboratory of the University Hospital Center of Réunion. Thus ILI samples tested negative for influenza are of unknown etiology.

Several biological tools allow identifying respiratory pathogens from nasal swab. In recent years, multiplex reverse transcriptase polymerase chain reaction (RT-PCR) has been developed to identify several viruses simultaneously [7–10]. We therefore used this new method to set up a retrospective study using swabs collected by sentinel GPs from 2011 to 2012.

The main objective of our study was to characterize respiratory pathogens responsible for ILI consultations in sentinel GPs in 2011 and 2012. Secondary objectives were to highlight seasonal trends on respiratory pathogens circulation and to describe occurrence of co-infections, especially during the flu season.

The primary study subjects were 5,298 patients, who underwent multiplex real-time polymerase chain reaction (PCR) for simultaneous detection of respiratory viruses, among who visited the emergency department or outpatient clinic with respiratory symptoms at Ulsan University Hospital from April 2013 to March 2016 (Figure 1). The medical records of all these patients were retrospectively reviewed in detail.

The role of respiratory infections as key causes of morbidity and mortality among military trainees is well-recognized. Compared to the young healthy adults’ population, military trainees undergoing basic military training course appear to be at increased risk of acquiring and transmitting respiratory infections (1). Every year, a large number of cases of respiratory infections occur in basic military trainees worldwide which the majority of them are resulting from viral infections. Respiratory infections have a tremendous impact on the military population and are responsible for 25–30% of hospitalization in the U.S. military (2). Affected trainees generally require a sufficient period of recovery which can lead to a longer training duration and a significant higher rate of viral transmission to newer cohorts (3). The higher vulnerability to respiratory disease epidemics observed in military trainees has been attributed to several causes including crowded habitation, demanding physical training program, stressful working environment, and insomnia (4, 5).

Numerous previous studies reported that adenoviruses, influenza A and B, human rhinoviruses, and coronaviruses are the predominant viruses detected in the military population. Outbreaks of adenovirus-associated respiratory disease have been reported globally in the military environments (3, 5-8). It has been suggested that adenovirus infection is associated with male gender, as well as direct contact with an infected person with respiratory symptoms 10 days prior to the onset of illness (8). Outbreaks of influenza viruses A and B have also been associated with much morbidity and mortality, especially influenza A (H1N1) pdm09 virus infection (9-13). It has been proposed that crowded living quarters, obesity, asthma, and age group (younger than 40 years) are amongst the major risk factors for acquiring influenza infections (14). Human rhinoviruses are the most important causative agents of the common cold and associated with more complicated upper respiratory tract infections (15,16). Approximately, all the human rhinoviruses have been detected in military trainees during respiratory infection (17). It has been also well documented that human rhinoviruses are associated with lower respiratory tract infections (18, 19). Nevertheless, there are other viruses associated with respiratory infections which are not well studied in military populations, including respiratory syncytial viruses (20-22), human bocaviruses (23-25), human parainfluenza viruses (26), metapneumoviruses (27), and echoviruses (28).

Until now, there is no study which aimed to investigate the prevalence of viral agents responsible for respiratory infections among the military population in Iran. Using micro-array technology, the objective of our study was to evaluate the molecular epidemiology of 17 viral pathogens causing respiratory infections among 400 military trainees in a large military training camp in Tehran, over a period of time from January to March 2017. The data resulted from this study can be employed to take preventive measures aimed to reduce the disease burden and prevent future outbreaks.

Globally, influenza-like illnesses (ILI), also known as acute respiratory illnesses, are common causes of morbidity and mortality in both developed and developing countries.1,2 In temperate climates, ILI is reported throughout the year amongst hospital patients with a marked increase in cases recorded during winter periods. There is also evidence of sporadic background activity of ILI transmission throughout the year amongst communities in tropical climates, with a slight increase in cases during the rainy season.3,4,5 However, little is known about the aetiologic agents of ILI in some developing countries, making it a challenge to plan and implement effective patient management and disease prevention and control efforts.6,7

As surveillance and monitoring programmes for ILI scale up in many countries, primarily triggered by the increased threat of zoonosis and the emergence of pandemic-prone respiratory viruses, there is a need to identify and document the incidence of endemic and circulating pathogens. This information is important for differential diagnosis, outbreak investigations, trend analysis, early recognition of emerging and re-emerging viruses and implementation of specific public health interventions such as mass vaccination campaigns. In Uganda, a tropical country lying along the equator, surveillance for influenza was started in July 2007. By June 2008, influenza viruses were confirmed in only 12% of patients presenting with ILI at health facilities, implying that the aetiologies in the remaining 88% were unknown.8 There are a few studies in Uganda that have identified influenza viruses, respiratory syncytial viruses, parainfluenza viruses, coxsackieviruses and echoviruses as being causative agents of ILI – but these studies were conducted during the 1970s.9,10,11 More recent results from other countries including Senegal, Cote d’Ivoire, Kenya and Madagascar have shown that these viruses are in circulation together with newly-discovered viruses such as coronaviruses, bocaviruses and polyomaviruses.12,13,14,15,16 In the current study, we identify the respiratory viruses that are associated with ILI patients seeking healthcare in Kampala city and Entebbe town, both located in the central region of Uganda.

On April 15th and 17th 2009, a novel swine-lineage influenza A (H1N1/2009) infection was reported to the World Health Organisation (WHO) by the Centers for Disease Control and Prevention (CDC) in Atlanta. The virus was detected in two children from adjacent counties in southern California presenting with febrile respiratory illness. These cases were not epidemiologically linked and neither child had exposure to swine. Subsequent phylogenetic characterisation of H1N1/2009 from the U.S. index case (A/California/04/2009) showed that the virus had a unique genome composition that had not been previously identified. Six genes (PB2, PB1, PA, HA, NP, and NS) were similar to viruses previously identified in triple-reassortant swine influenza viruses in North American pigs. The remaining two genes (NA and M) were derived from Eurasian swine influenza viruses. This particular gene constellation had never been previously identified in humans or other reservoirs.

Following the original identification of Influenza A/H1N1/2009 in the United States, sustained human-to-human transmission was seen in other countries, and on June 11, 2009, the WHO declared that the virus was responsible for the first influenza pandemic of the 21st century.

The first cases of H1N1/2009 in Scotland were detected at the end of April 2009 in a couple returning from their honeymoon in Mexico. The initial public health response to the outbreak was a containment exercise aimed at preventing the spread of infection, detecting cases and taking action to prevent these cases from infecting others. The exercise was initially based on clinical and epidemiological criteria (table 1). Patients who met these criteria were immediately given treatment and isolated while a rapid real time reverse transcriptase polymerase chain reaction (rtRT-PCR) for H1N1/2009 was initiated. Contact tracing was undertaken in order to treat those who had been in contact with confirmed cases. Soon after the first detections, person to person transmission was confirmed as having occurred in Scotland. Consequently, the epidemiological criteria were no longer useful and the containment exercise was then based on clinical criteria only. Testing continued to be carried out during this period.

During the outbreak period (April-July 2009) the West of Scotland Specialist Virology Centre (WoSSVC) tested 16 264 clinical samples for H1N1/2009 (Figure 1). Of these, only 1516 were positive (9% overall for the period of April-July; range 5-10% per month). Consequently, the clinical diagnosis was found to be wrong in the majority of cases.

A large number of viral infections, drugs and other diseases can cause disease presentations similar to those presented in Table 1. This is especially true for respiratory pathogens. The present study sought to determine what respiratory pathogens were diagnosed as cases of H1N1/2009 during the containment phase.