cord-000285-7p3b6tyf	2010	The primary goals of the study are: (i) to investigate both the acute and the long-term health consequences of varying severity and aetiology of clinically significant viral respiratory tract infections on the outcomes of allergic rhinitis (AR) and early childhood asthma; and (ii) to identify the potentially modifiable factors that define children who are at greatest risk of developing asthma following infant respiratory viral infection. Thus, we designed the prospective TCRI to establish a base for the evaluation of both the risks and benefits of documented significant infant viral respiratory infection of varying severity and aetiology and other environmental exposures on childhood atopy outcomes and to establish a biospecimen repository for analyses including biomarker testing and genotyping. The TCRI is a prospective cohort of mother-infant dyads enrolled in a longitudinal investigation of the relationship of infant viral respiratory infection severity and aetiology and the interaction of other risk factors on the development of childhood asthma and allergic diseases.
cord-000602-z5p3a64x	2012	Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies. Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies. The specific research-related demands of PERCH added to these constraints, requiring that our diagnostic strategy must exclude any prior assumptions regarding the likely importance of specific pathogens; must include a full range of respiratory tract specimens, including upper respiratory swab or aspirate, induced sputum, lung aspirate, bronchoalveolar lavage, and pleural fluid; must be comprehensive, yet realistic; must appropriately balance the demands of accuracy and efficiency; must account for both clinical and research ethical issues; and must be feasible for use and support at all participating field sites.
cord-000877-usz7pnvu	2013	title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Human bocavirus (HBoV) was first found in children with acute respiratory tract infections in 2005 [1] . The current study aims to screen the epidemiological status and molecular phylogeny of HBoV isolates prevailing in pediatric patients with respiratory infection in Saudi Arabia. The current study investigated the prevalence of HBoV in patients suffering from respiratory tract infections in Saudi Arabia. Furthermore, the phylogenetic analysis results of three selected sequences showed that the Saudi HBoV1 strains obtained from respiratory samples belonged to group I human bocaviruses (Fig. 1) . Detection of human bocavirus in Japanese children with lower respiratory tract infections Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction
cord-001070-zlzag6a8	2012	The role of rhinovirus asymptomatic infections in the transmission among close contacts subjects is unknown. We investigated HRV infections rates on selected populations of a pair of one child and one family member, health care workers (HCW), and immunocompromised patients with and without respiratory symptoms from June to September. One hundred and eleven health care workers (HCW) from São Paulo Hospital, 36 pairs of one child and one family member and 8 blood marrow transplanted hospitalized patients (BMT). Influenza and rhinovirus infections among health-care workers Acute Respiratory Infection and Influenza-Like Illness Viral Etiologies in Brazilian Adults Use of polymerase chain reaction for diagnosis of picornavirus infection in subjects with and without respiratory symptoms Rhinovirus transmission within families with children: Insidence of symptomatic and assymptomatic infections Viral respiratory infections in hospitalized and community control children in Alaska Frequent detection of respiratory viruses in adult recipients of stem cell transplants with the use of real-time polymerase chain reaction, compared with viral culture
cord-001162-z8cbbit3	2014	title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection While coinfections with viral pathogens including 2009 H1N1 have been described in patients with respiratory infections, few prospective studies have related these to clinical presentation and outcomes in adults since molecular diagnostics became available, and none in the setting of high background rates of adenovirus. [12] [13] [14] [15] [16] [17] We sought to describe the epidemiology of 2009 H1N1 and adenovirus in a basic training population, and to correlate differences in clinical presentations and outcomes with each respective pathogen and in coinfections. Subject enrollment was variable throughout the study period, depending on rates of clinical illness within the training population, as well as availability of study personnel to enroll trainees, and given that 2009 H1N1 influenza virus PCR was done as part of clinical care, there could have been some differences in those who enrolled vs.
cord-002227-x1ddi8wg	2016	In the process of nursing children with severe pneumonia, intensive care was provided, including condition assessment and diagnosis, close observation of disease, keeping the airway unblocked, rational oxygen therapy, prevention and treatment of respiratory and circulatory failure, support of vital organs, complications, and health education. As a result, severe pneumonia produces corresponding clinical symptoms, such as respiratory failure, heart failure, toxic encephalopathy and intestinal paralysis, which endanger the lives of children in the short term, and is the first cause of death of pediatric inpatients (6, 7) . Type I respiratory failure also refers to the coexistence of hypoxemia and hypercapnia, impairment of ventilatory function and gas exchange functions, severe lung lesion, obstruction of trachea and bronchia caused by sticky secretions, blood change of PaO 2 <60 mmHg, and PaCO 2 >50 mmHg. Main clinical manifestations of children patients with type I pneumonia with respiratory failure include, poor mental state or dysphoria, polypnea, cyanosis of lips, dyspnea, nasal flaring and three depression signs.
cord-002590-24o2viv3	2017	Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: A meta-analysis approach Antigen-specific B-cell responses to porcine reproductive and respiratory syndrome virus infection The Chinese highly pathogenic porcine reproductive and respiratory syndrome virus infection suppresses Th17 cells response in vivo Pathogenic and humoral immune responses to porcine reproductive and respiratory syndrome virus (PRRSV) are related to viral load in acute infection Porcine reproductive and respiratory syndrome virus-infected alveolar macrophages contain no detectable levels of viral proteins in their plasma membrane and are protected against antibody-dependent, complement-mediated cell lysis Polyclonal activation of B cells occurs in lymphoid organs from porcine reproductive and respiratory syndrome virus (PRRSV)-infected pigs The role of porcine reproductive and respiratory syndrome virus infection in immune phenotype and Th1/Th2 balance of dendritic cells Porcine reproductive and respiratory syndrome virus induces pronounced immune modulatory responses at mucosal tissues in the parental vaccine strain VR2332 infected pigs
cord-002801-6myqgme3	2017	title: Possible therapeutic effect of orally administered ribavirin for respiratory syncytial virus-induced acute respiratory distress syndrome in an immunocompetent patient: a case report Respiratory syncytial virus-induced severe pneumonia or acute respiratory distress syndrome in immunocompetent adults has been rarely described. We report a case of respiratory syncytial virus-induced acute respiratory distress syndrome occurring in a previously healthy man successfully treated with orally administered ribavirin. CONCLUSION: This case demonstrates the potential usefulness of orally administered ribavirin as a therapeutic option for severe respiratory syncytial virus infection, at least in an immunocompetent host. RSV-induced severe pneumonia or acute respiratory distress syndrome (ARDS) in immunocompromised patients is not uncommon. Here we report a case of ARDS due to RSV occurring in a previously healthy adult successfully treated with orally administered ribavirin. In addition, this case suggests that orally administered ribavirin could be a therapeutic option even for severe pneumonia or ARDS due to RSV, at least in immunocompetent hosts, especially if other antiviral agents are unavailable.
cord-003357-4qrg6lqu	2018	Conclusion: This study demonstrated that common respiratory viruses were partially responsible for hospitalized lower respiratory tract infections in adult patients from Harbin, China, with parainfluenza virus as the dominant viral pathogen. Viral infections played an important role in pediatric lower respiratory tract infections, and the corresponding common viral pathogens were influenza A and B virus (IAV and IBV), parainfluenza virus (PIV, type 1 to 3), respiratory syncytial virus (RSV) and human adenovirus (ADV) (Pavia, 2011) . In this report, the prevalence of common viruses in the lower respiratory tract infection of hospitalized adult patients from Harbin, China was explored in hopes of revealing the clinical and pathogenic features of respiratory viruses. The overall detection rate of viral infection among hospitalized adult patients in this report is 14.5%, which was consistent with the result of 16.8% in the age group above 14 years old by a national survey from 2009 to 2013 in China (Feng et al., 2014) .
cord-003488-pfzy8p5v	2017	Bronchiolitis is usually a self-limited disease, but some children may develop respiratory failure with increased work of breathing (WOB), hypoxemia and hypercarbia requiring mechanical ventilation (MV) in addition to usual supportive measures [7, 8] . These findings may seem unexpected and contradictory with the current understanding of severe bronchiolitis as a primarily obstructive airway disease with an increase in Abbreviations: mo months old, PF ratio PaO 2 /FIO 2 ratio, OI oxygenation index, PIM 2 Pediatric index of mortality 2, RSV respiratory syncytial virus, PNB preterm newborn, HMD hyaline membrane disease a Viral Studies were negative, but pneumococcal superinfection was diagnosed expiratory resistance, but they are supported by the observation done over a half century ago by Krieger et al. Correlation between respiratory system compliance and expiratory airway resistance measured in children on mechanical ventilation due to severe bronchiolitis.
cord-003492-rodqdtfj	2019	PRRSV is a complex disease and several gaps in the knowledge of its economic impact, biology and evolution, genetic polymorphism, mechanism of viral infections, elicitation of protective immune responses and novel control strategies, have been reviewed here (Box 1). Nonstructural proteins nsp2TF and nsp2N of porcine reproductive and respiratory syndrome virus (PRRSV) play important roles in suppressing host innate immune responses Immune responses in pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV) Immunodominant epitopes in nsp2 of porcine reproductive and respiratory syndrome virus are dispensable for replication, but play an important role in modulation of the host immune response Nonstructural protein 11 (nsp11) of porcine reproductive and respiratory syndrome virus (PRRSV) promotes PRRSV infection in MARC-145 cells Immune response to ORF5a protein immunization is not protective against porcine reproductive and respiratory syndrome virus infection
cord-003798-nki2sasr	2019	BACKGROUND: Information on the clinical, epidemiological and molecular characterization of human metapneumovirus in critically ill adult patients with severe community-acquired pneumonia (CAP) and the role of biomarkers identifying bacterial coinfection is scarce. METHODS: This is a retrospective epidemiological study of adult patients with hMPV severe CAP admitted to ICU during a ten-year period with admission PSI score ≥ 3. The main objective of this study was to describe the clinical and epidemiological characteristics of adults with severe pneumonia caused by hMPV who required intensive care unit (ICU) admission, over a long period of time. Interestingly, three patients (10.7%) were young adult patients without comorbidities and without bacterial coinfection that developed ARDS pointing out a main role of hMPV in the etiology of severe respiratory infections requiring mechanical ventilation. Main characteristics of immunosuppressed adult patients admitted to the Intensive Care Unit due to a severe community-acquired pneumonia associated with human metapneumovirus infection (Guipuzcoa, Basque Country, Spain, 2007-2017).
cord-003917-bswndfvk	2019	Filoviruses have become a worldwide public health concern, especially during the 2013–2016 Western Africa Ebola virus disease (EVD) outbreak—the largest outbreak, both by number of cases and geographical extension, recorded so far in medical history. During the 2013–2016 Western Africa outbreak, Ebola virus (EBOV) was detected in the lung of infected patients suggesting a role in lung pathogenesis. However, new evidences collected during the recent 2013-2016 Ebola outbreak hypothesized shedding of the virus in the lung and identified viral replication markers in sputum samples collected from EBOV infected patients [14] . However, new evidences collected during the recent 2013-2016 Ebola outbreak hypothesized shedding of the virus in the lung and identified viral replication markers in sputum samples collected from EBOV infected patients [14] . Interestingly, evidence collected in animal studies, in the epidemiological analysis of transmission chains, and in the most recent Ebola outbreaks suggests that EBOV may be able to cause primary pulmonary infection.
cord-004397-ypli7wtu	2020	title: Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. In the present study, we used the suspension microarray, a multipathogen detection platform, to simultaneously detect viral and bacterial respiratory pathogens in matched OPS and BALF specimens from pediatric patients for comparison of the sensitivities between the two sample types. To compare the OPS and paired BALF for pathogens detection in young children with RTI, we tested the two sample types using suspension microarray. In the present study, we used suspension array to simultaneously detect multiple viral and bacterial pathogens in paired BALF and OPS specimens from symptomatic patients hospitalized with respiratory illness. We used suspension-array to compare BALF and paired OPS specimens for detecting multiple pathogens in children hospitalized with respiratory illness.
cord-005583-hmv8jjfl	2013	In an individual patient, such a response to intervention should be indicated by their best, rather than worst, measure of gas exchange, Therefore, the purpose of the present prospective, single institution study of AHRF in children was to assess whether the best, early respiratory indices in non-survivors were significantly different from those who survived. Table 2 Comparison of previously published [2] [3] [4] [5] respiratory severity parameters with the present series (PPV positive predictive value for mortality, VI ventilation index, OI oxygenation index, PIP peak inspiratory pressure (cmH20), A-aDO 2 alveolar arterial oxygen gradient (mmHg), MAP mean airway pressure (cmH20), LR + the likelihood ratio for a positive test result, i.e. the ratio of finding the predictor in non-survivors to finding it in survivors) * indicates intermediate to high diagnostic impact, ns not significant Proposed PPV LR + PPV p predictors (95 % confidence interval) in present study
cord-005646-xhx9pzhj	1996	Aims and methods The aim of both a prospective and retrospective survey conducted in German pediatric intensive care units in 1993 was to accumulate data on the epidemiology, risk factors, natural history and treatment strategies in a large group of pediatric ARDS patients who were treated in the tt~ee year period from 1991 to 1993.All patients had acute bilateral alveolar infiltration of noncardiogenic origin and a pO2~iO2 ratio < 150mmHg. The influence of sex, underlying disease and single organ failure was analyzed using the Fischer''s exact test, the influence of additional organ failure on mortality was tested with the Cochran-Mantel-Haenszet statistics.
cord-005774-7z6uyn6p	1995	This review will focus on techniques which are used to measure thoracoabdominal asynchrony, tidal breathing flow-volume loops, small airway function (forced expiratory maneuvers), respiratory mechanics and lung volumes in critically ill infants and children. In 1989, Shannon [49] proposed in this Journal that the minimum physiological information needed for the intelligent use of mechanical ventilation (particularly if lower airway and/or pulmonary parenchymal disease was apparent) required the measurement of at least 4 variables: i) arterial partial pressure of carbon dioxide; ii) arterial oxygen saturation; iii) the mechanical time constant of the lung and iv) FRC. In 1989, Shannon [49] proposed in this Journal that the minimum physiological information needed for the intelligent use of mechanical ventilation (particularly if lower airway and/or pulmonary parenchymal disease was apparent) required the measurement of at least 4 variables: i) arterial partial pressure of carbon dioxide; ii) arterial oxygen saturation; iii) the mechanical time constant of the lung and iv) FRC.
cord-005814-ak5pq312	1995	Results: In 5 patients with treated SS, 16 tests were performed (VL n=8; Dobu n=4; NA n=4 Method: Septic shock was defined as severe sepsis with either persistent hypotension (mean arterial pressure; MAP<70 mmHg) or the requirement for a noradrenaline (NA) infusion ~> 0.1 ~g/kg/min with a MAP _< 90mmHg. Cardiovascular support was limited to NA + dobutamine (DB), 546C88 was administered for up to 8 h at a fixed dose-rate of either i, 2.5, 5, 10 or 20 mg/kg/h iv. Methods: Fourteen cases were s~udied,their gestational age ranged from(27-32)ws.Continnous positive air way pressure was applied to six cases at Peep level from (3-6)cm H2o through nasal pronge,(group I),the other 8 cases were managed as routine,(group II).Blood gases, TcPO2,TcCo2,resp.rate,depth and pattern were monitored for assessment of tissue Oxygenation and ventilation, Results: Our rasults showed that early application of CPAP improve ventilation among (83.3%)of cases,while (16.7%)of cases need IMV.The cases of group II need IMV among (75%)of the studied cases during the second or the third day of life.
cord-005818-3mzwliiy	2014	Die Surfactantsubstitution stellt einen entscheidenden Durchbruch in der Behandlung des Atemnotsyndroms dar.Durch eine prophylaktische Surfactantgabe oder die Therapie des manifesten Atemnotsyndroms konnten die akuten pulmonalen Komplikationen beatmeter Frühgeborener um 2/3 reduziert und die Sterblichkeit nahezu halbiert werden.Eine frühe Surfactantapplikation innerhalb der ersten 15 Lebensminuten ist besonders bei sehr unreifen Frühgeborenen einer späteren Behandlung bei manifestem Atemnotsyndrom überlegen.Als initiale Dosis werden 100 mg Phospholipide/kg empfohlen; einige Frühgeborene profitieren von einer Mehrfachbehandlung.Natürliche Surfactantpräparate haben eine bessere klinische Wirksamkeit als die zurzeit verfügbaren synthetischen Präparate.Es gibt einige Hinweise, dass eine Surfactanttherapie auch bei pulmonalen Erkrankungen Neugeborener einen therapeutischen Effekt haben kann; diese Erkrankungen wie Mekoniumaspirationssyndrom und neonatale Pneumonie führen u.a.über eine Inaktivierung von Surfactant zu einer sekundären Defizienz dieses oberflächenaktiven Systems. Fujiwara und Mitarbeiter (Morioka) berichteten 1980 erstmals von Frühgeborenen mit manifestem Atemnotsyndrom (engl: respiratory distress syndrom: RDS), die nach einer intratrachealen Applikation eines Rindersurfactants mit einer deutlichen Verbesserung des pulmonalen Gasaustausches reagierten [18] .
cord-006261-yw5k8qkz	2012	Few studies have investigated the common belief that moderate physical activity is beneficial in decreasing risk of respiratory tract infections and improving immune function. Laboratory and clinical studies suggest that changes in immune parameters associated with heavy train ing lead to adverse health effects, particularly an increase in the incidence or severity of upper respiratory tract infections. During this time, the women in the exercise group experienced fewer upper respiratory tract infection symptom days, improved cardiorespiratory fitness, and increased natural killer cell numbers compared with their sedentary controls. This study indicates that intensity of exercise may playa role, and that moderate activity may actually improve immune function and associated upper respiratory tract infection symptoms. Clinical studies examining the effects of moderate levels of physical activity have shown possible enhanced immune responses with a concomitant impact on the length and severity of an upper respiratory tract infection. The effects of moderate exercise training on natural killer cells and acute upper respiratory tract infections
cord-006325-3no74e74	2018	A more severe outcome was observed for RSV-bacteria-associated pneumonia compared with RSV pneumonia: length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). In conclusion, we did not observe major differences in the epidemiology of bacterial superinfections in RSV-positive pneumonia compared to reports on post-influenza pneumonia. RSV and bacteria coinfection was statistically associated with a more severe outcome than RSV-positive pneumonia as length of stay was significantly longer (16 days vs 10 days) and ICU hospitalization more frequent (66.7% vs 21.0%) (p < 0.05). It is probably due to the systematic testing strategy associated to a Species distribution of pathogenic bacteria involved in RSV-positive pneumonia (CAP) and hospital-acquired pneumonia (HAP) sampling bias toward influenza-like illness. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France
cord-007030-mewo9w43	2016	The purpose of this study is to determine the prevalence of respiratory illness and its associated factors among Malaysian hajj pilgrims in 2013 and to describe its preventive measures. Malaysian hajj pilgrims with previous experience of hajj (OR 0.24; 95% CI 0.10–0.56) or umrah (OR 0.19; 95% CI 0.07–0.52) and those who have practiced good hand hygiene (OR 0.35; 95% CI 0.16–0.79) were found to be significantly associated with lower risk of having respiratory illness. All preventive measures which include hand hygiene, wearing face masks and influenza vaccination must be practiced together as bundle of care to reduce respiratory illness effectively. Data based on the social demographic, co-morbid illness, smoking habits, symptoms of respiratory illness, history of contact with respiratory ill patients, previous experience of hajj or umrah, the practice of preventive measures, influenza and pneumococcal vaccination and supplement intake against respiratory illness were obtained by a self-administered proforma.
cord-007176-61e9obb3	1973	RS virus was estimated, from sucrose density gradient centrifugation studies, to be 90-120 nm in diameter [2] ; viral particles in infected cells measured 65 nm by electron microscopy. All adults tested possessed detectable levels of neutralizing antibody to RS virus before challenge, but the titer of naturally acquired antibody had no significant effect on subsequent RS infection of volunteers and was poorly correlated with development of mild clinical illnesses. The neutralization test is more sensitive than CF when serum from infants is used, but rises in neutralizing antibody have been detected in only half of the virus-positive infections in this age group. Virus structures were detected 6-8 hr later [17] .· Infection of WI-38 cells with strain 229E resulted in a reorganization of the cytoplasm, as determined by electron microscopy. Respiratory syncytial virus infection in adult volunteers. Respiratory syncytial virus infection in adult volunteers. Morphology and development of respiratory syncytial virus in cell culture
cord-007222-31o180fz	1973	From January 1, 1967 to December 1971, the temporal pattern of respiratory syncytial virus infection was investigated in infants and children younger than 18 months hospitalized for acute lower respiratory tract disease. Of 4696 infants and children with acute lower respiratory tract disease admitted to the Cook County Hospital, 2530 were tested for virus infection by virus isolation or serologic procedures or both. This report describes the periodic pattern of RSV infection in infants and children with lower respiratory tract disease admitted to the Cook County Hospital in Chicago, between January 1, 1967 and December 31, 1971. The study group comprised infants and children younger than 18 months of age admitted to the Cook County Hospital because of acute lower respiratory tract disease. DISCUSSION This continuing surveillance study of virus infections in infants and young children with acute lower respiratory tract disease describes the cyclical pattern of occurrence of RSV infections.
cord-007234-hcpa8ej5	2007	title: A Recently Identified Rhinovirus Genotype Is Associated with Severe Respiratory-Tract Infection in Children in Germany Here we report the investigation, by MassTag PCR, of pediatric respiratory-tract infections in Germany, studying 97 cases for which no pathogen was identified through routine laboratory evaluation. In an attempt to gather additional information on the potential pathogenicity, as well as temporal and geographic distribution, of rhinoviruses, including the recently identified genotype, we evaluated specimens collected, during the 2003-2006 seasons in Bad Kreuznach, Germany, from children hospitalized because of severe LRTI. In this study of samples collected, during a 3-year interval, from hospitalized children with severe undiagnosed respiratory infection, MassTag PCR allowed us to detect viral pathogens in 49 (51%) of 97 cases. Although we did not have samples to test for the presence of HRV in the lower respiratory tract, the high frequency at which HRV was identified as being the sole virus detected suggests a correlation between the agent and the observed LRTI symptoms.
cord-007417-az8xd66p	2008	Whether an infection induces disease depends on viral (type (E.g. RSV, RV)), host (genetic susceptibility, age, immune responses) and environmental (allergen exposure, season) factors. With respect to allergy RSV infection might only trigger defective immunity in genetically susceptible individuals or that allergic inflammatory and immune responses may promote the influx of virus-specific cells into the airways increasing inflammation and AHR (Schwarze et al., 1999c) . Nevertheless most studies suggest that Th1 responses may result in viral clearance and mild symptoms whereas an aberrant bias towards a Th2 phenotype may lead to more intense RSV-induced disease and promote the development of asthma . Animal models have been used to determine if RSV can induce the development of asthma by triggering pro-asthmatic immune responses that lead to variable airflow obstruction and airway inflammation. Further studies are required to elucidate the links between infection, immune responses and susceptibility to chronic respiratory diseases and why some individuals but not others develop persistent wheeze and asthma.
cord-007445-2folsh35	2000	To more comprehensively evaluate the relationships among virus infection, atopy (cytokine dysregulation of Thl / Th2 imbalance), and immune system or lung developmental components, a rat model of virus-induced airway dysfunction has been studied extensively.''l'' In this model, infection with PIV type 1 during a critical developmental time period (when the animals are weaning [ 3 4 weeks of age] as opposed to when they are neonates [4-5 days] or adults) produces chronic (8-12 weeks fol-lowing infection), episodic, reversible airway inflammation and remodeling with associated alterations in airway physiology (increased resistance and rnethacholine responsiveness) that resemble human asthma in high (brown Norway strain) but not low (F344 strain) IgEantibody producing rats.62 The temporal progression of this asthma-like syndrome is associated with a Thl / Th2 imbalance within the lung, and its development can be significantly attenuated by the exogenous administration of IFN-8 just prior to and during the viral infection in the brown Norway responder strain.lo2 This model further supports the concept of both genetic (atopy; cytokine dysregulation or imbalance) and environmental factors (virus infection) being important in the inception of the asthmatic phenotype, as well as a developmental component contributing.
cord-007796-zggk0x2q	2005	In respect to the role of viruses in the pathogenesis of acute and chronic airway disease in children, it is of utmost importance that we gain a proper understanding of the underlying mechanisms involved in order to design effective therapeutic and preventive strategies. Epithelial cells are key regulators of the innate immune response against viral infections (Garofalo and Haeberle, 2000) , producing a number of inflammatory mediators in response to RSV infection. In summary, in RSV lower respiratory tract infections, cytotoxic CD8Ï© T-cells are involved in viral clearance while the humoral response is required for the protection against reinfection. The innate immune defense to viral respiratory tract infections consists of the mucosal layer, type 1 interferons, activated phagocytes, and NK-cells. A key question is whether the association with the development of asthma is merely an expression of increased susceptibility to both asthma and RSV-induced lower respiratory tract infections or whether true causality is involved.
cord-008716-38sqkh9m	2001	
cord-009860-qebenhxz	2015	Serologic evidence of infection with respiratory syncytial virus (RSV) and parainfluenza were determined by enzyme immunoassay (EIA), and influenza by hemagglutination‐inhibition assay and EIA. This is despite the fact that each year many residents of nursing homes become ill with respiratory infections not proven to be influenza, either by culture or serology. The purpose of this study was to identify all common respiratory viruses which cause symptomatic dsease during the winter months in nursing home patients, by utilizing both viral cultures and serology, and to assess their clinical impact. Subjects Between December 11, 1989 and March 13, 1990 , the head nurse on each floor identified residents who had signs or symptoms of acute respiratory illness including nasal congestion, pharyngitis, cough, wheezing, or respiratory difficulty with or without fever. The groups of viruses responsible for most acute respiratory infections are rhinovirus, coronavirus, influenza, RSV, parainfluenza, and adeno~irus.~ An attempt was made to diagnose each of these pathogens, with the exception of coronavirus, utilizing either culture, serology, or both.
cord-010233-772e35kx	2002	The search terms used were picornavirus, rhinovirus, enterovirus, viral respiratory infection, upper respiratory infection, disease burden, economic, cost, complications, asthma, COPD, immunocompromised, elderly, otitis media, and sinusitis. In fact, because rhinovirus-induced illnesses are so common, they produce more restriction of activity and physician consultations annually than respiratory illnesses caused by other viruses or bacteria.s This article reviews the clinical impact and outcomes associated with picomavirusinduced respiratory infection in specific populations at risk for complications secondary to these infections. 15 In addition, these advances in technology have confirmed the results of earlier studies, further demonstrating the significance of rhinoviruses in causing or predisposing patients to otitis media and sinusitis and exacerbating other chronic respiratory diseases such as asthma, cystic fibrosis, and chronic obstructive pulmonary disease (COPD).
cord-010368-plpghewn	2020	Although not confirmed in all studies with a symmetric distribution of the 23 confounding factors investigated, the overall analyses showed that there was a relationship between childhood viral LRTI at < 5 years and serum test diagnosed-atopy (OR = 2.0, [95% CI = 1.0–4.1]), allergic rhinoconjunctivitis (OR = 1.7, [95% CI = 1.1–2.9]), hyperreactivity diagnosed by serum tests with food (OR = 5.3, [1.7–16.7]) or inhaled allergens (OR = 4.2, [95% CI = 2.1–8.5]), or furred animals (OR = 0.6, [95% CI = 0.5–0.9]). The purpose of this systematic review and meta-analysis of Long-term sEquelAe of lower Respiratory tract infections iN Early childhood (A LEARNED study) was to investigate the association between viral LRTI at <5 years and the atopy development at > 2 years. Pérez-Yarza in a systematic review including children younger than 3 years with HRSV respiratory infection from 1985 to 2006 also suggested controversial findings about the subsequent risk of allergic sensitization development defined by positive skin or serum tests specific for common allergens [11] .
cord-011095-79ce5900	2020	One study in children under age 5 years old found that respiratory syncytial virus (RSV), human metapneumovirus (HMPV), and parainfluenza viruses (PIV) were more likely to be causative of disease [8] . In an evaluation of children under 18 years old admitted to the hospital with a diagnosis of pneumonia, the most common cause of infection, whether bacterial or viral, was RSV quickly followed by rhinovirus [12] . While some studies do have RSV and rhinovirus as the leading cause of pneumonia in children, another important common viral contributor is influenza [15] . [55] did a systemic review of patients of all ages with respiratory illnesses and found that studies that recruited young children were more likely to report high rates of co-infection and that there were inconclusive results on risk of hospitalization or ICU admission. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children.
cord-015893-e0fofgxq	2011	Sulfur dioxide, nitrogen dioxide, ozone, and particulate matter in air pollution may • exacerbate asthma, and patients should be cautioned to stay indoors when levels of these irritants are high. A study of children aged 6-8 years with asthma concluded that an asthma exacerbation was of a greater severity if a viral infection was present as opposed to a nonviral illness (7) . Inhaled corticosteroids and leukotriene receptor antagonists (LTRAs) are well known to control the number of wheezing exacerbations in school-age children with chronic persistent asthma, an effect that appears to encompass those episodes caused by viral illness. Viral respiratory infections, and to a lesser extent air pollution, are common triggers of exacerbations and may interact with individuals to affect the development of some forms of asthma. By understanding and anticipating respiratory viral infections and air pollution as important causes of asthma, the health care provider can provide superior care for those who suffer from this chronic disease.
cord-016009-qa7bcsbu	2019	
cord-016020-awanrm9u	2007	In addition, despite the well-recognized association of viral infections with upper and lower respiratory tract infections, the current diagnostic virology procedures do not provide an answer rapidly enough to with parainfluenza virus type 4, human coronaviruses, rhinoviruses, and some enteroviruses would not ordinarily be identified without RNA detection methods. Published diagnostic methods for detection of respiratory pathogen DNA or RNA directly from clinical specimens utilize target amplification procedures such as polymerase chain reaction (PCR) or nucleic acid sequence-based amplification (NASBA).Although direct detection methods based on nucleic acid hybridization would be theoretically possible, the amount of target nucleic acid in specimens may be minimal and such methods would lack sensitivity compared to amplification methods, unless the organism was propagated before analysis. Thus, the molecular amplification procedures reported for direct detection of respiratory pathogens in clinical samples include PCR (e.g., Reference 19 and Figure 41 assays have utilized bacterial ribosomal RNA (rRNA; e.g., Reference 22 ).
cord-016070-e9ix35x3	2020	The SARS coronavirus and MERS-CoV are two pathogens from the coronavirus family that predominantly cause serious lower tract respiratory infections with a high mortality rate, but they are genetically different viruses. This observation suggests that camels are the reservoirs of the virus, which can be transmitted to humans through direct contact with these animals or through consumption of their milk: 1599 cases had been diagnosed by July 2015, with 574 deaths [World Health Organization (WHO)]. HCoV-NL63 and HCoV-HKU1 are viruses that tend to manifest as a common cold, just as the usual coronaviruses HCoV-229E and HCoV-OC43; nevertheless, in small children, elderly patients, and immunosuppressed patients, they can cause serious respiratory disease with a high mortality rate. Isolated cases of avian origin in humans caused by the influenza H10N8 virus and H6N1 have been observed in China.
cord-016451-k8m2xz0e	2020	Influenza, measles, SARS, MERS, and smallpox illnesses are caused by highly infectious viral pathogens that induce critical illness. Measles infects and disrupts tissues throughout the body; however, severe disease is primarily due to lower respiratory tract and neurological complications [72] . Global epidemiology of avian influenza A H5N1 virus infection in humans, 1997-2015: a systematic review of individual case data Transmission of Middle East respiratory syndrome coronavirus infections in healthcare settings Viral shedding and antibody response in 37 patients with Middle East respiratory syndrome coronavirus infection Viral RNA in blood as indicator of severe outcome in Middle East respiratory syndrome coronavirus infection Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection
cord-016499-5iqpl23p	2014	A convenience population of 15 healthy children (1-9 years old) without asthma were followed during at least three seasons, and picornaviruses were detected in 5 % of 740 specimens (21 % of infections) not associated with symptoms, The impact of HRV typing and of sampling based only on symptoms. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Comparison of results of detection of rhinovirus by PCR and viral culture in human nasal wash specimens from subjects with and without clinical symptoms of respiratory illness Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines
cord-016882-c9ts2g7w	2017	It''s well known that approximately 60% of total human respiratory and gastrointestinal infections are acquired indoor, since viruses have a rapid spread in the community and can be transmitted easily, especially in crowded and poorly ventilated environments, causing high morbidity and decline in quality of life and productivity. Viruses'' inductors of Severe Acute Respiratory Syndrome (SARS), influenza and norovirus are transmitted from patients primarily by contact and/or droplet routes, while airborne transmission occurs over a limited distance (Srikanth et al., 2008) . It is well-known that viruses are shed in large numbers, with transmission routes extraordinary diverse, including direct contact with infected persons, faecal-oral transmission (through contaminated food and water), droplet and airborne transmission, and can survive for long periods on surfaces or fomites, emphasizing the possible role of surfaces in the transmission of viruses (Barker et al., 2001; La Rosa et al., 2013) .
cord-016990-ot1wi3xi	2008	
cord-017107-sg8n12hs	2008	A recently completed, retrospective, community cohort study in Olmsted County, Minnesota included patients treated with NIV and found an even higher incidence of ALI, 156 per 100,000 person-years (personal communication, Rodrigo Cartin -Ceba), Mortality from ALI varies greatly depending upon the age of the patient, underlying chronic illnesses, ALI risk factors, and non-pulmonary organ dysfunctions [15] . In an international cohort study [4] , acute exacerbation of COPD was a principal indication for initiating mechanical ventilation in 13 % of patients with acute respiratory failure. The majority of patients with interstitial lung disease and acute respiratory failure admitted to the ICU require invasive mechanical ventilation . In a retrospective review [39] of 75 patients with interstitial lung disease who were mechanically ventilated at Mayo Clinic from 2003 to 2005, acute respiratory failure was the most common cause of ICU admiss ion (77 %), followed by sepsis (11 %) and cardiopulmonary arrest (4 %).
cord-017126-7ebo3cy3	2007	Nach der „American-European Consensus Conference" (Bernard et al., 1994) wird zwischen einem ARDS — acute respiratory distress syndrom und einem ALI — acute lung injury unterschieden. Bei Patienten mit ALI/ARDS kann das Auftreten apoptotischer Vorgänge an pulmonalen epithelialen Zellen (Song Y et al., 1999 , Li et al., 2004 , Martin et al., 2005 (Abraham, 2003) derselben, sodass es zur Aufrechterhaltung eines von Leukozyten geführten inflammatorischen Prozesses kommt, der typisch für eine akute Lungenschädigung ist (Wang et al., 1999 , Yum et al., 2001 Die verminderte Apoptose der Neutrophilen ist bedingt durch: 1. Beneficial effects of the "Open lung Approach" with low distending pressures in acute respiratory distress syndrom; A prospective randomized study on mechanical ventilation Combining high-frequency oscillatory ventilation and recruitment maneuvers in adults with early acute respiratory distress syndrome: the treatment with oscillation and an Open Lung Strategy (TOOLS) trial pilot study Effect of alveolar recruitment maneuver in early acute respiratory distress syndrome according to antiderecruitment strategy, etiological category of diffuse lung injury, and body position of the patient
cord-017140-k4lzwfge	2018	• Patient with suspected contagious respiratory infection-during transport, examination, treatment, etc.; use a face mask-also on the patient-to protect others and the environment from contamination. Department management is responsible for training, use and control of face masks, respirators and eye protection and that the equipment and written guidelines are available [5] . P3 mask is used by the surgical team and during all sterile procedures: in the case of operative treatment of patients with special types of airborne infection such as tuberculosis, etc., see above. However, surgical masks are not approved as protection against airborne infections: [5, 14, 24, 25] "Harmful microorganisms (bacteria, viruses, fungi) or components of microorganisms (e.g. endotoxins) may occur in air, either in dust, smoke or aerosols, or even finer distributed as droplet nuclei where all liquid has dried in. Transmission of microbes via small particles and droplet nuclei from influenza patients is not adequately controlled by the use of surgical mask [50] [51] [52] .
cord-017252-88b3preq	2014	Despite immunizations and public health initiatives, the most common bacterial causes of CAP have remained largely unchanged over the last several decades and include: Streptococcus pneumoniae , Staphylococcus aureus , Haemophilus infl uenzae (including non-typable strains) and Moraxella catarrhalis [ 7 , 8 , 21 , 23 ] . Chest CT is helpful to further evaluate diffi cult cases, particularly immunocompromised children with ill-defi ned infi ltrates on CXR, complex empyema or effusion, or recurrent or chronic pneumonia [ 11 ] . Respiratory failure in an immunocompromised child frequently necessitates a chest CT to better visualize the pattern and extent of disease, aid in diagnosis of the etiology, determine the need for more invasive procedures, and to increase the sensitivity of assessing treatment response [ 11 ] . Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections
cord-017364-d9zmdm23	2014	A virus causing a similar cytopathic effect in cultured cells was recovered from infants with respiratory illness shortly after, and studies of human antibodies in the serum of infants and children indicated that infection was common early in life [ 1 , 2 ] . Higher titers of virus in respiratory secretions usually are associated with increased severity of disease, in prospective studies of natural infection [ 114 ] or of clinical vaccine trials [ 115 ] . Most epidemiologic studies of MPV in children show that the virus is the second leading cause of lower respiratory infection after RSV. Acute lower respiratory tract infections by human metapneumovirus in children in Southwest China: a 2-year study The impact of infection with human metapneumovirus and other respiratory viruses in young infants and children at high risk for severe pulmonary disease Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children
cord-017499-51yy7y9n	2008	Thus, -selective opioids like morphine, fentanyl and sufentanil, due to the high density of binding sites, mediate their main action within the brain stem and the midbrain. This sterospecificity of opiate action supports the concept of selective receptor binding to a site, which is able to distinguish in "handedness or goodness of fit" of an opioid molecule maximal response induced by administration of the active agent. On the other hand mixed agonist/antagonists, such as pentazocine, nalorphine, levallorphan, nalbuphine and butorphanol, demonstrate characteristics, which enable them to displace a pure agonist at the receptor site (antagonistic effect), but at the same time when administered by themselves, they induce opioid related effects such as analgesia and respiratory depression (agonistic effects; Table II-7) . However, a less potent opioid like codeine or tramadol, even when given in dosages higher than their therapeutic margin, will not induce a clinically relevant respiratory depressive effect ( Figure II-34) .
cord-017715-99ri6x0y	2015	2. The patient has been to or lived in areas reported with infectious SARS patients and patients suffering from secondary infections 2 weeks before the disease onset, who also have abovementioned clinical symptoms, not high peripheral blood white cell count and pulmonary shadows on chest X-ray fi lms. 3. The patient has been to or lived in areas reported with infectious SARS patients and patients suffering from secondary infections 2 weeks before the disease onset, who also have abovementioned clinical symptoms, pulmonary shadows on chest X-ray fi lms, and no obvious response to anti-infectious treatment. If the foci could not be absorbed for a long term in SARS recovery phase or patients still have symptoms but normal chest presentations, CT scan need to be carried out for further observation as it can better visualize the subtle pulmonary interstitial changes, such as lung interlobular septum thickening, intralobular septum thickening, subpleural linear shadow, and small ground-glassdensity lesion and regional and segmental bronchiectasis, and therefore is helpful for clinical diagnosis of pulmonary interstitial fi brosis.
cord-017784-4r3fpmlb	2019	Severe community-acquired pneumonia and acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are causes of acute respiratory failure (ARF) in elderly patients. This process termed immunosenescence or immune dysregulation, together changes in lung function who occur with advancing age, play a critical role in the manifestation of age-related pulmonary diseases such as infections (i.e., pneumonia), chronic obstructive pulmonary disease (COPD), and increased the risk for develop sepsis [1] . Triggering causes of ARF in advanced aged patients are especially acute heart decompensation, severe community-acquired pneumonia (CAP), acute exacerbations of COPD (AECOPD), and pulmonary embolism. Lower respiratory tract infections, including pneumonia and exacerbation of chronic obstructive pulmonary disease, are among the most common causes of ARF in elderly people and the most important cause of hospitalization. Antibiotic therapy and treatment failure in patients hospitalized for acute exacerbations of chronic obstructive pulmonary disease
cord-017897-mbwm0ytg	2018	In order to guarantee a better patient adaptation to the ventilator, to reduce the oxygen consumption related to the respiratory muscle activity and to guarantee a protective transpulmonary pressure, the use of neuromuscular blockers is accepted in clinical practice [49] . The indications for the prone positioning have changed over time: once it was used to improve arterial oxygenation in the most severe forms of respiratory failure [53, 54] ; while nowadays it aims to achieve a more homogeneous distribution of stress and strain within the lung parenchyma, acting in synergy with the remaining therapies and protecting against the ventilator induced lung injury [55] . Lung recruitability is better estimated according to the Berlin definition of acute respiratory distress syndrome at standard 5 cm H2O rather than higher positive end-expiratory pressure: a retrospective cohort study Ventilation strategy using low tidal volumes, recruitment maneuvers, and high positive end-expiratory pressure for acute lung injury and acute respiratory distress syndrome: a randomized controlled trial
cord-018302-lmly43rd	2016	Respiratory viral infections due to respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause infections in immunocompromised transplant patients ranging from mild upper respiratory infections to severe lower respiratory tract disease with respiratory failure. Surveillance studies of respiratory viruses from transplant centers have established the high frequency and the signifi cant clinical impact of respiratory viral infections in HSCT recipients overall [ 8 -15 , 46 , 47 ] as well as the relative importance of RSV in terms of morbidity and mortality (Table 31 -2 ). A retrospective MDACC study of confi rmed RSV infections in 280 allogeneic HSCT recipients from 1996 to 2009 utilized multivariable logistic regression to demonstrate that lack of ribavirin aerosol therapy at the upper respiratory tract disease stage was an important risk factor associated with RSV LRTI and all-cause mortality [ 99 ] .
cord-018319-tylkbh4h	2011	Historically, the most common causes of respiratory infections in cancer patients were thought to be opportunistic bacteria and fungi, but newer diagnostic methods have revealed that respiratory viruses can cause serious morbidity and mortality in such patients, including leukemia patients and hematopoietic stem cell transplant (HSCT) recipients. Many viruses are known to cause respiratory tract infections, but the most common in hospitalized cancer patients are influenza viruses, respiratory syncytial virus (RSV), and parainfluenza viruses (PIV) [1, 2] . Although the combination of ribavirin and intravenous immunoglobulin (IVIG) or palivizumab has not been evaluated in a randomized trial, it is sometimes used in severely ill patients with RSV pneumonia, especially HSCT recipients, given that they have high mortality rates from this infection [3, 11, 14] . However, because other viruses can produce the same syndrome and influenza infection can produce other respiratory syndromes, a confirmatory test detecting the virus or viral antigens in nasal washes, throat swabs, respiratory tract secretions, or bronchoalveolar lavage specimens is needed in sporadic cases and in immunocompromised patients.
cord-018408-ttae193b	2008	Second, patients with genetic or acquired immune defi ciency commonly develop severe pneumonia with opportunistic infections that usually do not infect healthy children. These immunocompromised patients commonly have been given chemo-radiotherapy for cancer or are receiving immune-suppressive agents to prevent rejection episodes following solid organ and hematopoietic stem cell transplantation. The pathogens that commonly produce CAP or VAP, such as Streptococcus pneumoniae, Gram-negative bacilli, and Staphylococcus aureus, are relatively virulent bacteria so that only a small inoculum is required and the aspiration is usually subtle. Bacterial organisms recovered from tracheal secretions obtained through an endotracheal tube may or may not refl ect the causative agent(s) responsible for lower respiratory tract infection. In addition, recipients of solid organ and hematopoietic stem cell transplantation (HSCT) are frequently given life-long treatment with immunosuppressive agents designed to prevent graft rejection or graft-versus-host disease. Early-onset nosocomial pneumonia and VAP are commonly caused by antibiotic-sensitive, community-acquired organisms (e.g., Strep.
cord-018421-wy3mtafh	2016	Human rhinoviruses are the most common respiratory viruses detected in the upper respiratory tract of hematopoietic cell transplant and lung transplant recipients, and evidence on the impact on clinical outcomes is mounting. Due to the development of polymerase chain reaction (PCR) assays for viral detection, HRVs are now known to be the most common viruses detected from respiratory specimens in HCT recipients and can account for 25-40% of cases of viral respiratory infections in these patients [ 2 -4 ] (Figure 32-1 ). In that study, approximately one third of the adult HCT recipients who developed symptomatic HRV infections prior to engraftment had progression of upper respiratory tract symptoms to LRTI, and all cases with pneumonias were fatal. Rhinovirus as a cause of fatal lower respiratory tract infection in adult stem cell transplantation patients: a report of two cases Human Rhinovirus RNA Detection in the Lower Respiratory Tract of Hematopoietic Cell Transplant recipients: Association with Mortality.
cord-019051-gtruu1op	2009	
cord-019100-rce6kyu4	1998	
cord-020267-0axms5fp	1986	In Britain RSV accounts for yearly hospitaladmission rates of 12 -5 to 24'' 5 per 1000 among infants aged 1-3 months;3 and in North Carolina it is responsible for 24-50% of all admissions for pneumonia in children under 5 years of age.4 In hospital roughly 14% of RSV-infected infants require intensive care and 5% need assisted ventilation.s Although the mortality from RSV infection is generally low, it is especially high in infants with underlying congenital heart disease (37%, rising to 73% with concomitant pulmonary hypertension),5 and in the immunocompromised (23%),6 and is almost certainly raised in infants with bronchopulmonary dysplasia and cystic fibrosis. Striking improvements were noted in 2 infants treated with ribavirin aerosol for parainfluenza virus type 3 infection complicating severe combined immunodeficiency disease13,14-a combination often causing respiratory failure and death. Rather it should be considered for infants with bronchiolitis or pneumonia, and for high-risk patients with underlying cardiopulmonary disorders or immunodeficiency with probable RSV or influenza, and possibly parainfluenza infection.
cord-020700-iko8gy1e	2017	INTRODUCTION: It is known that infants with viral respiratory infections severe enough to require hospital admission have a high risk of developing recurrent wheezing. The main aim of this study was to analyse symptomatic and asymptomatic respiratory viral infections during the first year of life in a cohort of infants, recruited at birth, and the development of recurrent wheezing. The objective of our prospective study was to analyse asymptomatic and symptomatic infections of varying severity in a cohort of newborns during the first year of life and assess their role in the development of recurrent wheezing. We defined ''''first detected viral infection'''' as PCR detecting a respiratory virus in a sample for the first time in the life of a child, whether the infection was asymptomatic, symptomatic and managed at the outpatient level, or symptomatic and requiring hospital admission.
cord-021277-smw6owql	2013	key: cord-021277-smw6owql authors: nan title: Respiratory distress syndrome: recent research date: 2013-02-17 journal: nan DOI: 10.2165/00128413-199107860-00060 sha: doc_id: 21277 cord_uid: smw6owql nan In infants Effects In adults Use of corticosteroids in the adult respiratory distress syndrome -a clinical review Adult respiratory distress syndrome associated with parainfluenza virus type I in children Effects of prostaglandin EI on oxygen delivery and consumption in patients with the adult respiratory distress syndrome Prophylactic treatment with an aerosolized corticosteroid liposome in a porcine model of early ARDS induced by endotoxaemia Physiologic effects and side effects of prostaglandin E I in the adult respiratory distress syndrome respiratory distress and acute renal failure due to synergic bleomycin-cisplatin toxicity
cord-021894-lq8yr710	2018	Globally there are an estimated 33.8 million cases of RSV lower respiratory tract infection each year in children under 5 years of age, resulting in 3.4 million admissions to the hospital and 66 to 199 thousand deaths (with the majority in low-and middle-income countries). 42, 43 Severity of disease is associated with both infant risk factors (including lack of adaptive T cell response), 26,44 but also RSV virus specific factors (viral antigen load and direct cytotoxic effects). Respiratory syncytial virus genomic load and disease severity among children hospitalized with bronchiolitis: multicenter cohort studies in the United States and Finland Respiratory syncytial virus load, viral dynamics, and disease severity in previously healthy naturally infected children The risk of mortality among young children hospitalized for severe respiratory syncytial virus infection High incidence of pulmonary bacterial co-infection in children with severe respiratory syncytial virus (RSV) bronchiolitis
cord-022082-1dq623oe	2007	
cord-022084-hap7flng	2009	The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye'' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups.
cord-022337-f3a349cb	2007	There is also evidence that the viruses which cause wheezing with respiratory tract infections may be age dependent; for example, infants wheeze with RSV while older children have exacerbations of asthma with rhinovirus.^^ To extend these observations. However, as already discussed, the increased frequency of LARs to antigen was still noted 4 weeks after the viral infection, suggesting that a viral respiratory infection has a greater, and possibly more lasting, effect on factors that participate in the development of LARs. Virus-associated airway hyperresponsiveness is a multifactorial process involving a complex interplay of IgE-dependent reactions, epithelial activation or damage, autonomic nervous system dysfunction and, of particular interest and relevance to our discussion, enhanced allergic inflammation."^^ In IgE-mediated reactions, the tissue response, be it the skin, nose or airway, is influenced by I g E sensitization of mast cells and basophils, release of bronchospastic and inflammatory mediators from sensitized cells, and the response of the target organ, which in asthma is bronchial smooth muscle.
cord-022431-f6caajxy	2013	
cord-023509-tvqpv6fp	2011	As a general rule, exposure to silica dust extends over many years, often 20 or more, before the symptoms of silicosis first appear: by the time the disease becomes overt clinically, much irreparable damage has been inflicted on the lungs. Confusingly, the term ''acute silicosis'' has since been applied to a further effect of heavy dust exposure in tunnellers, sand blasters and silica flour workers, namely pulmonary alveolar lipoproteinosis (see below), 71, 72 whilst the terms ''accelerated silicosis'' or ''cellular phase silicosis'' have been substituted for ''acute silicosis'' in referring to the rapid development of early cellular lesions. Asbestosis is defined as diffuse interstitial fibrosis of the lung caused by exposure to asbestos dust. The finely divided fume of several metals is highly toxic to the lungs and capable of producing severe acute and chronic damage to both the conductive airways and the alveoli, resulting in acute tracheobronchitis and bronchiolitis, diffuse alveolar damage, obliterative bronchiolitis and pulmonary fibrosis.
cord-023528-z9rc0ubj	2009	First, restriction of the thorax or the abdomen can result in impaired ventilation, which can occur easily when one restrains a foal and may result in spuriously abnormal arterial blood gas values (see the discussion on arterial blood gas evaluation, Respiratory Diseases Associated with Hypoxemia in the Neonate). Hypoxic ischemic encephalopathy (HIE), currently referred to as neonatal encephalopathy in the human literature, is one systemic manifestation of a broader syndrome of perinatal asphyxia syndrome (PAS), and management of foals with signs consistent with a diagnosis of HIE requires the clinician to examine other body systems fully and to provide therapy directed at treating other involved systems. Therapy for the various manifestations of hypoxiaischemia involves control of seizures, general cerebral support, correction of metabolic abnormalities, maintenance of normal arterial blood gas values, maintenance of tissue perfusion, maintenance of renal function, treatment of gastrointestinal dysfunction, prevention and recognition and early treatment of secondary infections, and general supportive care.
cord-023711-xz5ftnat	2013	Acute respiratory disease in cattle is not attributable to a single etiological agent. However, if PI3 virus or BVDV has been isolated, you have diagnosed the infection but not an "acute respiratory/enteric disease", because other viruses and also bacteria might be etiologically involved. At the end of the 1950s, "shipping fever" was described as a disease following massive transports to or from the enormous feedlots of the USA, and PI3 virus was isolated as the first virus of a condition with a multiple viral etiology. The types 4, 5 and 7 have been described each as a single causative agent of acute respiratory-enteric disease in Hungary and Japan, respectively. The isolation of these viruses from apparently healthy cattle as well as from those with acute respiratory-enteric disease indicates that they are widespread. A serosurvey of viruses during outbreaks of acute respiratory and/or enteric disease in Swedish cattle
cord-023712-nptuuixw	2014	12 Influenza A and B viruses frequently cause lower respiratory tract disease among children younger than 2 years of age, but the proportion manifesting as bronchiolitis is less than that observed with RSV. Although rapid diagnostic testing is generally unnecessary, it may be useful at times for implementing appropriate infection control, monitoring seasonal patterns of respiratory pathogens, restricting antimicrobial use, or providing confirmation of the diagnosis in children with unusual clinical presentations or severe disease. Timely diagnosis of specific viral respiratory pathogens may occasionally be necessary to guide specific antiviral therapy in children with high-risk conditions or severe illness with influenza or RSV. Although the risk of respiratory failure is relatively low for most children with RSV bronchiolitis, a small number of severely affected infants will require assisted ventilation in most intensive care units each year. Comparison of risk factors for human metapneumovirus and respiratory syncytial virus disease severity in young children
cord-023721-e0zp2gux	2013	
cord-023728-fgcldn4e	2014	The term croup now generally refers to an acute respiratory tract illness characterized by a distinctive barking cough, hoarseness, and inspiratory stridor in a young child, usually between 6 months and 3 years old. From 1979 to 1997, croup cases associated with parainfluenza viruses, estimated from the National Hospital Discharge Survey, showed that the number of admissions among children younger than 5 years decreased by approximately one third. 14 The human coronaviruses (hCoV) have been identified in up to 7% of young children with acute respiratory tract infections, with the NL63 strain most often associated with croup. Although abrupt onset of stridor at night may be the initial indication of illness, most children have a prodrome of mild upper respiratory tract signs of rhinorrhea, cough, and sometimes fever 12 to 48 hours before the onset of the distinctive "rough and stridulous" cough of croup.
cord-023942-vrs3je1x	2011	
cord-024183-1mrdjc39	2013	
cord-024188-d7tnku8z	2010	
cord-026005-f2khcjdy	2017	Microscopic examination of properly collected, stored, and processed samples may reveal many erythrocytes and siderophages in pulmonary hemorrhage or left-sided heart failure; inclusion bodies or syncytial cells in viral pneumonias; increased number of leukocytes in pulmonary inflammation; abundant mucus in asthma or equine recurrent airway obstruction (RAO); the presence of pulmonary pathogens, such as parasites, fungi, and bacteria; or tumor cells in cases of pulmonary neoplasia. The portal of entry for the respiratory form is typically aerogenous, and the disease is generally transient; thus the primary viral-induced lesions in the nasal mucosa and lungs are rarely seen at necropsy unless complicated by secondary bacterial rhinitis, pharyngitis, or bronchopneumonia. Laryngeal edema occurs in pigs with edema disease; in horses with purpura hemorrhagica; in cattle with acute interstitial pneumonia; in cats with systemic anaphylaxis; and in all species as a result of trauma, improper endotracheal tubing, inhalation of irritant gases (e.g., smoke), local inflammation, and animal species is classified as fibrinous, catarrhal, purulent, or granulomatous (Figs.
cord-027550-yyqsatqw	2020	
cord-027693-a4up394g	2020	
cord-048197-9785vg6d	2001	The respiratory epithelial target cells respond to viral infection with specific alterations in gene expression, including production of chemoattractant cytokines, adhesion molecules, elements that are related to the apoptosis response, and others that remain incompletely understood. The transcription factor NF-IL-6 is also produced in response to RSV infection [13] , and participates in a co-operative manner with NF-κB in the regulation of IL-8 gene expression [11] , although later studies suggest that activator protein-1 may function preferentially in this role [14] . Again, as part of our systematic study of gene expression in response to pneumovirus infection, we found that human respiratory epithelial cells respond to RSV infection with increased expression of the cytoskeletal protein cytokeratin-17 [36] . Inhibiton of viral replication reverses respiratory syncytial virus-induced NF-κ κB activation and interleukin-8 gene expression in A549 cells Respiratory syncytial virus infection induces expression of the anti-apoptosis gene IEX-1L in human respiratory epithelial cells
cord-048447-chz8luni	2007	The primary objective of the systematic review is to assess the effect of the administration of pulmonary surfactant compared with no therapy or with placebo on all-cause mortality (at or before hospital discharge) in mechanically ventilated children with acute respiratory failure. We used the following characteristics to assess the methodologic quality: allocation concealment (sealed envelopes or central randomization were considered adequate), blinding (which of the trial personnel and caregivers were blinded, and the methods used to ensure blinding), completeness of followup (assessed by the number of patients randomized for whom there were no outcomes), similarity of the groups at baseline (with respect to known prognostic factors: age, aetiology, severity of illness as measured by the Pediatric Risk of Mortality score, and immunosuppression), whether a standard or recommended strategy for mechanical ventilation was used, and whether a priori criteria for the use of co-interventions were used.
cord-129086-ra2njvcz	2020	However, in more recent times, the focus has shifted towards the theoretical investigations of fluid flow mechanisms involved in the virus-laden particles prevention by facemasks. 44 While these experimental studies are essential for the broad characterization and design evaluation of respiratory facemasks, further theoretical and numerical methods and algorithm-based investigations provide a better insight into the facemask''s fluid flow dynamics and the droplet leakage through the facemask openings. The computational fluid flow models have shown their potentials in an improved prediction of the spreading of respiratory virus-laden droplets and aerosols, sensitive to the ambient environment, and crucial to the public health responses. The results revealed that the small droplets travel a larger distance and remain suspended in the air for a longer time under the influence of airflow, supporting the mandatory use of facemasks to prevent the virus. In recent years, the respiratory droplets flow behavior through the facemasks has typically well-predicted using the computational fluid dynamics (CFD) techniques.
cord-151024-qe7c2uks	2020	We further provide the impulse response of SARS-CoV2-ACE2 receptor binding event to determine the proportion of the virus population reaching different regions of the respiratory tract. These results are especially important to understand the effect of SARS-CoV2 on the different human populations at different ages who have different mucus flow rates and ACE2 receptor concentrations in the different regions of the respiratory tract. • Determining impulse response of SARS-CoV2 infection process for the first time in literature • Calculating ACE2 receptor densities in the different regions of the respiratory tract: Based on the available data on surface parameters, we calculate ACE2 receptor density crudely. Due to the cylindrical symmetry assumption, we can make a longitudinal Upon entering the mucus and periciliary layer, viruses use their viral S-spike proteins to bind to ACE2 receptors on host cell surfaces [43] .
cord-225826-bwghyhqx	2020	In this work, we perform the health screening through the combination of the RGB and thermal videos obtained from the dual-mode camera and deep learning architecture.We first accomplish a respiratory data capture technique for people wearing masks by using face recognition. In this study, we develop a portable and intelligent health screening device that uses thermal imaging to extract respiration data from masked people which is then used to do the health screening classification via deep learning architecture. After extracting breathing data from the video obtained from the thermal camera, a deep learning neural network is performed to work on the classification between healthy and abnormal respiration conditions. First, we combine the face recognition technology with dual-mode imaging to accomplish a respiratory data extraction method for people wearing masks, which is quite essential for current situation. Finally, we use a bidirectional GRU neural network with attention mechanism (BiGRU-AT) model to work on the classification task with the input respiration data.
cord-251986-ajlpb9li	2020	This virus shares highly homological sequence with SARS‐CoV, and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID‐19) with clinical symptoms similar to those reported for SARS‐CoV and MERS‐CoV. A growing body of evidence shows that neurotropism is one common feature of CoVs. 1, [9] [10] [11] [12] Therefore, it is urgent to make clear whether SARS-CoV-2 can gain access to the central nervous system (CNS) and induce neuronal injury leading to the acute respiratory distress. Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Exploring the pathogenesis of severe acute respiratory syndrome (SARS): the tissue distribution of the coronavirus (SARS-CoV) and its putative receptor, angiotensin-converting enzyme 2 (ACE2) Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients
cord-252012-hdjbxah8	2010	Traditionally associated with acute respiratory illness (ARI) or symptoms of the "common cold," the respiratory viruses implicated in asthma exacerbations predominantly possess RNA genomes with a distinct genome organization (positive [1] or negative [À] sense), virus particle (virion) morphology (enveloped or nonenveloped), host cell receptor interaction, and well-defined annual or seasonal prevalence. These "newly identified viruses" (NIVs) including human metapneumovirus (HMPV; described pre-SARS), the human rhinovirus (HRV) species C (HRV-Cs), human coronaviruses (HCoVs)-NL63 and -HKU1, human bocavirus (HBoV), and the KI and WU polyomaviruses (KIPyV and WUPyV) are now the focus of intense research, and their involvement in asthma exacerbations is slowly beginning to be determined. 34 In a retrospective study of clinical samples taken over a 20-year period from young children (median age 14.5 months), the percentage of lower respiratory tract illness (LRTI; including asthma exacerbations and bronchiolitis) associated with any HCoV, HCoV-NL63, or HCoV-OC43 was estimated to be 4.6%, 2.6%, and 1.9%, respectively.
cord-252037-rj61mzqj	2005	In this study, we examined: i) the circulation rate of hMPV among the other respiratory viruses during 3 consecutive winter-spring seasons; ii) the relative circulation of the 2 types and the 4 subtypes of hMPV during the same 3-year period; iii) the relative impact of hMPV as compared to hRSV in determining admission to the hospital of infants with acute respiratory infections. The relative distribution of different respiratory viruses causing severe infections requiring admission to the hospital of infants and young children in three consecutive winter-spring seasons from 2001 through 2004 is reported in Table 2 Within the aliquot of patients found positive for some respiratory virus, no difference in the circulation rate was observed for respiratory virus infections caused by influenzavirus B, hPIVs, hAdVs, hCoVs, and coinfections along the three years studied.
cord-253145-1fbj1rdv	2007	Assays based on nucleic acid amplification and detection can be designed against a broad range of respiratory viruses and have been particularly useful for detection of recently identified viruses such as human metapneumovirus and coronaviruses NL63 and HKU1. Use of NATs allows assessment of the impact of a wider array of potential pathogens on respiratory infections than previously possible and target-specific (multiplex) approaches have proved feasible for enhanced broadspectrum respiratory virus diagnosis. Many feasibility studies have confirmed that NATs improve detection of potential pathogens from lower respiratory tract specimens as well as from respiratory swabs even where alternative methods such as DFA and culture are available (Hibbitts and Fox, 2002; Moore et al., 2004; Lee et al., 2006) . If individual NATs are utilized, multiple infections are identified frequently but use of real-time multiplex reactions may lead to competition between amplification and detection Table 1 Enhanced detection of respiratory viruses using NATs
cord-253148-3t4o27xp	2008	STUDY DESIGN: From October 2005 through October 2006, we screened respiratory samples from children and adults negative for common respiratory pathogens for HBoV by PCR. CONCLUSIONS: HBoV circulates in Cleveland, OH, in children and adults with similar frequencies, and can warrant hospitalization and intensive care. We sought to further define the clinical and epidemiologic characteristics of HBoV in adult and pediatric patients in Cleveland, OH. Isolates positive for HBoV were screened for common respiratory viruses by RT-PCR with published primer sets. Forty samples (2.2%) tested positive for HBoV by PCR: 36 (90%) pediatric patients and 4 (10%) adult patients. Of pediatric patients who screened positive for HBoV, 27 (84.4%) were admitted to the hospital, including 9 (28.1%) who required intensive care. However, this report suggests that clinical disease associated with HBoV alone may be severe enough to require admission to the hospital in both adults and children and to the intensive care unit in children.
cord-253223-us0ey8dq	2009	[38] [39] [40] [42] [43] [44] In a recent casecontrol study on acute gastroenteritis, Arthur and colleagues 13 examined stool specimens for potential pathogens, including all three species of human bocavirus. The large percentage of coinfections associated with human bocavirus infections suggests that evaluation for further pathogens should be undertaken for any patient diagnosed with HBoV-1. Human bocavirus infection in children with respiratory tract disease Human bocavirus detection in nasopharyngeal aspirates of children without clinical symptoms of respiratory infection Detection of human bocavirus in Japanese children with lower respiratory tract infections High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Human bocavirus DNA detected by quantitative real-time PCR in two children hospitalized for lower respiratory tract infection
cord-253279-8j7esl8j	2017	
cord-253502-v2hh3w3r	2004	
cord-253761-wjm8ju3v	2010	To define the epidemiological profile and the clinical characteristics associated with HBoV infection in a population of children hospitalized with respiratory tract infection. MATERIAL AND METHODS: During a one-year period throat swab samples were collected from 370 previously healthy children, aged 14 days to 13 years, admitted to two different paediatric wards because of respiratory tract infection. The aim of the present study was to define the epidemiological profile and the clinical characteristics associated with HBoV in hospitalized children with respiratory tract infection (RTI) in Greece. One may argue that the fact that HBoV is prevalent in samples from patients with respiratory tract infection does not guarantee a causative role for the symptoms, especially when -as in this case -it is frequently detected in combination with other respiratory viruses of known pathogenic potential. Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus
cord-254265-8i86c8kt	2008	In 67/99 children (67%) at least one viral pathogen was identified, the viruses detected most frequently were respiratory syncytial virus (35%), human metapneumovirus (25%) and rhinovirus (19%). The aim of the present study was to describe the role of human metapneumovirus and other common respiratory viruses including: influenza virus A, B, and C, parainfluenza 1-4 viruses, adenoviruses, respiratory syncytial virus A and B, rhinovirus, coronavirus 229E and OC43 and enterovirus as bronchiolitis, and bronchopneumonia pathogens among hospitalized children younger than 1 year, taking into account that in this age group respiratory viruses are the main etiological agents of lower respiratory tract infections [Shay et al., 1999; Smyth and Openshaw, 2006; Bush and Thomson, 2007] . Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis
cord-254766-585iu5ey	2008	This review summarizes the evidence associated with factors that may contribute to the development or exacerbation of asthma including age, host factors, genetic polymorphisms, altered immune responses, and aspects of viral antigen expression. These observations suggest that respiratory viral infections lead to a prolonged period of increased antigen presentation in the airways resulting in de novo and memory T-cell responses not only to the virus but also to unrelated antigens including allergens. In addition to studies of primary infections, models studying the interactions between respiratory viral infections and allergen sensitization are essential in understanding the mechanisms of virus induced asthma exacerbations. These studies show that the immune responses to allergen sensitization and respiratory viral infections interact to cause persistent inflammation and AHR, symptomatic of the asthmatic response (Fig. 2) [53] . Recurrent respiratory syncytial virus infections in allergen sensitized mice lead to persistent airway inflammation and hyperresponsiveness
cord-254770-ot9ys10r	2009	20 In Switzerland, pre-emptive therapy in cases of low-grade immunosuppression, prophylaxis in severe immunosuppression, and combined treatment with immunoglobulin (Ig), ribavirin, and palivizumab in cases of proven infection have been suggested for both BMT recipients and LTRs. 20 To get a better overview on the clinical evolution of RSV infections in LTRs we retrospectively searched our virology reports and identified 10 adult LTRs with proven lower respiratory tract RSV infection. Two patients were treated with ribavirin for 7 days (orally with 1,600 mg/day or intravenously with 10 mg/kg 3 times daily) concomitant with intravenous palivizumab (a single dose of 15 mg/kg) ( Table 1) , including Patient 3, who required anti-thymocyte globulins for non-responding conThe detection of RSV by PCR in respiratory secretions is highly sensitive and specific, 24 and is currently considered the best available test for the diagnosis of respiratory tract infections in adult lung transplant recipients.
cord-255011-7oqfod62	2008	
cord-255166-sar50ej0	2007	
cord-255623-qdpdsye9	2020	
cord-255711-8lojw5cz	2019	
cord-255734-038xu4hq	2006	
cord-255901-nl9k8uwd	2016	Studies conducted in community or health care settings found facemasks to be generally effective against influenza-like illness (ILI) or even against severe acute respiratory syndrome (SARS) but its effectiveness against respiratory infections at MGs remains unknown. 15, 17 A review of non-pharmaceutical interventions against respiratory tract infections among Hajj pilgrims presented data on the uptake of facemask and acknowledged that compliance was generally poor, but did not evaluate its effectiveness during Hajj. A few studies showed that providing educational session on protective measures against respiratory infections (including facemask) before Hajj was associated with significantly higher uptake of facemasks among pilgrims. 68 Focused studies are required to investigate factors influencing facemask compliance among attendees of Hajj and other MGs. In this systematic review, pooled data of facemask effectiveness showed that participants who used facemask during Hajj are about 20% less likely to suffer from respiratory infections compared to those who do not use it.
cord-256065-zz2907h0	2020	title: A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. RSV additionally induced over-representation of differential expressed pattern recognition receptor genes as compared to healthy controls (Table S3 ): (i) Toll-like receptors (TLR) cascades (R-HSA-168898; adjusted p-value = 1.23 × 10 −3 ), including TLR3 (R-HSA-168164; adjusted p-value = 2.45 × 10 −2 ), which are specialized in the recognition of conserved molecular features of different pathogens such as bacteria, viruses, fungi, and parasites; and (ii) C-type lectin receptors (R-HSA-5621481; adjusted p-value = 5.12 × 10 −6 ), capable of sensing glycans present in viral pathogens to activate antiviral immune responses such as phagocytosis, cytokine production, antigen processing and presentation, and subsequent T cell activation.
cord-256788-h4iv8crq	2012	9 In that regard a decrease in IFN-g production from cord blood mononuclear cells (CBMCs) stimulated by PHA or allergens has been associated with increased risk for acute respiratory tract illness during infancy. We assessed whether each of these immune end points could predict the development of respiratory tract illness during the first year of life in a prospective birth cohort of children at high risk for asthma and allergic disease. Together, these findings reinforce the association of a decreased IFN-g response to RSV with the development of increased viral respiratory tract infections in the first year of life. In this study we provide evidence that a decreased antiviral interferon response at the time of birth is selectively associated with an increase in acute respiratory tract infections in the first year of life among infants at high risk for asthma and allergic disease.
cord-256827-tht5h1tu	2001	Common cold is caused by viruses in most circumstances and does not require antimicrobial agent unless it is complicated by acute otitis media with effusion, tonsillitis, sinusitis, and lower respiratory tract infection. Five to six days after initiation of treatment, cephalexin and placebo groups did not differ in the presence of nasal discharge, incidence of complications, or parental opinion of benefit of medicationY Cough occurs in 60-80% of common cold and does not suggest a bacterial etiology. n Even in uncomplicated viral upper respiratory infection, as occurs in common cold, there is inflammation and congestion of both the nasal and the sinus mucosa. Persistence of signs and symptoms of upper respiratory infection i.e. rhinorrhea or cough for more than 10-14 days is a pointer towards sinusitis.
cord-256930-bz80uxnx	2013	
cord-257073-dm80bxnd	2011	OBJECTIVE: We examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. Conclusions: Combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. We tested the feasibility of combining real-time symptomatic surveillance with nasal self-swabbing for the prospective collection of epidemiologic and virological data on acute respiratory infections. Combining e-mail-based active symptomatic surveillance with self-collection of nasal swabs ensured prospective, accurate collection of data on incident episodes of acute respiratory infections and timely sample collection for the detection of respiratory pathogens.
cord-257171-kp2huia0	2012	
cord-257220-fe2sacjj	2014	LDV elevates IgG levels in mice with little production of virus-specific antibodies [11, 21] , which is almost identical to what is seen in isolator piglets infected with PRRSV [22] (''''The effect of age, rearing, complement and the role of mucosal immunity'''' section). Polyclonal activation of B cells occurs in lymphoid organs from porcine reproductive and respiratory syndrome virus (PRRSV)-induced pigs The presence of alpha interferon at the time of infection alters the innate and adaptive immune responses to porcine reproductive and respiratory syndrome virus Interferon type I response in porcine reproductive and respiratory syndrome virus-infected MARC-145 cells Antigen-specific B cell responses to porcine reproductive and respiratory syndrome virus infection Antibody production and blastogenesis response in pigs experimentally infected with porcine reproductive and respiratory syndrome virus Neutralizing antibody responses of pigs infected with natural GP5 N-glycan mutants of porcine reproductive and respiratory syndrome virus
cord-257244-gryp0khc	2017	Despite these important associations, the use of antiinfectives (antibiotics, antivirals, antifungals, vaccines) that specifically target known pathogens, or drugs that are based on or exploit microbe-host receptor interactions (toll-like receptor agonists, bacterial lysates) or are immunomodulators (vitamin D), and/or may work in part by altering our associated microbiology (probiotics) are, with the exception of severe asthma, seldom considered in asthma treatment, prevention and guidelines. Overall, antibiotic use is associated with asthma risk rather than protection at most stages of human development, including pregnancy, 10, 11 early life 12 and childhood, 13 although why this is so is a subject widely debated. 10 In retrospective studies, the association between antibiotic use and increased risk of asthma or wheezing in children is further confused due to the potential of reverse causation. Inhibiting virus replication through interfering with viral enzymes active within cells poses additional problems in drug discovery; however, several useful inhibitors for respiratory tract viruses have found their way into phase I/II clinical trials.
cord-257299-z9u12yqb	2009	Common childhood viral infections, such as measles and mumps are probably an unrecognized cause of acute or progressive damage to hearing [5] . Measles infection can be avoided by administering a reduced, live-virus vaccine to children between the ages of 12 and 15 months (MMR). The etiology of the acute forms in the respiratory airways is, initially, of a viral nature in most patients, with later, secondary bacterial infections on the mucous lesions caused by the viral agents [31] . Herpangina is an extremely contagious illness caused by a coxackievirus characterized by a presence of a vesicular exanthema at the velopharyngeal mucous level and acute or croup laryngotracheitis [38] [39] [40] [41] when viral infections are associated. The most common manifestation of the primary infection of this organism is infective mononucleosis (IM), a sometimes acute, but often asymptomatic clinical syndrome which more often strikes children, adolescents, and young adults [82] . Viral etiology and epidemiology of acute lower respiratory tract infections in children
cord-257656-z7zx46gd	2019	title: The Emerging Role of Rhinoviruses in Lower Respiratory Tract Infections in Children – Clinical and Molecular Epidemiological Study From Croatia, 2017–2019 Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. Therefore, we investigated the rhinovirus (RV) infection prevalence over a 2-year period, compared it with prevalence patterns of other common respiratory viruses, and explored clinical and molecular epidemiology of RV infections among 590 children hospitalized with acute respiratory infection in north-western and central parts of Croatia. This study aims to determine the RV prevalence, compare it with prevalence patterns of other common respiratory viruses, as well as to explore clinical and molecular epidemiological features of RV infections among hospitalized children with acute respiratory infection.
cord-257805-pcp3qgn0	2020	
cord-258139-x4js9vqe	2005	Alternatively, when the causative pathogens are endemic in a population and individual susceptibility is dependent on numerous interrelated factors, the management of animal resistance and risk factors may be proportionally more important for disease prevention than biosecurity practices. The authors emphasize five areas of biosecurity management that should be more rigorously applied for the reduction of respiratory disease prevalence in cattle, including (1) strategic vaccination, (2) calf biosecurity, (3) housing ventilation, (4) commingling and animal contact, and (5) bovine viral diarrhea virus control. Airborne pathogen concentration is a function of many factors, including animal type, housing system, stocking rate, bedding, humidity, dust particle density and size, and finally, elimination through ventilation. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical.
cord-258336-zs04l3s0	2017	Abstract Objectives To report epidemiological features, clinical characteristics, and outcomes of human rhinovirus (HRV) infections in comparison with other community acquired respiratory virus (CRV) infections in patients hospitalized for two consecutive years. The present study reports the epidemiological features, clinical characteristics, and outcomes of HRV infections in comparison with other CRV infections in patients hospitalized in a referral hospital in Southern Brazil, for two consecutive years. Patients hospitalized at an academic tertiary care center in Southern Brazil from whom respiratory samples were collected and sent for investigation, or who were diagnosed with SARI in 2012 or 2013, were included in the study. The medical records and influenza notification forms of patients with detectable respiratory virus were reviewed, focusing on epidemiology, clinical manifestation, outcome, laboratory findings, and diagnosis of SARI. In conclusion, HRV has a high prevalence in the hospitalized children and was present in cases of severe disease, including death.
cord-258366-fu9b446y	2012	
cord-258386-aiwzgkq3	2020	Of the remaining nine who continued to need respiratory support, seven 39 (77.8%) had iatrogenic preterm deliveries (six by cesarean delivery) for maternal respiratory 40 distress (needing increasing levels of respiratory support without improved oxygen saturation), 41 one had an early term delivery due to PROM, and one, now 30 weeks, has required intensive 42 care with high-flow nasal cannula for three weeks. Of the eight patients delivering with maternal respiratory distress, seven did not require 45 intubation, and one was intubated for emergent cesarean delivery, and remained on a ventilator 46 for 19 days. Of the eight patients delivering with maternal respiratory distress, seven did not require 45 intubation, and one was intubated for emergent cesarean delivery, and remained on a ventilator 46 for 19 days.
cord-259422-5ex12eun	2003	
cord-259927-xh9cw9ao	2017	
cord-259997-8f8di4eu	2018	
cord-260225-bc1hr0fr	2020	Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4).
cord-260238-2p209g2p	2004	
cord-260457-m1jbpo5l	2007	
cord-260472-xvvfguht	2007	The association between upper respiratory viral infections and asthma exacerbations in children was demonstrated almost three decades ago using virus cultures and serological techniques [5] . Abbreviations: RTePCR, reverse transcriptionepolymerase chain reaction; RV, rhinovirus; PIV, parainfluenza virus; RSV, respiratory syncytial virus; MPV, human metapneumovirus; ICAM-1, intracellular adhesion molecule-1; IFN-b, interferon-beta; NGF, nerve growth factor; SP, substance P; NK1, neurokinin 1 receptor; MBL, mannose-binding lectin; LABA, long-acting b 2 agonists. In the human respiratory tract, all the above agents are able to produce a spectrum of clinical acute infection phenotypes, ranging from the common cold, croup and acute bronchiolitis, to pneumonia, although each virus has increased propensity for a particular clinical disease (e.g. parainfluenza for croup, RSV for severe bronchiolitis, influenza for pneumonia) [21, 22] . Rhinovirus is the key virus accounting for the majority of exacerbations both in children and adults and thus the effective treatment or prevention of that infection would be a major asset in asthma therapy.
cord-260630-vvpzp73r	2005	In this issue of Clinical Infectious Diseases, there are 2 articles that provide us with some insight into the various etiologic agents that can cause acute respiratory tract infection (ARTI) in general practice patients in The Netherlands [1] and into the significance of the human metapneumovirus (hMPV) in patients with community-acquired pneumonia (CAP) and exacerbations of chronic obstructive pulmonary disease (COPD) in Quebec, Canada [2] . The objectives of the Dutch study were to estimate the incidence of influenza-like illnesses (ILIs) and of other ARTIs in patients visiting their general practitioners (to determine the etiologic agents) and to test the hypothesis that asymptomatic persons with subclinical infection may act as sources of transmission [1] . Nose and throat swab specimens were obtained from case patients and control subjects, and viral cultures and PCR tests were performed for detection of adenovirus, coronavirus, enterovirus, hMPV, influenza virus, parainfluenza virus, rhinovirus, and respiratory syncytial virus (RSV), as well as for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Chlamydophila psittaci.
cord-260750-utbuj5iz	2013	
cord-260871-dtn5t8ka	2020	Besides, several neurological manifestations had been described as complications of two other previous outbreaks of CoV diseases (SARS ad Middle East respiratory syndrome). Several neurological manifestations were described as complications of two other previous outbreaks of CoV diseases, namely, SARS and the Middle East respiratory syndrome (MERS). Stroke is one of the most frequent neurological diseases associated with SARS-CoV-2 infection, 8 and large-vessel stroke in younger patients was recently reported in five patients. Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Central nervous system involvement by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the central nervous system
cord-261025-y49su5uc	2003	Severe acute respiratory syndrome (SARS) is a recently recognized febrile respiratory illness that first appeared in southern China in November 2002, has since spread to several countries, and has resulted in more than 8000 cases and more than 750 deaths. This article summarizes currently available information regarding the epidemiology, clinical features, etiologic agent, and modes of transmission of the disease, as well as infection control measures appropriate to contain SARS. An RT-PCR test specific for RNA from the SARS-CoV has been positive within the first 10 days after fever onset in respiratory specimens from most patients considered probable cases of SARS who have been tested and in stool samples in the second week of illness. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with patients with SARS or travel to SARS-affected areas) and a combination of fever and respiratory symptoms, with or without chest radiographic changes. Severe Acute Respiratory Syndrome (SARS) in Singapore: clinical features of index patient and initial contacts
cord-261598-w2tyongu	2014	The FilmArray Respiratory Panel (RP) (BioFire Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. The FilmArray Respiratory Panel (RP) (BioFire Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. Although the infection usually remains limited to the upper respiratory tract in most patients, complications due to influenza viruses have been reported in HSCT and SOT patients, especially lung transplant recipients [18, 22, 23] . In 2008, the FDA cleared the first broadly multiplexed molecular assay, the xTAG Ò respiratory viral panel ( Two studies have evaluated the performance of the eSensor RVP compared to other multiplex respiratory panels including the FilmArray RP, the xTAG RVP and the xTAG RVP FAST and to laboratory developed tests [58, 59] .
cord-261756-4lybl57r	2020	
cord-261908-olcuq6tm	2011	
cord-261941-xf1k5uj1	2005	Recommendations for limiting secondary transmission are given based on the Centers for Disease Control and Prevention guidelines on infection control in health care facilities. It is confirmed through laboratory testing showing an acute rise in SARS-CoV antibody titers within 4 weeks of developing the disease. Patients who meet the criteria for suspect SARS should immediately be placed in a private respiratory isolation room that has been specially engineered to contain negative pressure in relation to the outside hallway and have a minimum of 12 air exchanges per hour. Prevention of transmission in medical facilities requires a combination of early identification, isolation, and treatment of infectious individuals with active disease, engineering controls, basic infection control measures, and the use of personal protective equipment. Hospital infection control guidance for severe acute respiratory syndrome (SARS) California Department of Health Services: severe acute respiratory syndrome (SARS)-infection control recommendations Infection control measures for operative procedures in severe acute respiratory syndrome-related patients
cord-262347-ejhz9rra	2015	
cord-262366-cmjnb0al	2006	title: Genetic variability of human coronavirus OC43‐, 229E‐, and NL63‐like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients In the winter–spring seasons 2003–2004 and 2004–2005, 47 (5.7%) patients with acute respiratory infection associated with human coronavirus (hCoV) 229E‐, NL63‐, and OC43‐like strains were identified among 823 (597 immunocompetent and 226 immunocompromised) patients admitted to hospital with acute respiratory syndromes. © 2006 Wiley‐Liss, Inc. In the winter-spring seasons 2003-2004 and 2004-2005, 47 (5.7%) patients with acute respiratory infection associated with human coronavirus (hCoV) 229E-, NL63-, and OC43-like strains were identified among 823 (597 immunocompetent and 226 immunocompromised) patients admitted to hospital with acute respiratory syndromes.
cord-262623-lmf2h6oc	2009	
cord-262673-j2ot35lt	2020	Furthermore, respiratory epithelial cells and lung macrophages are capable of secreting a broad range of chemokines like IL-8, Macrophage inflammatory protein-1 (MIP-1), RANTES and cytokines including TNF-α, IL-6, IL-1β that influence the types of immune cells being recruited to the area in response to acute viral infections (177, 178) . Both Influenza and SARS virus can induce acute lung injury (ALI) which is accompanied by high levels of C5a, leading to the influx and activation of innate immune cells (199) (Figure 1) . Innate immune response of human alveolar type II cells infected with severe acute respiratory syndrome-coronavirus Middle East respiratory syndrome coronavirus shows poor replication but significant induction of antiviral responses in human monocytederived macrophages and dendritic cells Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells
cord-263141-n200x6z1	2016	
cord-263749-bbhh5xb1	2020	
cord-263764-2ewz8ok4	2018	
cord-263927-hnsyas9q	2012	Objectives To describe respiratory viruses, including co‐infection and associated attributes such as age, sex or comorbidity, in patients presenting with influenza‐like illness to a community sentinel network, during the pandemic A(H1N1)pdm09 in Ontario, Canada. In multinomial logistic regression analyses adjusted for age, sex, comorbidity, and timeliness of sample collection, single infection was less often detected in the elderly and co‐infection more often in patients <30 years of age. Co‐infection, but not single infection, was more likely detected in patients who had a sample collected within 2 days of symptom onset as compared to 3–7 days. [8] [9] [10] [11] [12] [13] Higher proportions of influenza A, respiratory syncytial virus (RSV), parainfluenza viruses, and rhinovirus, compared with other circulating viruses have been detected in patients with co-infections. 9, 15, 16, 20, 21 This study enrolled community patients presenting with (ILI) to a community sentinel network, during the influenza pandemic A(H1N1)pdm09 in Ontario, Canada and documented the profile of respiratory viruses causing ILI symptoms.
cord-264059-jf4j00bp	2019	3 Initial studies demonstrated that such POC multiplex PCR systems identified previously under-evaluated viral or atypical infections in ED dyspneic patients, and the additional information on rapid respiratory infection testing may also change the physician''s antibiotic-prescribing behavior, enabling more timely and appropriate treatment. In this study, we aimed to assess the impact of implementing a diagnostic algorithm that combines rapid respiratory viral surveillance and PCT tests on older patients presenting to the ED with severe acute respiratory illness. This prospective cohort study reports the clinical impact of rapid molecular diagnosis of respiratory pathogens in conjunction with PCT testing on older adult patients presenting to the ED with severe acute respiratory illness. The findings of our study support the use of rapid multiplex PCR respiratory panels in conjunction with the PCT test for early diagnosis of respiratory viral infection and to inform optimizing antibiotic use in older adult patients presenting to the ED with severe acute respiratory illness.
cord-264079-u0nkjexi	1981	title: The use of gowns and masks to control respiratory illness in pediatric hospital personnel Nosocomial disease often lengthens the hospital stay and, in some instances, may be severe or even fatal> ~ For certain viruses, particularly respiratory syncytial virus, there is a high frequency of infection in nursing, medical, and other stafP ..... Children with respiratory disease are usually placed in isolation and hospital personnel may be cohorted or required to wear gowns when administering patient care. The efficacy of this approach in the control of RSV therefore designed a prospective study to examine the effect of various control methods on the acquisition of symptomatic respiratory infections by medical personnel caring for infants with respiratory disease. We were unable to demonstrate any effect of adding the use of both gown and mask to the usual handwashing routine on the development of illness in personnel caring for infants with respiratory disease.
cord-264255-q5izs39f	2007	
cord-265054-52eqdlef	2006	
cord-265257-p9f0pl3y	2019	
cord-265354-ajfjrnr9	2011	
cord-265380-2gs34xcw	2019	
cord-265445-bazcczdj	2020	title: Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study Objective: To investigate the relationship of overnutrition (obese and overweight) with severity of illness in children hospitalized with acute lower respiratory infections (ALRIs), frequency of viral coinfections and leptin levels. However, the empirical evidence needed to estimate the impact of overnutrition (including overweight and obese conditions) on the severity of viral respiratory infections in children is still lacking (10) . Hence, the objective of this study was to estimate the relationship of overnutrition on severity of illness in infants (aged between 0 and 5 months) and children (aged between 6 and 24 months) hospitalized with ALRIs. Moreover, frequency of viral coinfection, RSV viral load and levels of leptin according to nutritional status were evaluated.
cord-265751-q1ecpfyg	2017	
cord-266260-t02jngq0	2019	
cord-266516-0ure8256	2017	
cord-266716-pghnl980	2018	
cord-266822-ecq50ye2	2017	Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Standardized measures of disease severity are urgently needed for clinical trials of vaccines and antivirals currently in development for ARI caused by influenza (FLU), respiratory syncytial virus (RSV), human metapneumovirus (HMPV), adenovirus (ADV), or human rhinovirus (HRV) [9] [10] [11] [12] [13] [14] [15] [16] [17] . Considering the variability in disease presentations and courses of illness with influenza and other respiratory viral infections in children, the ViVI Disease Severity Score is not intended to be validated against future clinical events or outcomes. Our contributions are the following: (A) The design of a hospital-based surveillance program and a unique QM cohort of more than 6000 children, where an independent QM team monitored patients daily using standardized clinical assessments and virology at the National Reference Centre for Influenza and Other Respiratory Viruses.
cord-267003-k7eo2c26	2015	
cord-267274-3ygl3stc	2020	We analysed three separate datasets from the SCHN electronic records from Jan 1, 2015, to June 30, 2020, in children younger than 16 years: (1) laboratory tests for respiratory syncytial virus by PCR; (2) hospital admissions for bronchiolitis coded by the ICD-10 Australian Modification (J21.0, J21.1, J21.8, and J21.9); and (3) emergency department attendances for acute respiratory illness coded by the Systematised Nomenclature of Medicine Clinical Terminology (appendix p 4). We observed concurrent lower frequencies of respiratory syncytial virus (A and B) detection, admission to hospital for bronchiolitis, and emergency department attendance for acute respiratory illnesses (appendix p 1) in 2020 compared with preceding years. The small uptick in emergency department attendances and bronchiolitis admissions in June, 2020 (appendix p 1) was not associated with increased respiratory syncytial virus detections.
cord-267436-mivxm8oh	2005	
cord-267973-uvz7kavu	2016	
cord-268038-9jjpc1a2	2015	These results indicate the potential of RI-002 to improve outcome of RSV infection in immunocompromised subjects not only by controlling viral replication, but also by reducing damage to lung parenchyma and epithelial airway lining, but further studies are needed. In this case, treatment with a drug that has strong antiviral activity may have a higher therapeutic efficacy in immunosuppressed patients compared with immunocompetent individuals infected with RSV because of the reduction in pulmonary damage caused by excessive viral replication. Although normal cotton rats treated with saline cleared RSV by day 10 post infection, immunosuppressed saline-treated animals had~6 log 10 PFU of virus in their lungs and noses at that time. To determine whether RI-002 has an effect on pulmonary pathology associated with prolonged RSV replication in immunosuppressed animals, lung tissue was collected for histopathology analysis on day 10 post infection.
cord-268251-mcg1v24t	2014	
cord-268324-86a0n0dc	2020	The severe acute respiratory syndrome-coronavirus-2 (commonly known as SARS-CoV-2) is a novel coronavirus (designated as 2019-nCoV), which was isolated for the first time after the Chinese health authorities reported a cluster of pneumonia cases in Wuhan, China in December 2019. The clinical picture of critical patients with severe inflammatory-induced lung disease and with sepsis or septic shock needing intensive care support and mechanical ventilation is characterized by a wide range of signs and symptoms of life-threatening multiorgan dysfunction or failure, including dyspnoea, tachypnoea (respiratory rate of > 30/min), tachycardia, chest pain or tightness, hypoxemia, virus-induced distributive shock, cardiac dysfunction, elevations in multiple inflammatory cytokines, renal impairment with oliguria, altered mental status, functional alterations of organs expressed as laboratory data of hyperbilirubinemia, acidosis [serum lactate level > 2 mmol/L (18 mg/dL)], coagulopathy, and thrombocytopenia.
cord-268388-kkhuzf3p	2014	Two years have passed since the initial description of the Middle East respiratory syndrome coronavirus (MERS-CoV), yet the epidemic is far from being controlled. First reported in 2012 [1] , Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus and the first lineage 2C Betacoronavirus known to infect humans [2] . Middle east respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies in milk collected according to local customs from dromedary camels, qatar Middle east respiratory syndrome coronavirus (MERS-CoV) in dromedary camels Epidemiological, demographic, and clinical characteristics of 47 cases of middle east respiratory syndrome coronavirus disease from saudi arabia: A descriptive study Clinical features and viral diagnosis of two cases of infection with middle east respiratory syndrome coronavirus: A report of nosocomial transmission Clinical features and virological analysis of a case of middle east respiratory syndrome coronavirus infection Ribavirin and interferon therapy in patients infected with the middle east respiratory syndrome coronavirus: An observational study
cord-268490-e8jub01m	2007	
cord-268729-n7slf5tx	2008	
cord-269437-0pvqvhqs	2013	
cord-269508-d82qjyyr	2013	
cord-270258-9vgpphiu	2016	To identify factors which can predict pneumonia development and progression to respiratory failure at the early course of the disease, we evaluated MERS-CoV infected patients managed in a tertiary care center during the 2015 MERS outbreak in Korea. To identify factors which can predict pneumonia development and progression to respiratory failure at the early course of the disease, we reviewed the electronic medical records of who were diagnosed with MERS-CoV infection and admitted at Samsung Medical Center, a 1950 tertiary care university hospital which managed the largest number of MERS-CoV infected patients as a single center during the 2015 Korean MERS outbreak. The present analysis of predictive factors for pneumonia development and progression to respiratory failure using variables obtained by day 3 of symptom onset could be conducted owing to the observation of entire clinical course of the disease from the exposure to MERS-CoV.
cord-270647-vn4kirrx	2018	OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively. Both groups differ with respect to the associated virus and bacteria: while asthma exacerbations have been associated to a specific rhinovirus infection, pneumonia can be related to a wide range of bacterial, fungal and viral agents, with a high prevalence of Respiratory Syncytial Virus (RSV) [2, 7] . Here we describe the virome and bacteriome present in the Upper Respiratory Tract of hospitalized children clinically diagnosed with asthma and pneumonia, during an acute exacerbation and an ARI episode respectively, at the National Institute of Respiratory Diseases (INER, Mexico City) during 2014 and 2015 winter seasons. Prevalence of respiratory viral infection in children hospitalized for acute lower respiratory tract diseases, and association of rhinovirus and influenza virus with asthma exacerbations
cord-270947-6e5cw2q9	2017	
cord-271172-y48dovux	1998	
cord-271669-dkg6229j	2019	
cord-271822-ohkki0ke	2020	
cord-272143-6ej3eibd	2018	We have evaluated these infections in children with humoral immunodeficiencies who required immunoglobulin replacement therapy, considering their relationship with symptoms, lung function, bacterial co‐infection, and outcomes. CONCLUSIONS: In our experience, viral respiratory tract infections can cause significant respiratory symptoms and impaired lung function, in children with HID, despite immunoglobulin replacement therapy. Children with severe T-cell immunodeficiencies present impaired clearance of respiratory viruses, and pulmonary complications of viral infections are leading causes of morbidity and mortality in this group of patients. 1 However, the role of respiratory viruses in children with other types of primary immunodeficiency (PID), mainly those with humoral immunodeficiencies (HID) or diseases of immune dysregulation, has hardly been studied. 2, 7 We report, to the best of our knowledge, the first study that analyses respiratory viruses in pediatric patients with predominantly antibody deficiency who required IRT, considering their relationship with clinical symptoms and pulmonary function, bacterial co-infection, treatment and outcomes.
cord-272179-wvw5mmy3	2020	
cord-272538-gclrtie7	2018	
cord-272596-yxvg8357	2014	title: Detection of Human Bocavirus in Children with Acute Respiratory Tract Infections in Lanzhou and Nanjing, China In our study, 72.34% of HBoV1-positive patients had co-infection with 10 different respiratory viruses, which is similar to previous reports [12] [13] [14] [46] [47] [48] . Detection of human bocavirus in children with upper respiratory tract infection by polymerase chain reaction Detection of bocavirus in children suffering from acute respiratory tract infections in Saudi Arabia Detection of human bocavirus from children and adults with acute respiratory tract illness in Guangzhou, southern China Clinical relevance of human bocavirus with acute respiratory tract infection and diarrhea in children: a prospective case-control study Frequent detection of bocavirus DNA in German children with respiratory tract infections Human bocavirus infection in children with acute respiratory tract infection in India Human bocavirus in children with acute respiratory infections in Vietnam Human bocavirus infection in young children with acute respiratory tract infection in Lanzhou
cord-272878-6f0q661e	2011	In the two academic hospitals, Saint-Louis hospital (SLS) in Paris and Tours hospital (TRS), influenza-like illness (ILI) was defined as a patient suffering from at least one general symptom (fever above 38uC, asthenia, myalgia, shivers or headache) and one respiratory symptom (cough, dyspnoea, rhinitis or pharyngitis), in agreement with the guidelines from the French Institut de Veille Sanitaire (InVS), a governmental institution responsible for surveillance and alert in all domains of public health [12] . Two hundred and twelve were positive for non influenza pathogens (189 single infections and 23 mixed infections with two, three or four viruses) and three additional single infections by influenza A were identified in SLS, including two by pandemic H1N1v and one by seasonal H3N2, as determined after molecular typing (data not shown). As RHV was the most frequent aetiology in ILI, we also compared clinical symptoms observed in patients with a single infection by RHV or by H1N1v (data not shown).
cord-273620-gn8g6suq	2012	
cord-274007-zndtddty	2020	
cord-274127-12x5cc8i	2014	Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The detection rates of respiratory viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real‐time multiplex RT‐PCR. The aim of this study was to compare the detection rates of respiratory viruses in paired nasopharyngeal swabs and sputum samples from adult patients with respiratory symptoms using multiplex real-time RT-PCR. The present study found that the overall detection rate from sputum samples in adults was significantly higher than from nasopharyngeal swabs using multiplex real-time RT-PCR. In conclusion, the detection rates of respiratory viruses from sputum samples are significantly higher than those from nasopharyngeal swabs in adults using multiple real-time RT-PCR.
cord-274749-ji91qq9q	2015	
cord-274763-i6e3g3te	2018	
cord-274900-s7ft1491	2019	title: Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study Whilst epidemiology and clinical features of viral respiratory tract infections (VRTIs) were mainly explored in children and outpatients [7, 8] , a few data show increasing prevalence rates also in hospitalized patients, particularly in elderly and in presence of comorbidities such as asthma, chronic obstructive pulmonary disease or immunosuppression [9] [10] [11] . CAP was defined as acute lower respiratory tract infection characterized by the presence of two or more signs and symptoms (among fever, cough, dyspnoea, pleuritic pain, crackles or bronchial breath at pulmonary auscultation), associated with at least one among (a) radiological findings (opacity or infiltrate at radiography or computed tomography interpreted as pneumonia by the attending physician), (b) serum levels of inflammatory markers above normal values and (c) neutrophilic leucocytosis, in patients hospitalized no longer than 48 h [1] .
cord-275166-qduf08kp	2018	Adenovirus was the most prevalent virus (50%; n = 81), followed by influenza virus (45.68%, n = 74), rhinovirus (40.12%; n = 65), enterovirus (25.31%; n = 41), and respiratory syncytial virus (16.05%; n = 26), whereas Streptococcus pneumoniae (17%; n = 29), Moraxella catarrhalis (15.43%; n = 25), and Haemophilus influenzae (8.02%; n = 13) were the most commonly isolated bacteria. Respiratory tract infections (RTIs) such as acute otitis media, sinusitis, bronchitis, and community-acquired pneumonia are a leading cause of infectious disease-related morbidity, hospitalization, and mortality among children worldwide, particularly in low-income countries. 1 According to World Health Organization (WHO), the prevalence of hospitalized children under 5 years with acute respiratory infections (ARIs) is estimated to be 20% and 90% of those were due to pneumonia. 4, 5 However, primary infections with viral pathogens can predispose to secondary bacterial infections, and the most frequently isolated bacteria in ARIs include Streptococcus pneumonia and Haemophilus influenzae.
cord-275512-7yik78yc	2015	
cord-275605-mbiojk39	2018	METHOD: The MEDLINE/PubMed and Scopus databases were searched for all relevant papers published prior to February 2018 that evaluated the prevalence of clinical symptoms of respiratory infections, including pneumonia, among Hajj pilgrims, as well as their influenza and pneumococcal vaccination status. We carried out a systematic review of cohort and hospital studies that reported the prevalence of clinical symptoms of respiratory infections and pneumonia among pilgrims during the Hajj, and both their influenza and pneumococcal vaccination status, with the aim to provide data allowing the investigation of the impact of this large mass-gathering event on public health policies and services and to identify potential targets for preventive measures. For inclusion, the article had to meet the following criteria: (1) Original study involving Hajj pilgrims; (2) detailed description of the study population, including influenza and pneumococcal vaccination status when available; (3) clinical or self-reported respiratory symptoms and diseases.
cord-275828-c6d6nk7x	2016	-SBT/ABPC, intravenous drip, 3 g/3e4 times a day -CTRX, intravenous drip, 1 g/twice a day or 2 g/once a day -CTX, intravenous drip, 1e2 g/2e3 times a day -LVFX, intravenous drip, 500 mg/once a day (2) Cases of late-onset hospital-acquired pneumonia or ventilator-associated pneumonia in which the risk of resistant bacteria is high An antimicrobial drug with anti-pseudomonal activity that targets non-glucose-fermentative gram-negative rod should be administered [50, 51, 68] -To treat polymicrobial infection, the administration of an antimicrobial drug with an activity against obligate anaerobe is not always necessary [67, 70] . -SBT/ABPC, intravenous drip, 3 g/3e4 times a day -CTRX, intravenous drip, 2 g/once a day or 1 g/twice a day -CTX, intravenous drip, 1e2 g/2e3 times a day -LVFX, intravenous drip, 500 mg/once a day (2) Late-onset hospital-acquired pneumonia or cases in which there is a risk of multi-drug-resistant bacteria In addition to the above pathogens, the involvement of non-glucose-fermentative gram negative bacteria or ESBLproducing enteric bacteria must be considered. For the treatment of immunodeficiency-/blood disease-related pneumonia in children, antimicrobial drug therapy should also be basically selected, considering causative microorganisms.
cord-276005-ifn88mjd	2012	We investigated the clinical impact of human coronaviruses (HCoV) OC43, 229E, HKU1 and NL63 in pediatric patients with cystic fibrosis (CF) during routine and exacerbation visits. The proportion of cases with acute respiratory exacerbation among patients infected with different HCoV species was compared by χ 2 or Fisher exact tests. The identification of new species of HCoV [7, 8] and the emergence of SARS HCoV [6] highlighted the potential role of these viruses as causative agents of severe lower respiratory tract infections. However, most of the studies on the clinical impact of different HCoV species were only performed among children who were hospitalized for acute respiratory tract infections, with small sample sizes and short periods of sample collection [10] . New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia
cord-276348-vr5fit8r	2004	
cord-276927-rxudwp2v	2012	Rapid administration of antibiotics and resuscitative measures in case of sepsis and septic shock associated with protective ventilatory strategies and early short-term paralysis associated with differential ventilatory techniques (recruitment maneuvers with adequate positive end-expiratory pressure titration, prone position, and new extracorporeal membrane oxygenation techniques) in severe ARDS can help improve its prognosis. Incorporation of modified risk factors such as acute increase of respiratory rate, presence of tachypnea, detection of pulse oximeter desaturation, increased necessity of oxygen supplementation, presence of low pH, acidosis, or hypoxemia in an arterial blood gas sample in clinical practice can improve the clinicians'' ability to perform early diagnosis and prompt therapeutic intervention in ARDS [17] .
cord-277276-j2qzhvzi	2014	
cord-277327-il8uaavn	1997	
cord-278031-vpq4yghn	2013	3 Clinicians are often unaware of the presence of more than one pathogen, although co-infections of bacteria 4 or other respiratory viruses 5 and infl uenza are well described, as are bacterial, viral, or parasitic infections with pulmonary tuberculosis. Global scientifi c and political attention is currently focused on two new viruses associated with severe RTIs and high mortality: the avian infl uenza A H7N9 virus from China and novel coronavirus from the Arabian Peninsula. 11 Although several new rapid molecular diagnostic plat forms capable of simultaneously identifying both pathogens and the genetic determinants of anti microbial resistance are emerging, 12 they do not seem to be well suited to clinical presentations or downstream manage ment strategies for patients with RTIs. Furthermore, none can identify new emerging organisms for which genetic sequences are unavailable.
cord-278935-3lgud7l8	2014	title: Clinical and epidemiological profiles of lower respiratory tract infection in hospitalized children due to human bocavirus in a subtropical area of China Furthermore, epidemiological data shows that HBoV is present year-round with different incidence rates from 2.2% to 19% in children with lower respiratory tract infection [Manning et al., 2006; Weissbrich et al., 2006; Allander et al., 2007; Canducci et al., 2008] . The purpose of this study was to ascertain the frequency, seasonal, and clinical characteristics in hospitalized children with lower respiratory tract infection and evaluate the effects of meteorological factors on the incidence of HBoV in a subtropical region of China. Based on the data from this study, HBoV was the third most common pathogen after RSV and Mycoplasma pneumoniae with an incidence of 6.6% in all hospitalized children with lower respiratory tract infection in Suzhou area.
cord-279257-a7d9a2w1	2008	
cord-279421-rxocrgfu	2016	
cord-280732-u0pncmp0	1976	
cord-280857-0o1ikwks	2020	This review summarizes practical strategies for achieving lung and diaphragm-protective targets at the bedside, focusing on inspiratory and expiratory ventilator settings, monitoring of inspiratory effort or respiratory drive, management of dyssynchrony, and sedation considerations. Several strategies can be used to facilitate lung and diaphragm protective ventilation, including modulation of ventilator inspiratory and expiratory assist, drugs that modify respiratory drive and/or effort, extracorporeal CO 2 removal (ECCO 2 R) and electrical stimulation of the respiratory muscles, as shown in Fig. 2 . [7] also showed that higher ECCO 2 R support reduced P 0.1 , respiratory muscle effort, and transpulmonary pressure in spontaneously breathing patients recovering from severe ARDS [74] . These preliminary findings suggest that partial neuromuscular blockade could be a feasible approach to achieving lung and diaphragm-protective ventilation targets in patients with high respiratory effort.
cord-281051-i229xv0o	2017	This protocol outlines our process for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. This paper outlines a protocol for conducting a systematic review to investigate whether associations between ARI and seasonal or meteorological parameters differ between Indigenous and non-Indigenous groups residing in the same geographical region. This research builds from the United Nations Declaration of the Rights of Indigenous Peoples [13] understanding of the term Indigenous peoples, which states that an Indigenous person self-identifies as Indigenous; has historical continuity Table 1 Inclusion and exclusion criteria for a systematic literature review investigating the impact of seasonal and meteorological parameters on acute respiratory infection (ARI) in Indigenous and non-Indigenous peoples
cord-281085-lqniqui0	2006	As the pathological cough (especially its chronic form) has significant impact on patient''s quality of life, observed either in physical activity or psychosocial domain, various treatment attitudes are used for different forms of cough (acute, subacute, chronic, productive, nonproductive, psychogenic, asthma-associated, or painful). The most important defensive reflex of the airways is cough, which, together with the mucociliary transport system, forms the main mechanism for cleaning of the respiratory tract (Korpas and Nosalova, 1991; Chung and Chang, 2002; Belvisi and Geppetti, 2004) . Although respiratory-modulated receptors play an important role in the function of the upper airways, they are not generally viewed as a primary factor in the elicitation of cough reflex. The antitussive activity of these agents is associated with their ability to lower the sensitivity of the cough center to nerve impulses coming from airways receptors (Fox, 1996b) .
cord-281418-mvgp6qfv	2010	The aim of this study was to assess the association among the presence of a respiratory virus detected by molecular assays in bronchoalveolar lavage (BAL) fluid, respiratory symptoms, and acute rejection in adult lung transplant recipients. Upper (nasopharyngeal swab) and lower (BAL) respiratory tract specimens from 77 lung transplant recipients enrolled in a cohort study and undergoing bronchoscopy with BAL and transbronchial biopsies were screened using 17 different polymerase chain reaction—based assays. The present investigation was specifically designed to assess the epidemiology of respiratory viruses in bronchoalveolar lavage (BAL) fluid from lung transplant recipients and to analyze the relationship between these viruses and the presence of acute graft rejection. Because BAL fluid specimens were collected for a variety of clinical conditions, we were able to analyze the association among symptoms, the diagnosis suspected by the physician in charge, and the subsequent presence of a proven upper and/ or lower respiratory tract viral infection.
cord-281754-auqh3vtr	2017	As a human virus the range of disease is broad, from cold like to severe multisystem involvement (These CoV infections are associated with short incubation periods (2-7 days), such as those found in SARS [2, 5, 6, 17, 18, 24, 25] . The etiology causing his illness was identified as severe acute respiratory syndrome coronavirus (SARS CoV); it was likely transmitted to at least 10 additional persons. Other pathogens, including members of the Paramyxoviridae family, and human metapneumovirus (hMPV) were considered as causative of this new clinical illness which became known as Severe Acute Respiratory Syndrome or SARS. Genomic sequence analysis seems to support the hypothesis that of SARS-CoV is an animal virus for which the normal host is still unknown and that developed the ability to productively infect humans or has the ability to cross species barriers [25] .
cord-281916-v6u5mr2i	2016	
cord-282303-idh7io9v	2019	With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. Respiratory viral and bacterial pathogens, including Staphylococcus aureus, Streptococcus pyogenes, influenza viruses, respiratory syncytial virus, adenovirus, rhinoviruses and novel coronavirus strains, can survive on hospital surfaces for days, weeks or even months. This study identified that hospital surfaces in these Bangladeshi hospitals, were frequently contaminated with respiratory pathogens and pose a potential threat for fomite-borne transmission of respiratory infections to patients, healthcare workers and family caregivers.
cord-282420-0fcyjw7l	2020	key: cord-282420-0fcyjw7l authors: Lu, Cheng-wei; Liu, Xiu-fen; Jia, Zhi-fang cord_uid: 0fcyjw7l On Jan 22, Guangfa Wang, a member of the national expert panel on pneumonia, reported that he was infected by 2019nCoV during the inspection in Wuhan. Unprotected exposure of the eyes to 2019nCoV in the Wuhan Fever Clinic might have allowed the virus to infect the body. 4 Severe acute respiratory syndrome coronavirus (SARSCoV) is predominantly transmitted through direct or indirect contact with mucous membranes in the eyes, mouth, or nose. 5 The fact that exposed mucous membranes and unprotected eyes increased the risk of SARSCoV transmission 4 suggests that exposure of unprotected eyes to 2019nCoV could cause acute respiratory infection. The respiratory tract is probably not the only transmission route for 2019nCoV, and all ophthalmologists examining suspected cases should wear protective eyewear. *Cheng-wei Lu, Xiu-fen Liu, Zhi-fang Jia The severe acute respiratory syndrome
cord-282533-w6kl74c8	2018	METHODS: Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. CONCLUSIONS: FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3429-6) contains supplementary material, which is available to authorized users. The aim of this study was to evaluate the application of FilmArray RP for the detection of respiratory organisms, and to provide information about the seasonality and prevalence of these organisms in pediatric patients with RTIs in a large children''s hospital in China.
cord-282668-bs634hti	2017	In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenzalike Illness cases. From January 2012 to December 2015 we collected specimens (nasal-pharyngeal and oral-pharyngeal swabs) and surveillance data for influenza and other viral respiratory pathogens from outpatients presenting with influenza-like-illness (ILI) at different sentinel sites in Senegal. So the circulation of such HAdV genome types in Senegal emphasizes the need to reinforce HAdV surveillance, especially in hospitalized patients, by including HAdV genome detection and genotyping in the documentation of severe respiratory infections. Molecular epidemiology of human adenovirus isolated from children hospitalized with acute respiratory infection in São Paulo, Brazil
cord-282867-kbyxdegu	2020	The main aim of this study is to review and summarize the evidence regarding the supportive role of physical rehabilitation techniques in managing COVID-19-associated pneumonia. In this review, we also emphasize the use of rehabilitation techniques in the management of pneumonia in COVID-19-infected patients. The purpose of this study was to review the evidence regarding the supportive role of treatment options available in physical rehabilitation to manage COVID-19 pneumonia effectively. Evidence strongly supports that many rehabilitation techniques including chest physiotherapy and physical therapy modalities can be of great support to manage COVID-19-associated pneumonia [9, 10] . Common problems identified in COVID-19 patients that could be managed by rehabilitation specialists in the postacute phase include musculoskeletal pain, joint pain, reduced range of motion, muscular weakness, neuropathy and myopathy, pulmonary dysfunction, dysphagia, dyspnea, confusion, and impaired activities of daily living.
cord-283399-iz4l9i0d	2006	This study was carried out to further the available information on adult cases of human metapneumovirus (hMPV), a recently described cause of respiratory infection. For adults presenting with respiratory symptoms and a background of pre-existing respiratory disease or who are immunocompromised, nucleic acid-based techniques are a cost-effective means of making the viral diagnosis in a clinically relevant time frame. In young children and elderly patients hMPV is most commonly associated with a clinical diagnosis of bronchiolitis or bronchitis, respectively, whereas in middle-aged adults, it may produce an influenza-like illness, which can be complicated by pneumonitis in the presence of immunocompromising factors [5] . This retrospective observational study reviewed all cases of hMPV detected in patients over 18 years of age, from the time the RT-PCR method was adopted in July 2003 through to January 2005.
cord-283604-fqc9jp0l	2015	To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. The comparison results of the penton base, hexon, and fiber gene sequences between the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and the strains from the GenBank database indicated significant conservation and stability of the sequences within the genome across time and space.
cord-283910-k10j5dzd	2017	Recent advances in laboratory diagnostic methods confer to the identifi cation of different viruses as etiologic pathogens of bronchiolitis, although respiratory syncytial virus (RSV) remains the main culprit The aim of this review was to present the clinical picture of bronchiolitis as a whole entity irrespective of the virology as well as in relation to the particular viral parthogens that are incriminated as etiological factors. We searched the databases with the following key words: viral bronchiolitis, clinical features, definition, epidemiology, etiology, guidelines, severity score, adenovirus, bocavirus, coronavirus, influenza, metapneumovirus, parainfluenza, respiratory synchytial virus, and rhinovirus. In 2006 American Academy of Pediatrics (AAP) published a clinical practice guideline for bronchiolitis, [3] that was updated in 2014 [4] according to which bronchiolitis is "a constellation of signs and symptoms including children younger than 2 years including a viral upper respiratory tract prodrome followed by increased respiratory effort and wheezing".
cord-284266-tbndldhr	2020	Our results indicated that infants with more severe bronchiolitis disease, caused by RSV-A infection, present significant perturbations of both the nasal microbiota structure and the microbial relationships. Evaluation of α diversity by the Shannon and Simpson indexes, as well as the number of observed OTUs, showed a significant lower biodiversity in the RSV-positive group with respect to the virus-negative one, suggesting the presence of a microbial shifts in the nasal microbiota of RSV-positive subjects (Figure 1a) . Evaluation of α diversity by the Shannon and Simpson indexes, as well as the number of observed OTUs, showed a significant lower biodiversity in the RSV-positive group with respect to the virus-negative one, suggesting the presence of a microbial shifts in the nasal microbiota of RSVpositive subjects (Figure 1a) . The main aim of the present study was to characterize the nasal microbiota in pediatric patients hospitalized for bronchiolitis from RSV and in infants affected by bronchiolitis but negative for a respiratory virus.
cord-284332-p4c1fneh	2012	[47] Although both of these studies were conducted prior to the 1994 AECC definition, ARDS was strictly defined in the aforementioned studies, including a PaO 2 /FiO 2 ratio <150 or intrapulmonary shunt >20% in patients requiring mechanical ventilation and who had diffuse infiltrates on chest radiograph without clinical evidence of heart failure as pulmonary arterial occlusion pressures were <18 mmHg. Building on the results of these two studies, Sinuff and colleagues [48] developed practice guidelines for prophylactic ketoconazole use, and tested the implementation and efficacy of these guidelines in two ICUs (one control and one active comparator). [119] A phase II study enrolling 98 patients with ALI compared an antioxidant enteral feeding formula containing eicosapentaenoic acid, g-linolenic acid and antioxidant vitamins with placebo, and observed improved oxygenation, reduced pulmonary inflammation, fewer days of mechanical ventilation and fewer non-pulmonary organ failures in the treatment arm, although there was no difference in mortality between this approach and the control group.
cord-284372-v95fzp8n	2004	title: A touchdown nucleic acid amplification protocol as an alternative to culture backup for immunofluorescence in the routine diagnosis of acute viral respiratory tract infections To overcome this problem we developed a diagnostic molecular strip which combined a generic nested touchdown protocol with in-house primer master-mixes that could recognise 12 common respiratory viruses. CONCLUSIONS: The touchdown protocol with pre-dispensed primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses which were negative by immunofluorescence. To test the feasibility of its routine use we needed to clinically validate its performance in a routine setting on specimens tested in parallel with our standard immunofluorescence protocol for the diagnosis of acute virus respiratory infections. In conclusion the use of the touchdown protocol with pre-dispensed and quality checked primer master-mixes was suitable for replacing virus culture for the diagnosis of respiratory viruses for immunofluorescence negative specimens.
cord-284858-hrljsc8l	2013	
cord-284889-hth8nf5b	2013	Previous studies have shown that respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and human enterovirus infections may be associated with virus-induced asthma. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma. More than 200 different types of viruses are known to cause ARI, with respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), and human parainfluenza virus (HPIV) most commonly identified in ARI patients. In this review, we focus on molecular epidemiological studies of respiratory viruses, including RSV, HRV, HMPV, and HPIV infections, associated with virus-induced asthma. Thus, both the antigenicity of the viruses and host immune conditions may play important roles in the pathophysiology of severe respiratory infections such as bronchiolitis, pneumonia, and virus-induced asthma (Awomoyi et al., 2007) .
cord-284905-h8xovybl	2008	Background and objective: To investigate the association between serological evidence of past infections with common respiratory pathogens and lung function in members of an isolated community of Aborigines from tropical coastal north‐western Australia. 3 Studies of members of an isolated coastal Australian Aboriginal community in the tropical Kimberley region of Western Australia have shown that levels of lung function measured by FEV1 and FVC were lower than those of Australians of European descent. In this tropical Aboriginal community, serological evidence of the burden of previous infections with known viral and other respiratory pathogens was associated with significant decreases in the levels of airway function, consistent with airflow obstruction. The relationship of FEV1 and FEV1/FVC ratio with the total number of positive titres in this study suggests that repeated infections with common respiratory pathogens may have a cumulative detrimental effect on airway function or increase susceptibility to other agents such as tobacco smoke.
cord-285096-g9y3au1a	2013	Following experimental infection in dogs, all five CRCoV isolates gave rise to clinical signs of respiratory disease consistent with that observed during natural infection. Following experimental infection in dogs, all five CRCoV isolates gave rise to clinical signs of respiratory disease consistent with that observed during natural infection. In that study we demonstrated that young dogs were susceptible to experimental infection with both CRCoV isolates, which gave rise to clinical signs of respiratory disease consistent with naturally occurring infection. Analyses specifically focused on the histopathological changes in the canine upper and lower respiratory tissues, virulence differences among CRCoV isolates derived from CIRD cases representing wide geographical locations; UK and USA [MO, NE, UT and MI] , and the demonstration of Koch''s postulates. Consistent with observations made during naturally occurring infection, dogs in this study also displayed clinical signs of mild respiratory disease following viral challenge (nasal discharge, sneezing, and coughing); whilst the control group remained healthy.
cord-285557-my16g91c	2004	
cord-285587-rggfg60a	2015	
cord-286337-qk90xb3a	2018	While the effects of these alterations on risk of secondary bacterial pneumonia have not been studied, potential mechanisms by which these changes might modulate susceptibility to secondary bacterial infections include alterations in the nature and magnitude of the immune response in the host (microbiome on host effects) and facilitating growth of pathogens in the absence of normal commensals (inter-microbial effects). Given the effects of viruses on enhancing bacterial adherence to the epithelium (86) (87) (88) , it is perhaps not surprising that multiple studies of human subjects as well as in animal models have shown that viral infections are associated with increased colonization by potentially pathogenic bacteria (known as "pathobionts"). Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included; however, the authors suggested that flu is associated with an expansion of Proteobacteria (109) which is generally less abundant in healthy hosts.
cord-286443-t0asknzu	2013	title: Home Self-Collection of Nasal Swabs for Diagnosis of Acute Respiratory Virus Infections in Children With Cystic Fibrosis In the current study, we investigated the feasibility of home self-collection of NS in children with CF experiencing onset of new respiratory illness, with samples mailed to a central laboratory for respiratory virus detection by real-time PCR. If respiratory illness with onset of symptoms in the previous 7 days was present at a clinic visit, subjects were first asked to blow their nose to remove mucus that might inhibit PCR, and paired swabs were obtained as follows: a deep nasal (mid-turbinate) sample was collected by research staff, by first measuring from the opening of one naris to the nasal bridge, and then inserting a standard flexible nasopharyngeal flocked nylon swab (Copan Diagnostics Inc, Murrieta, CA; catalog No. 503CS01) until mild resistance was encountered, approximately one-half to two-thirds the length of the nose.
cord-286449-ekvzaae2	2008	A respiratory virus was detected in 37% of exacerbations, 12% of stable COPD patients and 12% of non-obstructed smokers, p < 0.0005. Studies using serology and viral culture identified respiratory viruses in 30% of patients during acute exacerbations of COPD. 8 The hypothesis tested in the present study was that acute respiratory viral infection is implicated in the pathogenesis of COPD exacerbations. The detection rate of respiratory viruses during exacerbations of COPD in this study (37%) is comparable to results obtained by Seemungal 9 Lower detection rates may be related to time of sampling as patients presenting to hospital had developed symptoms for a median of 5 days prior to admission. 21 However, several of the patients were seen at different time points during this study and the same virus was not detected by repeat sampling suggesting that those testing positive using the PCR screen were experiencing an acute viral infection.
cord-286472-pqtem19t	2020	This newly identified respiratory viral illness was caused by a novel coronavirus, which was initially designated as human betacoronavirus (2) (3) (4) (5) , but was eventually named Middle East Respiratory Syndrome Coronavirus (MERS CoV). It is important to consider multisystem function as well as pulmonary status in patients with severe respiratory illness, including suspected MERS CoV, especially those returning from regions where aggressive pathogens are noted. Patients recently returning from the Middle East, presenting with significant respiratory illness, with CT findings of peribronchial region abnormalities, organizing pneumonia, should be considered for MERS CoV infection, and if possible, queried about international travel and occupational exposures. Middle East Respiratory Syndrome Coronavirus (MERS CoV) Infection Feasibility, safety, clinical and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol
cord-286602-cdueeg47	2020	
cord-286924-zk7hzcla	2017	
cord-286930-c1zkjdgf	2014	
cord-287156-3plpi6i9	2020	Among the seven coronaviruses that affect humans (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV, and the most recent coronavirus disease 2019 (COVID-19) represent potential life-threatening diseases worldwide. Children appear to be less susceptible to develop severe clinical disease and present usually with mild and aspecific symptoms similar to other respiratory infections typical of childhood. 8, 9 Additionally, three HCoVs responsible for outbreaks involving high case fatality rates have been detected in humans in the last two decades: the severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the new coronavirus disease 2019 (COVID-19) ( Table 1) . Principal features of severe acute respiratory syndrome (SARS)-CoV, the Middle East respiratory syndrome (MERS)-CoV and the most recent coronavirus disease 2019 (COVID19) . Clinical features and viral diagnosis of two cases of infection with Middle East Respiratory Syndrome coronavirus: a report of nosocomial transmission
cord-287178-hu6vlc9u	2015	
cord-289050-9w7ks01n	2008	
cord-289139-5ljqnc39	2014	title: The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit BACKGROUND: The use of a multiplex molecular technique to identify the etiological pathogen of respiratory viral infections might be a support as clinical signs are not characteristic. OBJECTIVES: The aim of the study was to evaluate a multiplex molecular real-time assay for the routine diagnosis of respiratory viruses, to analyze the symptoms associated with the pathogens detected and to determine the spread of virus during the period. This assay can detect 15 viruses: influenza viruses (IV) types A and B, parainfluenza viruses 1 to 4 (PiV), respiratory syncytial viruses A and B (RSV), rhinovirus (RV), coronaviruses 229E, OC43 and NL63 (CoV), human metapneumovirus (MPV) and adenovirus (ADV). RSV and RV were the most prevalent pathogens, particularly in the youngest children, and co-infections were associated with more severe respiratory symptoms.
cord-289282-4oz6r7op	2020	title: Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS‐CoV. Clinical presentations and outcome of severe acute respiratory syndrome in children Clinical features, diagnosis, treatment and short-term outcome of severe acute respiratory syndrome (SARS) in children Severe acute respiratory syndrome (SARS) in children: epidemiology, presentation and management Screening for Middle East respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study Middle East respiratory syndrome coronavirus in pediatrics: a report of seven cases from Saudi Arabia The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China Comparative analysis of eleven healthcare-associated outbreaks of Middle East respiratory syndrome coronavirus (Mers-Cov) from 2015 to 2017 Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS
cord-289697-g24xib4l	2005	
cord-290505-omszep7u	2019	
cord-291217-fpte1q9m	2009	The most recent Cochrane review of 22 trials involving 1428 infants with bronchiolitis who received inhaled bronchodilators (including β 2 agonists, ipratropium and adrenergic agents) reported a significant improvement in overall average clinical score, but had no effect on either pulse oximetry measurements or on risk of hospitalization. However, a recent placebo-controlled study of montelukast in 53 infants with a first episode of bronchiolitis demonstrated absence of benefit, with no significant differences in length of hospitalization, clinical severity score, or inflammatory mediators between the two groups. Fluids (either enteral or parenteral) and oxygen are the mainstays, although cpap or mechanical ventilation are effective for respiratory failure • there is no role for bronchodilators, corticosteroids, antiviral agents, physiotherapy, nebulized dnase or antibiotics, but nebulized 3% hypertonic saline administered with a bronchodilator may decrease length of stay in hospital
cord-291618-166wvdbt	2013	Viral respiratory tract infections (VRTI) are an important cause of morbidity and mortality in patients with hematologic malignancies, particularly in allogeneic haematopoietic stem cell transplantation (HSCT) recipients [1] [2] [3] . The symptoms of VRTI were divided into three main categories, and the rate of positive virological results was as follows: ILI 38 % (25 out of 65), fever only 30 % (9 out of 30) and upper VRTI symptoms 22 % (15 out of 67) (Fig. 1) Six patients had pneumonia; thus, BAL was performed and four viruses were detected (co-pathogens are reported in Table 2 ): one influenza A, two RSV and one coronavirus. Prospective study of the incidence, clinical features, and outcome of symptomatic upper and lower respiratory tract infections by respiratory viruses in adult recipients of hematopoietic stem cell transplants for hematologic malignancies
cord-291639-hioh2s35	2007	Many epidemiological and clinical studies have suggested a role for respiratory viral infections in the natural history of chronic obstructive pulmonary disease (COPD), particularly during their exacerbations highlighting the need for development of effective vaccines and/or treatment for these viruses. In this review we will provide an overview of the relationship between respiratory virus infection and the molecular mechanisms involved in the activation of airway infl ammation in COPD exacerbations. It has been postulated that bacterial colonization could contribute to increased susceptibility to viral infection in COPD patients for example by increasing ICAM-1 expression in bronchial epithelial cells either directly or through induced infl ammation (Sajjan et al 2006) . Despite growing clinical evidence for a role of respiratory viral infections in the pathogenesis of COPD exacerbations, the precise mechanisms of respiratory virus-induced airway infl ammation and of host defenses against respiratory viruses are poorly understood (Johnston 2005) .
cord-291961-usl8z6ep	2015	METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Previous studies have indicated that a number of HPyVs are associated with human diseases, such as progressive multifocal leukoencephalopathy (JCPyV), hemorrhagic cystitis (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV) [3, 7, 9, [17] [18] [19] . Because initial infections with most HPyVs occur in infancy, the prevalence of HPyV6 in NPAs from children was detected with real-time PCR. The detection rate for HPyV6 by real-time PCR assay was 1.7 % in 887 NPA samples collected from hospitalized children with RTI.
cord-292261-gh9cifjr	2020	
cord-292587-hp4zd8lr	2017	We expect that the development of technologies that overcome the existing challenges in current respiratory protective devices will lead to a timely and effective response to the next outbreak. We expect that the development of technologies that overcome the existing challenges in current respiratory protective devices will lead to a timely and effective response to the next outbreak. While effective management and availability of control measures are crucial to an outbreak response, the pathogens [ 1 1 4 _ T D $ D I F F ] (virus/bacteria/ fungi) captured on filters are an intrinsic concern because of fear of cross-infection, new aerosol release, and contaminated waste. Hence, production of a filter that inactivates the collected pathogens would bring key improvements to current surgical masks and respirators, resulting in increased protection, reduced risk of cross[ 1 0 9 _ T D $ D I F F ] -infection, and recyclability without decontamination ( Figure 1 ).
cord-292828-29jbf9ik	2014	title: Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies. Importantly, when using highly sensitive polymerase chain reaction (PCR) assays the detection rates for respiratory viruses are similar in both anterior nasal swab specimens and samples collected by the more traditional method of nasopharyngeal aspiration [18, 19] . The ORChID project is an ongoing comprehensive community-based study using PCR assays to detect respiratory viruses in anterior nasal swab specimens taken weekly by parents from their infants throughout the first 2-years of life.
cord-292836-1o2ynvy3	2020	In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus. By contrast SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic in humans, with high rates of severe pneumonia and fatal outcomes [21] . A large prospective surveillance study conducted in Norway from 2006 to 2015 that enrolled all hospitalized children aged ≤16 years with respiratory tract infections revealed that HCoVs OC43 and NL63 were detected most frequently and were epidemic every second winter [35] . Large surveillance studies of children and adults to evaluate the prevalence of all major respiratory viruses using multiplex PCR have been conducted in many settings, showing that HCoV infections are the fourth or sixth most common virus detected overall and across all age groups [33, 43] .
cord-292871-vgposxom	2015	
cord-293354-55nawxos	2016	title: Viral etiology of severe acute respiratory infections in hospitalized children in Cameroon, 2011–2013 This study was conducted to gain new insights into the timeliness of virus circulation and viral etiology among children aged ≤15 years, hospitalized for SARI. hBoV occurred intermittently all over the study period, while the prevalence of remaining viral etiologies was low, ranging from 0 to 5 positive samples per month for each virus, numbers which appeared insufficient to allow for the description of seasonal patterns. Viral etiology of hospitalized acute lower respiratory infections in children under 5 years of age -a systematic review and meta-analysis Viral etiology of acute lower respiratory tract infections in hospitalized young children in Northern Taiwan Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years
cord-293897-p30wz7b7	2020	14,15 Many immunocompromised adults with PIV infection first present with symptoms of mild upper respiratory tract disease, but in contrast to RSV, influenza, and HMPV, detection of PIV-1 and PIV-3 in asymptomatic HCT recipients is relatively common, reported in 6 of 17 (35%) infection episodes in a prospective study. In immunocompromised hosts, including hematopoietic cell transplant recipients, solid organ transplant recipients, and oncology patients, respiratory viruses can be associated with significant clinical manifestations, including prolonged viral shedding, lower respiratory tract disease, the need for supplemental oxygen, late airflow obstruction, and even death. In immunocompromised hosts, including hematopoietic cell transplant recipients, solid organ transplant recipients, and oncology patients, respiratory viruses can be associated with significant clinical manifestations, including prolonged viral shedding, lower respiratory tract disease, the need for supplemental oxygen, late airflow obstruction, and even death.
cord-294062-3esrg1jw	2018	
cord-294155-94skyx5f	2007	
cord-294544-iutcduix	2007	1 This has enabled the identification of many viruses, including those commonly causing respiratory infections -influenza, RSV, PIV 1-4, adenoviruses, measles, enteroviruses, rhinoviruses, VZV, CMV and HSV. 3 After 24-72 h of culture, using pooled or single fluorescein isothiocyanate (FITC)-labelled monoclonal antibodies directed against influenza A and B, RSV, parainfluenza 1-3 and adenoviruses, rapid identification of a respiratory virus infection can be established. Diagnosis of rhinovirus infection rarely requires laboratory testing but virus isolation, detection of viral RNA by RT-PCR, antigen detection by DIF in cells from respiratory secretions or detection of a fourfold rise in antibody titres by neutralization test or EIA can be performed if required. Diagnosis of the specific cause of an acute pneumonia due to a particular viral agent is complicated by difficulty in obtaining appropriate lower respiratory tract samples for culture and in isolating or detecting certain pathogens, and additionally by the frequent asymptomatic shedding of some viruses, e.g. herpes simplex virus or adenoviruses.
cord-294568-12eyo13f	2017	
cord-294933-oc2glu4a	2020	The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The document provides clinical recommendations for the noninvasive respiratory support (noninvasive ventilation, high flow oxygen therapy with nasal cannula) in any patient with suspected or confirmed presentation of COVID-19 with acute respiratory failure. The present document has been developed by consensus among the scientific societies involved in acute respiratory failure in adult patients, and seeks to provide a more detailed description of the recommendations on the use of non-invasive respiratory support (NIRS) in the management of acute respiratory failure (ARF) secondary to infection by the newly emergent SARS-CoV-2 coronavirus, which causes so-called COVID-19 disease, as a complement to the information emitted by the Spanish Ministry of Health, Consumer Affairs and Social Wellbeing (Ministerio de Sanidad, Consumo y Bienestar Social [MSC]), 1,2 which is frequently updated and establishes a series of general recommendations.
cord-295074-fsbp4fky	2013	Rates of respiratory virus-associated hospitalization in children aged <5 years in rural northern India Introduction Acute respiratory infections are recognized as an important cause of mortality, hospitalization, and healthcare utilization in young children globally. 17e20 Using data from population-based surveillance of approximately 9500 children for hospitalizations for acute medical illness in rural northern India and concomitant testing for respiratory viruses by real-time reverse transcription polymerase chain reaction (rRT-PCR), we estimate the incidence of respiratory virus-associated hospitalizations among children aged <5 years. Incidences were also calculated for children aged <6 months for RSV and influenza since maternal immunization with RSV and Among the 98 children with respiratory virus-associated illness, history of fever (82%) and cough (69%) were the most commonly reported symptoms. RSV and influenza viruses circulated with clearly defined but different seasonality and were infrequently detected among children without fever or respiratory symptoms or signs, similar to prior studies.
cord-295189-bz3gi15h	2015	STUDY DESIGN: Data were collected from travellers arriving at Christchurch International Airport, New Zealand, during the winter 2008, via a symptom questionnaire, temperature testing, and respiratory sampling. CONCLUSIONS: The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptotology to influenza, has important implications for any screening strategies for the prediction of influenza in airline travellers. In a 2008 study, we sought to assess the prevalence of influenza infection in symptomatic and asymptomatic arriving international airline travellers and whether using a symptom-screening questionnaire and temperature measurement could reliably predict seasonal influenza infection [16] . The high prevalence of respiratory virus infections caused by viruses other than influenza in this study, many with overlapping symptoms to influenza, has important implications for any screening strategy for the prediction of influenza in airline travellers.
cord-296605-p67twx7a	2004	title: Management of Critically Ill Patients with Severe Acute Respiratory Syndrome (SARS) Most SARS patients would require high flow oxygen supplementation, 20–30% required intensive care unit (ICU) or high dependency care, and 13–26% developed acute respiratory distress syndrome (ARDS). The management of critically ill SARS patients requires timely institution of pharmacotherapy where applicable and supportive treatment (oxygen therapy, noninvasive and invasive ventilation). More than onethird of all the SARS patients required high flow oxygen therapy [4] , 20-30% required intensive care unit (ICU) admission or high dependency care, and 13-26% developed acute respiratory distress syndrome (ARDS) [5, 6] . Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China Evaluation of non-invasive positive pressure ventilation in treatment for patients with severe acute respiratory syndrome Clinical observation of non-invasive positive pressure ventilation (NIPPV) in the treatment of severe acute respiratory syndrome (SARS)
cord-296777-6xz2aslj	2009	title: Fatal lower respiratory tract disease with human corona virus NL63 in an adult haematopoietic cell transplant recipient Community-acquired respiratory viruses are known to account for many cases of interstitial pneumonia as a common complication following allo-haematopoietic cell transplantation (HCT). 7 We present a case of fatal HCoV NL63 pulmonary infection during the late-engraftment phase, 5 months after an allo-HCT with a matched unrelated donor in a patient without active GVHD and receiving only modest immune suppressive treatment. The BAL fluid at day 11 of admission and the final PCR analysis post mortem were negative for HCoV NL63, suggesting that the patient had cleared the virus. Although evaluation for corona virus in symptomatic HCT patients is not routinely performed, we believe it should be considered in the differential diagnoses of respiratory failure or as a possible causative agent before the development of IPS after allo-HCT for haematological disease.
cord-296836-aizquh16	2020	We assessed the prevalence of vitamin D insufficiency and deficiency, defined by 25-hydroxyvitamin D (25(OH)D) blood levels of 30–50 and <30 nmol/L, respectively, and their association with mortality from respiratory diseases during 15 years of follow-up in a cohort of 9548 adults aged 50–75 years from Saarland, Germany. Vitamin D insufficiency and deficiency are common and account for a large proportion of respiratory disease mortality in older adults, supporting the hypothesis that vitamin D(3) supplementation could be helpful to limit the burden of the COVID-19 pandemic, particularly among women. We previously assessed the prevalence of vitamin D insufficiency and deficiency and their association with all-cause mortality and mortality from cardiovascular, cancer and respiratory diseases during a mean follow-up of 9.5 years in a cohort of 9548 adults aged 50-75 years from Saarland, Germany [4] [5] [6] [7] [8] .
cord-299379-ch7a39d6	2019	title: Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy() The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs. Acute respiratory tract infections (ARTIs) are a persistent public health problem (Lu et al., 2013) . This three-year (October 2012-September 2015) hospital-based survey in Parma (Northern Italy) aimed to determine the prevalence of respiratory virus infections, their seasonality, and any patterns of mixed infections in children with ARTIs by using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays.
cord-299835-92karhpl	2004	title: Mild Illness Associated with Severe Acute Respiratory Syndrome Coronavirus Infection: Lessons from a Prospective Seroepidemiologic Study of Health-Care Workers in a Teaching Hospital in Singapore Participating HCWs completed a questionnaire and provided paired serum samples, which were analyzed by 2 different laboratories blinded to clinical data, by use of an enzyme-linked immunosorbent assay based on a protocol developed by the Centers for Disease Control and Prevention and a dot-blot immunoassay, with confirmation by a viral neutralization assay. Of the 372 HCWs participating in the present study, 8 were found to have positive antibodies to the SARS coronavirus in both samples by use of both test methods, and 6 had pneumonia and had been hospitalized for either probable or suspected SARS infection, whereas 2 had fever but did not have changes on chest radiographs.
cord-299952-xvtt8fz8	2010	title: A randomized controlled trial of low-dose recombinant human interferons α-2b nasal spray to prevent acute viral respiratory infections in military recruits To assess the efficacy and safety of a low-dose recombinant human interferon α-2b (rIFNα-2b) nasal spray in preventing acute viral respiratory infections in military population, we performed this randomized controlled trial. To evaluate the efficacy and safety of this new nasal spray in preventing acute respiratory infections in military population, we performed this randomized, placebo-controlled, double-blind trial. In summary, this randomized controlled trial suggested that the recombinant human interferon ␣-2b nasal spray can be used to prevent common acute viral respiratory infections caused by Flu-A, Flu-B, PIV1-3 and ADV and was generally well tolerated among military recruits. The efficacy of preventing viral respiratory infections by the rIFN␣-2b nasal spray should be evaluated further in different population groups, such as children and the elderly, and more samples should be involved in the further study.
cord-300019-8vxqr3mc	2019	We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Although influenza virus (Flu) is the most widely recognized viral infection associated with respiratory illness, >25 viruses have been linked to pneumonia, causing a substantial disease burden in adults and elderly individuals. Therefore, we aimed to conduct a similar systematic review to identify all case-control studies since 1996 investigating the potential role of respiratory viruses in the etiology of ARIs in older adults aged ≥65 years.
cord-300116-r93w4jm3	2014	METHODS: We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing. In this study, our aim was to determine whether a viral infection-related bacterial profile exists in the respiratory tract and evaluate any disparities in the microbiota structure that develops depending on the infectious virus species. The microbiota profiles of healthy-adult and patient groups also differed in the relative composition of the microbiome, which was highlighted in the graph showing the abundant bacterial genera observed in the tested samples ( Figure 2 and Additional file 3: Figure S2 ).
cord-300510-fhpkdqr0	2020	7. Perform early intubation if poor response to continuous positive airway pressure in terms of oxygenation: do not trust patients'' relatively good respiratory mechanics and feeling of improved dyspnoea, since these patients may have relatively normal lung compliance and the only clinical sign of fatigue may be high respiratory rate. As soon as possible according to gas exchanges (PaO 2 /FiO 2 > 150 with FiO2 < 50%) and lung ultrasound score (≤ 12), start assisted ventilation with a sigh while maintaining moderate to high positive end-expiratory pressure to prevent derecruitment. Abbreviations SARS-CoV-2: Severe acute respiratory syndrome coronavirus 2; ICU: Intensive care unit Assessment of lung aeration and recruitment by CT scan and ultrasound in acute respiratory distress syndrome patients Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China The authors read and approved the final manuscript.
cord-300711-yibdumij	2014	This study was performed to detect viruses in children with respiratory infections and describe their epidemiology and clinical characteristics. Methods: In this descriptive cross sectional study, throat swabs and wash specimens from 202 children younger than six years of age with diagnosis of a respiratory tract infection from a total of 897 specimens were evaluated using multiplex PCR method. Results: Respiratory viruses were detected in 92 children: respiratory synsytial virus, 16.8%; influenza virus, 5.4%; parainfluenza virus, 8.4%; adenovirus, 14.4% and human metapneumo virus 0.49% with male predominance and higher distribution in children younger than 1 year of age with preference in the cold months of year. In this study, AdVs followed by RSV were the most frequently detected viral agents in our patients (14.4%) which occurred mostly in the summer and winter months (August, September and February) in male children in all age groups.
cord-301011-xbuqd0j5	2020	In line with international initiatives, this article aims to provide guidance and detailed recommendations for hospital-based physical therapists managing patients hospitalized with COVID-19 through a national approach in the Netherlands. A working group conducted a purposive scan of the literature and drafted initial recommendations based on the knowledge of symptoms in patients with COVID-19, and current practice for physical therapist management for patients hospitalized with lung disease and patients admitted to the intensive care unit (ICU). 12 In line with this international study 12 and the consensus statement of Italian respiratory therapists 13 we aim to provide guidance and detailed recommendations for hospital-based physical therapists managing patients hospitalized with COVID-19 through a national approach in the Netherlands. Physical therapist management for patients hospitalized with COVID-19 comprises elements of respiratory support and active mobilization. Physical therapist management for patients hospitalized with COVID-19 comprises elements of respiratory support and active mobilization.
cord-301254-093yih5n	2010	OBJECTIVES: The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. CONCLUSIONS: Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates. All patients still positive for the same agent on follow-up had a higher Ct-value (corresponding to a lower Table 2 Follow-up (10 ± 2 days after initial visit) test result from analysis with real-time PCR of nasopharyngeal/throat swab specimens.
cord-301988-cevv81h3	2015	BACKGROUND: The purpose of this study was to determine the seasonal variance of potentially pathogenic bacterial and viral organisms in nasopharyngeal specimens obtained from asymptomatic health care professionals (HCPs) during the 2014 winter and summer months. Although asymptomatic HCPs certainly harbor a number of different potentially infectious agents, future studies are needed to determine whether colonized pathogens are transmitted or initiate infection in at-risk patient populations. Here, we describe the frequency and seasonal variation of bacterial and viral detections in asymptomatic health care professionals (HCPs) during the winter and summer months of 2014. 4 By elucidating changes in pathogen colonization rates in asymptomatic HCPs during different time periods in the year, health care organizations can monitor which potentially pathogenic agents are most prevalent in carriers in a health care setting and observe correlations with infection levels in at-risk hospitalized patients.
cord-302111-kg0dmgq0	2020	Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Given the rapidly emerging pandemic associated with the novel severe acute respiratory syndrome coronavirus 2 causing coronavirus disease 2019, it is important to review the clinical presentation and immunologic changes associated with viral pneumonia. Key Words: coronavirus; immunology; influenza virus; severe acute respiratory syndrome; viral pneumonia P neumonia is the leading infectious cause of hospitalization among adults and children in the United States (1) . Given the rapid spread of this virus and its association with severe pulmonary disease, the purpose of this review is to provide an overview of the presentation and immunology of viral pneumonia, principles of early management, and application to COVID-19.
cord-302833-6kntd89t	2016	BACKGROUND: Although N95 filtering facepiece respirators and medical masks are commonly used for protection against respiratory infections in healthcare settings, more clinical evidence is needed to understand the optimal settings and exposure circumstances for healthcare personnel to use these devices. Healthcare personnel who work in outpatient settings will be cluster-randomized to wear N95 respirators or medical masks for protection against infections during respiratory virus season. Abbreviations ARI, acute respiratory illness; CDC, centers for disease control and prevention; DSMB, data safety monitoring board; HAI, hemagglutination inhibition antibody; HCP, healthcare personnel; ILI, influenza like illness; LCRI, Laboratory confirmed respiratory illness; MM, medical mask; N95, N95 respirator; NIOSH, National Institute for Occupational Safety and Health; OSHA, Occupational Safety and Health Administration; PPE, occupational protective equipment; ResPECT, respiratory protection effectiveness clinical trial; RPD, respiratory protective devices; RT-PCR, reverse-transcriptase polymerase chain reaction; US, United States.
cord-303040-ha8gufh8	2015	In the event of an outbreak of an acute febrile illness of a highly infective nature in facilities used by a young adult group, RSV should be considered among the possible causative agents. Recent studies indicate that RSV is an important cause of respiratory infection in elderly patients, either those with compromised immunity or inflicted with chronic illness, as well as in adult populations in a special environment, such as military personnel [7] [8] [9] [10] [11] . A case patient was a person, among military recruits in this boot camp, who was admitted to the medical care center in the boot camp with chief complaints of fever and symptoms of upper respiratory tract illness after May 26, 2011. In the event of an epidemic of acute febrile respiratory illness of a highly infective nature, it is recommended to conduct a test for RSV in the young adult population in the military facilities.
cord-303299-p15irs4e	2020	The infection caused by the human corona virus COVID-19 (SARS-CoV2) resulted in a worldwide pandemic affecting several million people and causing severe disease and fatality mostly based on virus mediated lung failure [1, 2] . However, epidemics with respiratory virus such as not only influenza but also human corona viruses are prevalent in the Northern hemisphere over several months during the cold season and then disappear whereas influenza remains prevalent in tropical regions throughout the whole year [5] [6] [7] . The grey lines indicate seasons where no specific pandemic respiratory infections are recorded. If COVID-19 would behave similar to other respiratory viruses causing respiratory infections including human corona viruses which peak during winter time and early spring, there is hope that the COVID-19 pandemic can be slowed down by this seasonal trend [7, 9] . However, pandemics with new viruses such as the influenza H1N1v can circulate independent of typical respiratory viral seasons throughout the whole year [10] .
cord-303322-d69o3z8d	2011	Our randomised, placebo-controlled trial of azithromycin in Indigenous infants hospitalised with bronchiolitis is designed to determine whether it can reduce short-term (and potentially long-term) morbidity from respiratory illness in Australian Indigenous infants who are at high risk of developing chronic respiratory illness. Indigenous infants (aged ≤ 24-months, expected number = 200) admitted to one of two regional hospitals (Darwin, Northern Territory and Townsville, Queensland) with a clinical diagnosis of bronchiolitis and fulfilling inclusion criteria are randomised (allocation concealed) to either azithromycin (30 mg/kg/dose) or placebo administered once weekly for three doses. Indigenous infants (aged ≤ 24-months, expected number = 200) admitted to one of two regional hospitals (Darwin, Northern Territory and Townsville, Queensland) with a clinical diagnosis of bronchiolitis and fulfilling inclusion criteria are randomised (allocation concealed) to either azithromycin (30 mg/kg/dose) or placebo administered once weekly for three doses.
cord-303606-ypkia5x1	2011	We performed a prospective cohort study from September 2003 to December 2004 to delineate attributing the effect of different respiratory viral infections including newly discovered ones to asthma exacerbations in children in Hong Kong. Plausible explanations for much lower virus detection rate than previously reported include improved personal hygiene and precautionary measures taken during respiratory tract infections in the immediate post-severe acute respiratory syndrome period together with a significant contribution of other adverse factors like environmental air pollution. Plausible explanations for much lower virus detection rate than previously reported include improved personal hygiene and precautionary measures taken during respiratory tract infections in the immediate post-severe acute respiratory syndrome period together with a significant contribution of other adverse factors like environmental air pollution. Thus, we carried out a prospective study to delineate the current role of different viral respiratory tract infections including newly discovered respiratory viruses in asthma exacerbation in children in our locality.
cord-303935-qdehf6rb	2015	title: Changes in Clinical Presentation and Epidemiology of Respiratory Pathogens Associated With Acute Respiratory Illness in Military Trainees After Reintroduction of Adenovirus Vaccine The Center for Advanced Molecular Detection at Joint Base San Antonio-Lackland prospectively collects demographic, clinical, and polymerase chain reaction data from respiratory specimens (throat swab and nasal wash) among Air Force trainees presenting for care of ARI. Acute respiratory illness in military trainees post-VI is associated with decreased severity of systemic symptoms and reduced fever and heart rate. The purpose of this study was to evaluate (1) changes in clinical presentations of ARI pre-and post-VI, and (2) reductions in proportions of disease due to Ad. We also sought to further evaluate for evidence of nonvaccine type serotype shift and to determine whether the frequencies of common non-Ad respiratory pathogens have changed after VI, in trainees presenting for care of ARI, which have not previously been described in the published literature.
cord-304876-txaoz7oh	2018	42 Viral polymerase: An important molecular target for antiviral therapy Nucleoside analogs represent one of the dominant classes of antiviral agents due to their widespread use against the common chronic infections caused by human immunodeficiency virus (HIV), hepatitis B virus, and herpesviruses. 43 After being metabolized by host kinases to their triphosphate form, antiviral nucleotides compete with natural nucleoside triphosphates (NTPs) to bind to the active site of viral polymerases and alter DNA or RNA synthesis. 122 However, the results summarized here indicate that nucleoside analogs targeting the viral RNA polymerase of rhinovirus, EV71, and other enteroviruses have the potential to be efficacious in preclinical animal models, providing a rationale to conduct human studies with safer molecules sharing the same mode of action. Structure and functional analysis of the RNA-and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein
cord-306266-8qdrshz3	2014	Other factors that have been studied include: ■ air pollution -There is an association between air pollution and aggravation of existing asthma ■ allergen avoidance -There is no consistent evidence of benefit ■ breast-feeding -There is evidence of a protective effect in relation to early asthma ■ electrolytes -There is no consistent evidence of benefit ■ fish oils and fatty acid -There is no consistent evidence of benefit ■ house dust mites -Measures to reduce the numbers of house dust mites do not affect asthma severity ■ immunotherapy -Allergenspecific immunotherapy is beneficial in allergic asthma ■ microbial exposure -There is insufficient evidence to indicate that the use of probiotics in pregnancy reduces the incidence of childhood asthma ■ modified milk formulae -There is no consistent evidence of benefit pets -There are no controlled trials on the benefits of removing pets from the home ■ tobacco -Exposure to cigarette smoke adversely affects quality of life, lung function, need for rescue medications and longterm control with inhaled steroids.
cord-306278-c4q4la5c	2016	To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. To evaluate the circulation of the different HAdV types and the possible relationship between viral load, viral genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children consecutively attending the Emergency Room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection. However, further studies are needed to identify the potential pathogenetic role of the different species and types of HAdV and the importance of viral load in the severity of infection.
cord-306315-vt2e0crh	2020	CONCLUSIONS: Viruses are frequently identified in the respiratory tract of HIV-infected patients with acute respiratory failure that requires ICU admission, but with a non-viral copathogen in two-thirds of cases. Indeed, using nucleic acid amplification test such as multiplex polymerase chain reaction (mPCR), these pathogens have been shown highly prevalent (20-56%) in large cohorts of adult patients admitted to the ICU for all-cause ARF [7, 8] , community-acquired pneumonia [9, 10] , hospitalacquired pneumonia [11] , acute exacerbation of COPD [12, 13] , and asthma [14] , compared to asymptomatic adults [15, 16] . We investigated whether a respiratory virus-associated infection Table 2 Causative diagnosis of acute respiratory failure in 123 HIV-infected patients admitted to the ICU Data are presented as number (%). Viruses are frequently identified in the respiratory tract of HIV-infected patients with ARF that required ICU admission, but with a non-viral copathogen in two-thirds of cases.
cord-306411-dutbxfl4	2017	title: Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital This retrospective cohort study aimed to determine the etiological agents responsible for respiratory tract infections by Anyplex II RV16 detection kit (RV16, Seegene), involving 2266 pediatric patients with respiratory infections admitted to the Department of Pediatrics at King Abdul-Aziz Medical City, Ministry of National Guard, Riyadh, from July 2014 to June 2015. Different studies reported the detection of viruses like human respiratory syncytial virus A (RSV A), human respiratory syncytial virus B (RSV B), human adenovirus (AdV), Human metapneumovirus (HMPV), human coronavirus, and human parainfluenza virus (PIV). This study aimed to determine the distribution of 16 different viruses causing respiratory infections in children, by using RV16, and to compare data on demographic characteristics, symptoms, and single infections or coinfections.
cord-306450-sh2mrhoq	2019	The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. where coinfections were the most frequent cause of the respiratory infections in the studied group and followed by RV/EV and influenza A/B, respectively ( Figure 1B ). In our study, the age relation was significant for RSV and HMPV which were detected in 89% (260 of 292) and 81% (84 of 104) of children under 5 years, respectively. Similar to RSV, HMPV infections were frequently seen in winter and spring months as it was the case in our study while 90% of the HMPV cases were detected between January and April. Epidemiologic analysis of respiratory viral infections mainly in hospitalized children and adults in Midwest University Medical Center after the implementation of a 14-virus multiplex nucleic acid amplification test
cord-306480-wgl4zrnb	2020	BACKGROUND: Respiratory syncytial virus (RSV) is a common cause of severe respiratory illness in young children (< 5 years old) and older adults (≥ 65 years old) leading the World Health Organization (WHO) to recommend the implementation of a dedicated surveillance in countries. AIM: We tested the capacity of the severe acute respiratory infection (SARI) hospital network to contribute to RSV surveillance in Belgium. CONCLUSION: With only marginal modifications in the case definition and the period of surveillance, the Belgian SARI network would be able to substantially contribute to RSV surveillance and burden evaluation in children and older adults, the two groups of particular interest for WHO. Nevertheless, the SARI case definition we used, even with a less strict fever criterion, allowed to follow RSV circulation in the children population aged < 5 years and to identify comorbidities/indicators potentially associated with disease severity.
cord-307261-0a3iztns	2012	title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Two broadly multiplexed PCR systems were compared to each other and to a panel of laboratory developed tests for the detection of respiratory viral pathogens in clinical respiratory tract specimens from pediatric immunocompromised children. FilmArray detected viral targets: adenovirus, bocavirus, coronavirus 229E, HKU1, NL63, OC43, enterovirus, hMPV, human rhinovirus, influenza virus types A and B, parainfluenza viruses 1, 2, 3 and 4, and RSV. The current study, to our knowledge, is the first reported that compares the FilmArray with the ResPlex II v2.0 for the direct detection of viral agents in clinical respiratory tract specimens from immunocompromised children.
cord-307874-0obomty2	2020	Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity.
cord-308201-lavcsqov	2019	Viruses infecting human CNS cells could then cause different types of encephalopathy, including encephalitis, and long-term neurological diseases. Even though no clear cause and effect link has ever been made with the onset of human neurological diseases, their neuropathogenicity is being increasingly recognized in humans, as several recent reports associated cases of encephalitis [244] , acute flaccid paralysis [271] and other neurological symptoms, including possible complications of HCoV infection such as Guillain-Barré syndrome or ADEM [249, [272] [273] [274] [275] [276] [277] [278] [279] . Like for several other respiratory viruses, accumulating evidence now indicate that HCoV are neuroinvasive in humans and we hypothesize that these recognized respiratory pathogens are potentially neurovirulent as well, as they could participate in short-and long-term neurological disorders either as a result of inadequate host immune responses and/or viral propagation in the CNS, which directly induces damage to resident cells.
cord-308979-qhlvd2mt	2005	BackgroundInfections with common respiratory tract viruses can cause high mortality, especially in immunocompromised hosts, but the impact of human metapneumovirus (hMPV) in this setting was previously unknown MethodsWe evaluated consecutive bronchoalveolar lavage and bronchial wash fluid samples from 688 patients—72% were immunocompromised and were predominantly lung transplant recipients—for hMPV by use of quantitative real-time polymerase chain reaction (PCR), and positive results were correlated with clinical outcome and results of viral cultures, in situ hybridization, and lung histopathological assessment ResultsSix cases of hMPV infection were identified, and they had a similar frequency and occurred in a similar age range as other paramyxoviral infections. Each patient with high titers of hMPV exhibited a complicated clinical course requiring prolonged hospitalization ConclusionsOur results provide in situ evidence of hMPV infection in humans and suggest that hMPV is a cause of clinically severe lower respiratory tract infection that can be detected during bronchoscopy by use of real-time PCR and routine histopathological assessment
cord-309120-05bg7rfa	2020	title: The role of respiratory droplet physicochemistry in limiting and promoting the airborne transmission of human coronaviruses: A critical review() Airborne transmission is an accepted potential route for the spread of some viral infections (measles, chickenpox); however, aerosol features and infectious inoculum vary from one respiratory virus to another. This critical review identifies studies reporting instances of infected patients producing airborne human pathogenic coronaviruses, and evidence for the role of physical/chemical characteristics of human-generated droplets in altering embedded viruses'' viability. Based on previous literature, healthy subjects can produce particles between 0.01 The aerosols generated through speech, coughing, sneezing, and breathing have been 178 surveyed in several studies (Table 1) 290 Hygroscopic salts influence the transport of water vapor, and allow for humidity dependent 359 droplet sizes as described by Köhler theory (Köhler, 1936) . Measurements of airborne influenza virus in 839 aerosol particles from human coughs Measurements of airborne influenza virus in 839 aerosol particles from human coughs
cord-310508-zgqbfmzl	2020	This report to World Health Organization (WHO), raised global public health concern because this is the third coronavirus âȂŞassociated acute respiratory illness outbreak. Clinical care of patients with suspected 2019-nCoV should focus on early recognition, immediate isolation (separation), implementation of appropriate infection prevention and control (IPC) measures and provision optimized supportive care. Both the health care worker (HCW) and the suspected case of acute respiratory illness (ALI) should wear a medical mask and the patient should better be directed to a separate area, an isolation room if available. At the time being, emergency preparedness and response for providing appropriate care to the patients suspected to coronavirus-associated acute respiratory illness (abovementioned plans) should be developed and implemented in the emergency departments, as the frontline of treating human infections of 2019-nCov in the hospitals. Clinical management of severe acute respiratory infection when novel coronavirus (2019-nCoV) infection is suspected: interim guidance
cord-311275-ysr9nqun	2019	There were a few data of adult hospitalized patients with RSV infection, with high complications, in Thailand; [3, 12, 13] however, additional clinical data are required for planning patient management and also disease prevention in this region. RSV, respiratory syncytial virus; ARI, acute respiratory illness; COPD, chronic obstructive pulmonary disease; HAP, hospital-acquired pneumonia; VAP, ventilator-associated pneumonia. The pre-existing coronary arterial disease (CAD) was the risk factor of overall cardiovascular complications in hospitalized adult patients with RSV infection with odds ratio 6.18, (95% CI 1.18-32.5), p = 0.03, adjusted for age, sex, HT, DLP, DM, pre-existing CHF, arrhythmia, and VHD. The prospective study of all adult hospitalized patients with acute respiratory illness should be conducted to determine the prevalence, clinical manifestations, and outcomes of the virus. Most of the adult hospitalized patients with RSV infections aged ≥ 50 years old and had pre-existing cardiopulmonary diseases, hematologic malignancy, immunocompromised hosts, and DM.
cord-312024-qdgqif5j	2010	The increasing availability of new rapid and sensitive molecular diagnostics such as polymerase chain reaction testing, should provide more accurate and timely diagnoses of viral respiratory infections in older adults in the near future. This article summarizes what is known about the diagnosis of viral respiratory diseases in elderly adults, with the hope of increasing understanding of the utility and limitations of the currently available diagnostic tests for viral respiratory pathogens, such as culture, rapid antigen testing, polymerase chain reaction (PCR) testing, and serologic analysis. Compared with previous studies that have used viral culture for diagnosis, studies using PCR have more accurately detected the presence of viruses (including influenza virus, RSV, hMPV, parainfluenza virus, rhinoviruses, and coronaviruses) in the lower respiratory tract illness in older adults [5, 13, 31, 36, 40, 42] .
cord-312613-1nl7q6cy	2016	Respiratory viral infections, particularly respiratory syncytial virus (RSV) and rhinovirus, are the most importance risk factors for the onset of wheezing in infants and small children. The association between bronchiolitis caused by RSV and the development of recurrent wheezing and/or asthma was first described more than 40 years ago, but it is still unclear whether bronchiolitis causes chronic respiratory symptoms, or if it is a marker for children with a genetic predisposition for developing asthma in the medium or long term. In the Childhood Origins of Asthma (COAST) study, which followed a cohort of 289 newborns with high risk of developing asthma, lower respiratory tract infection associated with rhinovirus was the main risk factor for presenting recurrent wheezing at 3 and 6 years of life, with an odds ratio of 10 for rhinovirus bronchiolitis compared to 2.6 for RSV bronchiolitis. 3 found that 80% of asthma exacerbations in asthmatic children aged 9-11 years were associated with viral respiratory infection, of which two thirds were caused by rhinovirus.
cord-312615-q333qgps	2019	The aim of this study was to identity the various respiratory pathogens causing acute respiratory tract infections in children below 5 years of age visiting a sub-urban primary care clinic in Senegal. CONCLUSIONS: This case-control study in a primary care setting in sub-Saharan Africa found influenza virus A and B, RSV, and S pneumoniae to be the main causes of acute respiratory tract infections in children below 5 years of age. Therefore, the aim of this case-control study was to investigate the prevalence of the different viruses and bacteria colonizing the airways and their association with the occurrence of ARTIs and severity of disease in children less than 5 years of age, visiting a sub-urban primary care clinic in Dakar, Senegal. This case-control study investigates the prevalence of the different viruses and bacteria colonizing the airways and their 6 Microbiology Insights association with the occurrence of ARTIs in children visiting a sub-urban primary care clinic in Senegal.
cord-312691-ynh84b98	2016	title: Predictors of MERS-CoV infection: A large case control study of patients presenting with ILI at a MERS-CoV referral hospital in Saudi Arabia BACKGROUND: A case control study to better characterize the clinical features, laboratory, and radiological abnormalities associated with MERS-CoV infection in order to help with early identification of this syndrome from other respiratory infections. METHODS: Eighty patients admitted to a hospital in Riyadh, diagnosed with MERS-CoV infection based on RT-PCR were matched on age, sex, and the presence of a co-morbid condition on a basis of 1:2 to other patients admitted with respiratory symptoms and tested negative for MERS-CoV on RT-PCR. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Laboratory-confirmed case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection in Malaysia: preparedness and response Middle East Respiratory Syndrome Coronavirus: a case-control study of hospitalized patients
cord-312741-0au4nctt	2020	160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein
cord-312797-hohzjx74	2004	Despite the fact that prospective and case-control studies have been limited, the epidemiology and clinical manifestations associated with hMPV have been found to be reminiscent of those of the human respiratory syncytial virus, with most severe respiratory tract infections occurring in infants, elderly subjects, and immunocompromised hosts. In addition, studies have shown that hMPV is not a new pathogen, with serological evidence of human infection dating from 1958 in The Netherlands [4] and viral isolation for the past 10-20 years in Europe and Canada [4, 7] . Symptoms of both upper and lower respiratory tract infections have been associated with hMPV in young children, although most reports are biased towards description of the most severe symptomatology in hospitalized subjects. Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups
cord-312928-ef8hqs4s	2008	title: Viral Upper Respiratory Tract Infection and Otitis Media Complication in Young Children [1] conducted a large, longitudinal observational study of children with upper respiratory infection and examined for otitis complicationeither acute otitis media or otitis media with effusion. Indeed, in this study, the rate of respiratory syncitial virus infection was found to be low, probably as a result of the method used (conventional assays, type of molecular technique, RT-PCR vs. In this study, children aged !1 year and those who attended day care centers had a greater risk of acquiring upper respiratory tract infection and otitis media, compared with older children and those who were cared for at home. This article is important, especially because the rate of complications of otitis in upper respiratory tract infection was longitudinally studied. Viral upper respiratory tract infection and otitis media complication in young children Rates of hospitalisation for influenza, respiratory syncytial virus and human metapneumovirus among infants and young children
cord-312952-9gbb4own	2020	While the majority of studies indicate that the detection rate of respiratory viruses in patients with asthma and healthy subjects is similar [10] , they have been found to differ with regard to the bacterial composition of the airways [11] . This technique was chosen for the present study, to test the hypothesis that elderly patients with asthma display a different profile of respiratory pathogens in the airways as compared to non-elderly asthmatics, and that this profile may be related to local airway and/or systemic inflammation. This study is the first to use the IS technique to compare detection rates of respiratory pathogens in the airways of elderly and non-elderly patients with asthma. Although the detection rate and profile of respiratory viruses in IS was similar in elderly and non-elderly patients with asthma, the presence of pathogens was associated with some clinical characteristics only in older subjects.
cord-313749-f2ct57em	2007	title: Multiplex real-time PCR for detection of respiratory tract infections STUDY DESIGN: An assay targeting influenza virus A (IfA) and B (IfB), parainfluenza 1-3 (PIV), human metapneumovirus (MPV), respiratory syncytial virus (RSV), rhinovirus (RV), enterovirus (EV), adenovirus (AdV), human coronaviruses (229E, OC43, NL63), M. We developed a real-time PCR procedure, based on automated specimen extraction and multiplex amplification, at a relatively low cost (D 33). We believe that a combination of low cost, high accuracy and prompt result delivery is the key to achieving a wide clinical use of molecular diagnostics of respiratory infections. Further studies of respiratory infection aetiologies in different patient categories, and of the clinical utility of this and similar multiplex assays, need to be carried out. Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4
cord-314190-fvdock94	2017	The evidence and guideline recommendations consistently support a clinical diagnosis with the limited role for diagnostic testing for children presenting with the typical clinical syndrome of viral upper respiratory infection progressing to the lower respiratory tract. 24, 25, 27, 29, 30 Studies have investigated whether severity of illness, as measured by need for hospital admission, length of hospital stay, intensive care unit admission, repeated emergency department visits, and apnoea, is associated with specifi c viral infections or co-infections, but the evidence is confl icting. Recent studies suggest that higher respiratory syncytial virus genomic load, measured using quantitative PCR, might be associated with increased length of stay, use of respiratory support, and need for intensive care, in addition to recurrent wheezing, compared with lower viral loads. Systematic literature review assessing tobacco smoke exposure as a risk factor for serious respiratory syncytial virus disease among infants and young children
cord-314841-b5l6epy3	2019	Analysis of the host transcriptional response during respiratory viral infection using in-vitro, animal models and natural and experimental human challenge have furthered the understanding of the mechanisms and predictors of severe disease and may identify potential therapeutic targets to prevent and ameliorate illness. In addition to sensitive and rapid diagnostic testing, new molecular techniques allow an understanding of viral evolution, mechanisms and predictors of severe disease, interrogation of vaccine responses, improved bacterial and viral diagnostics and associations of viral infections with non-respiratory medical events. A number of candidate genes influencing respiratory virus susceptibility have been identified in animal and human studies and involve host virus interactions, innate immune signaling, interferon related pathways and cytokine responses (Table 1) [49] [50] [51] [69] [70] [71] [72] [73] [74] [75] . In addition, two compartments, the respiratory epithelium and blood can be sampled in human studies and interrogated using different viruses or viral strains to develop gene signatures for prognosis, as indicators of severity and to identify potential therapeutic targets.
cord-315037-lmur80te	2020	We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. 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. For children with respiratory symptoms and with a clinical suspicion of virus infection, a test for RSV antigen test, human parainfluenza virus (PIV) type 3 antigen test, viral PCR for enterovirus, or viral cultures was prescribed by the judgment of pediatricians. The following multiplex PCR assays were performed for each sample to detect RNA/DNA of 15 respiratory viruses, including RSV A or B, FluA, FluB, human enterovirus (EV), MPV, human parainfluenza virus types 1-4, human rhinovirus (RV), coronavirus OC43/NL63/229E, human adenovirus (ADV), and human bocavirus (Boca). The present study demonstrates that PCR has higher detectability for respiratory viruses compared to traditional antigen tests and viral cultures.
cord-315339-dcui85lw	2015	Although neutralizing antibodies directed against the HA globular head are highly efficient at preventing and clearing influenza virus infection, they can also FIGURE 3 In the memory phase, migratory lung DCs capture viral antigen retained on follicular DCs (FDCs) in tertiary lymphoid organs and present it to specific T cells in the respiratory draining lymph nodes. This explains why passively transferred IgG is effective at preventing severe disease from respiratory infections in experimental animals and why serum IgG antibodies are the main correlate of protection for parentally administered inactivated influenza vaccines in humans (Section Respiratory Virus Vaccines). Nasal administration of influenza vaccine with type I IFN was effective at inducing serum antigen-specific IgG2a and mucosal IgA antibody responses and at providing full protection against influenza virus challenge (Proietti et al., 2002) .
cord-315598-qwh72inx	2020	De otorgarse un Consentimiento Informado amplio, éste debería ser única y exclusivamente para los procesos asociados con COVID-19".(71) AMCI ® Se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de COVID-19 sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( Manejo de secreciones -Tratamiento del dolor -Tratamiento de la disnea -Sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. En cuanto hace referencia a la situación actual de pandemia por SARS-CoV-2 y compromiso pulmonar; Wu y cols, en Marzo de 2.020 realizaron un estudio retrospectivo de 201 pacientes con COVID-19 en China; para aquellos pacientes que desarrollaron SDRA, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte (23/50 [46%] con esteroides vs 21/34 [62%] sin esteroides; HR, 0.38 [IC 95%, 0.20-0.72]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes (400).
cord-315934-h70j2jmt	2019	During July 2007–June 2015, we enrolled 4,225 hospitalized children with pneumonia in a study to determine the seasonality of respiratory syncytial virus (RSV) infection in Beijing, China. R espiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection in young children worldwide (1-3); 2.7-3.8 million hospitalizations and 94,600-149,400 deaths occur each year among children <5 years of age as a result of RSV infection (4) . Several previous studies reported an RSV prevalence of 17%-33% among children with severe acute respiratory illness (15, 16) , but few have assessed the seasonality or trends of RSV infections in China. A sharp decrease in sample number and samples positive for RSV were observed each year during this event, resulting in a bimodal distribution curve ( Figure 1, During the study, 335 (8%) hospitalized children with pneumonia were admitted into the PICU, and 8 died (median age 1.4 years, range 4 months-13 years).
cord-315949-7id5mitl	2013	8, 9 The purpose of this study was to describe during a limited period of time the viral etiology of acute lower respiratory infections (ALRI) in patients hospitalized in two Lao hospitals by using a set of five multiplex RT-PCR/PCR targeting 18 common respiratory viruses. In this study, we report for the first time in Lao PDR the viral etiologies in patients hospitalized for ALRIs. We identified 186 respiratory viruses in 162 (55%) patients of all ages using 5 multiplex PCR/RT-PCR. Human respiratory syncytial virus is frequently defined as the predominant virus associated with hospitalizations for ALRI in children aged ≤5 years. Respiratory virus coinfections being frequent, 5, 19, 44 it demonstrates the usefulness of the multiplex RT-PCR approach, which allows the detection of the most important viruses in only few reactions while multiple infections are often undetected in viral culture or by direct immunofluorescence.
cord-316727-ktrlohm9	2014	title: Treatment and prevention of acute respiratory infections among Iranian hajj pilgrims: a 5-year follow up study and review of the literature Background Respiratory diseases/syndromes are the most common causes of referring to physicians among pilgrims in Hajj. The main aim of our study was to determine types, frequencies, etiologies, and epidemiologic factors of respiratory diseases among Iranian Hajj pilgrims and to suggest some preventive and treatment strategies. The aim of our study was to determine types, frequencies, etiologies, and some of other epidemiologic factors of respiratory diseases among Iranian Hajj pilgrims and to suggest some preventive and treatment strategies based on our 10 years of experience and literature review. We used the results of above mentioned studies and reviewed the literature, and offered a guideline for the treatment and prevention of acute respiratory infections (ARIs) in Hajj.  Significant difference values of NBT test before and after travel showed that respiratory diseases of pilgrims might have infectious origins.
cord-316956-nnqi0dj1	2016	title: Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico Respiratory syncytial virus (RSV) is the major infectious cause of lower respiratory tract illness in infants and young children around the world. 11 In the present study, 570 cases of RSV infection identified during four epidemic years in Mexico were evaluated to clarify the epidemiology of this infection and to assess the possible variations in demographic and clinical characteristics according to viral groups. 6 In this report, we analyzed the characteristics of 570 patients (399 children and 171 adults) with confirmed RSV infection included in the study during a 4-year period. Epidemiological and clinical data of hospitalizations associated with respiratory syncytial virus infection in children under 5 years of age in Spain: FIVE multicenter study Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico
cord-317619-o7qfugjw	2016	While the overall incidence of respiratory virus infection, in particular RSV and influenza A (H1N1) virus, leading to lower respiratory tract disease is widely studied (12, 13), the frequency of progression to pediatric ARDS has yet to be clearly determined. While post-pandemic studies suggest a decrease in influenza A (H1N1) virus disease severity and burden (20, 21), it continues to be a significant cause of severe illness and pediatric ARDS (22). In RSV infection, development of lower respiratory track disease in premature infants, with or without chronic neonatal lung disease is associated with a significantly higher risk of hospitalization, intensive care unit admission, need for mechanical ventilation, and death (12, [70] [71] [72] [73] . Disease severity and viral load are correlated in infants with primary respiratory syncytial virus infection in the community Motavizumab treatment of infants hospitalized with respiratory syncytial virus infection does not decrease viral load or severity of illness
cord-318229-29cgwivt	2018	An outbreak case is a patient with a positive RSV laboratory testing in samples from the upper or lower respiratory tract and a definite or possible nosocomial onset. Considering bed and room occupancy on the ward during the outbreak, direct patient to patient transmission (e.g. via droplets or contaminated surfaces) in cases 1 and 2 as well as 3 and 4 seemed epidemiologically possible as each pair was accommodated in the same room before samples were tested positive for RSV. Overlying sequence information from different quasispecies detected in the samples are highlighted in a box measures, in particular single room accommodation for contact patients (quarantine), suspension of all social activities, and surgical masks for all HCWs and visitors at any time, addressed the postulated RSV transmission pathways during this outbreak. Outbreak of respiratory syncytial virus (RSV) infection in immunocompromised adults on a hematology ward
cord-318591-ssnlfjap	2020	We used the severe acute respiratory infection (SARI) definition to describe the etiology, clinical, and epidemiological characteristics in this population. [4] [5] [6] After the recent influenza A (H1N1, H5N1, and H7N9) and the Middle East Respiratory Virus (MERS-CoV) outbreaks, the WHO is encouraging and supporting countries to strengthen surveillance on severe acute respiratory infections (SARI) 7 but with limited information on PLWH regarding etiology and prognosis, despite their increased risk for respiratory infections and adverse outcomes. [8] [9] [10] So, in this study, we described how SARI is represented, according to clinical presentation, epidemiology and etiology in a population of PLWH with respiratory infection residing in a high-prevalence TB area. We observed two cases of influenza in the non-SARI group, respectively 20 and 30 days after symptom onset, and both patients developed respiratory failure that led to death (data not shown).
cord-319675-mwy3t1ny	2016	At admission (on day 5–7 after illness onset), the patients in fatal cases presented higher initial viral loads in respiratory tract secretions (8.578 ± 2.115 vs 6.263 ± 1.225 Log(10) copies/ml, p = 0.023). Our results suggest that a higher initial viral load (10 8 copy/ml) in the respiratory tract samples on day 5-7 after disease onset is a predictor for fatal clinical outcome. In one case, as shown in Fig 2, even though the patient presented with a higher viral load (10 8.32 copies / ml) in tracheal aspiration, which may be associated fatal outcome, his clinical manifestation recovered gradually with a downward trend in the viral load in respiratory tract and whole blood samples. A higher initial viral load (10 8 copy/ml) in the respiratory tract on day 5-7 after disease onset and sustained viremia for 2 weeks or more may be associated with fatal clinical outcomes.
cord-319814-tyqb473m	2014	METHODS: In this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using PCR/RT-PCR from nasopharyngeal swabs. Flu viruses were detected in 2632 specimens (18.50%), RSV in 1120 (7.86%), PIV in 494 (3.47%), ADV in 493 (3.47%), hMPV in 319 (2.24%), HCoV in 351 (2.47%), and HBoV in 180 (1.26%). A decline in the incidence of viral infections with age was observed for respiratory viruses, except for Flu. The detection rates of RSV, PIV, ADV, hMPV, HCoV, and HBoV among children ( 14 years) were higher than among adults (>14 years old). The total detection rates for the seven respiratory viruses in spring, summer, autumn, and winter were 44.31%, 41.15%, 41.66%, and 30.52%, respectively.
cord-319877-izn315hb	2016	Scientific advancements since the 2002–2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. The downregulation of ACE2 results in the excessive production of angiotensin II by the related enzyme ACE, and it has been suggested that the stimulation of type 1a angiotensin II receptor and Middle East respiratory syndrome coronavirus (MERS-CoV) encode two large polyproteins, pp1a and pp1ab, which are proteolytically cleaved into 16 non-structural proteins (nsps), including papain-like protease (PLpro), 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), helicase (Hel) and exonuclease (ExoN). Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have developed mechanisms to interfere with these signalling pathways, as shown; these subversion strategies involve both structural proteins (membrane (M) and nucleocapsid (N)) and non-structural proteins (nsp1, nsp3b, nsp4a, nsp4b, nsp5, nsp6 and papain-like protease (PLpro); indicated in the figure by just their nsp numbers and letters).
cord-320107-wels9wt7	2018	Resolution of respiratory virus infection requires not only the elimination of the Keywords ► lung transplantation ► community-acquired respiratory viruses ► ribavirin ► bronchiolitis obliterns syndrome The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). The incidence of community-acquired respiratory viruses (CARVs) is $15 cases per 100 patient-years after lung transplantation (LTx). 8 In contrast to the nonimmunosuppressed host, CARV infection usually leads to more severe illness in the lung transplanted recipient with a higher incidence of respiratory failure. ALN-RSV01 for prevention of bronchiolitis obliterans syndrome after respiratory syncytial virus infection in lung transplant recipients Incidence and outcomes of respiratory viral infections in lung transplant recipients: a prospective study Upper and lower respiratory tract viral infections and acute graft rejection in lung transplant recipients Community-acquired respiratory viral infections in lung transplant recipients: a single season cohort study
cord-320286-9tumplp3	2006	The virus was identified in clinical specimens from infants and children with respiratory tract illness. All specimens were negative for influenza viruses A and B; parainfluenza viruses 1, 2, and 3; adenovirus; and respiratory syncytial virus (RSV) by direct or indirect fluorescence assays or virus isolation and for human metapneumovirus (HMPV) by reverse transcription-polymerase chain reaction. Although a causal relationship still needs to be demonstrated by including a control group of healthy persons, detection of HBoV in respiratory tract specimens from patients with undiagnosed ARI suggests that this virus may be associated with respiratory illness. Most (89%) hospitalizations were in persons <5 years of age, which suggests that HBoV may cause more severe respiratory illness in infants and children, similar to disease caused by RSV (4, 5) , HMPV (6,7), human coronavirus NL63 (8) (9) (10) (11) (12) (13) (14) , and human coronavirus 229E (15) .
cord-320950-x02zp349	2019	A systematic review and meta-analysis (Huang et al., 2018) of studies on the accuracy of FA-RP, Nanosphere Verigene RV+ test (Hologic, 2018; Luminex, 2018) Gen-Probe Prodesse assays (Hologic, 2018) in the detection of IV A, IV B virus, RSV, hMPV, and AV showed that all of these assays had high diagnostic accuracy, with an area under the receiver operating characteristic curve (AUROC) equal to or >0.98 for all tested viruses. In a study involving 46 children aged 6-36 months with bocavirus infection, it was shown that in 22% of cases, the virus persisted in the respiratory secretions for more than 30 days, despite the rapid disappearance of clinical manifestations (Wagner et al., 2016) . In conclusion, multiplex platforms, despite significantly increasing the possibility to detect which pathogens are present in the respiratory secretions of a child with a respiratory infection, do not offer any advantage in comparison to tradition diagnostic tests regarding the identification of the true etiologic agent of the disease.
cord-321284-0y69n1ea	2016	title: The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. Forty healthy age-matched asymptomatic children with no history of a recent respiratory tract infection during the previous 2 weeks, who were not admitted to the hospital, and who do not have any chronic underlying illness were included as a control group. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR) among hospitalized children admitted with severe acute respiratory infection, as well as the high rate of detection of multiple viruses.
cord-321756-a7eh4dkb	2012	The study was done to identify viruses associated with acute lower respiratory tract infection among children less than 5 years. Majority of acute lower respiratory tract infections (ALRTI) in developed countries have been reported to be often due to viral pathogens of which most common are RSV, PIV, influenza viruses, Adv, human Coronaviruses and Bocaviruses [5] [6] [7] . This study was done to determine the burden of respiratory viruses among children hospitalized at the Komfo Anokye Teaching Hospital for acute lower respiratory illness using the Real Time Polymerase Chain Reaction (RT-PCR). The overall prevalence is comparable to previous studies done in other developing countries [24] and the predominance of RSV is in accordance with the assertion that this virus is the single most frequent lower respiratory tract pathogen in infants and young children worldwide [25] [26] [27] .
cord-321851-ku4z34lu	2020	Our results showed a downregulation of Th2, inadequate (partial) Th1 immune response and high expression levels of inflammatory cytokines IL-1α and IL-1β and the neutrophil chemoattractant chemokine IL-8 (CXCL8) in the lower respiratory tract of MERS-CoV infected patients. The lower respiratory tract samples from MERS-CoV infected patients and healthy non-infected controls were used to quantify expression levels of the main 12 human pro-inflammatory cytokines and chemokines (IL-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17A, IFN-γ, TNF-α, and GM-CSF). A side-by-side analysis of the data derived from the RT 2 -PCR profiling of pulmonary Th1/Th2 responses showed that genes encoding Th1 and Th2-related cytokines and chemokines were largely downregulated in the lower respiratory tract of MERS-CoV infected patients. Therefore, the high expression of inflammatory cytokines and downregulation of the Th1 and Th2 immune responses in the lower respiratory tracts of MERS-CoV infected patients may contribute to a more severe infection, higher case fatality, lung inflammation, and immunopathology.
cord-322524-bq9ok8h1	2018	Studies conducted in the 1980s and 1990s first identified RSV as a cause of acute respiratory illness in a variety of adult populations, including older adults, working-age adults, hospitalized patients, and residents of long-term care facilities [5] [6] [7] [8] [9] . A 6-season study of adults ≥50 years old with predominantly outpatient acute respiratory illness found that RSV was the third most common viral pathogen (after influenza and human rhinovirus) [19] . The objective of this study was to describe the clinical characteristics, severity, clinical outcomes, and long-term incidence of medically attended RSV illness in a community cohort of adults ≥60 years of age from the 2004-2005 through 2015-2016 influenza seasons. Seasonal incidence of medically attended respiratory syncytial virus infection in a community cohort of adults ≥50 years old
cord-322573-1fw1ehzd	2007	To determine the prevalence and clinical characteristics of HBoV, we investigated the presence of this virus in children with respiratory tract infection in our region (Gipúzkoa, Basque Country, Spain). To rule out the possibility that this result could have been due to fecal contamination resulting from swallowing respiratory secretions, and to determine whether the gastrointestinal tract is affected by this new respiratory virus, we studied its presence in patient feces in 527 episodes of acute gastroenteritis, unrelated to respiratory infection, in children <3 years of age, mainly from nonhospital centers (ambulatory clinics). From a second group of 520 children <3 years of age who came to the pediatric emergency unit of our hospital with an episode of acute respiratory infection during the same period, a similar frequency of HBoV detection was obtained (40/520, 7.7%) when nasopharyngeal aspirates were tested. Detection of human bocavirus in Japanese children with lower respiratory tract infections
cord-322657-q4aeood2	2004	We studied the viral etiology of acute expiratory wheezing (bronchiolitis, acute asthma) in 293 hospitalized children in a 2-year prospective study in Finland. To prevent and treat acute expiratory wheezing illnesses in children, efforts should be focused on RSV, enterovirus, and rhinovirus infections. The purpose of the study was to investigate the role of 11 respiratory viruses in children hospitalized for acute expiratory wheezing. The supernatants of cell cultures exhibiting a cytopathogenic effect were further studied by antigen detection for adenovirus; influenza A and B viruses; parainfluenza virus types 1, 2, and 3; and RSV or by reverse transcription (RT)-PCR for enterovirus-es and rhinovirus. First, respiratory virus infection was detected in up to 90% of hospitalized children with acute expiratory wheezing. In conclusion, this study showed that acute expiratory wheezing necessitating hospitalization was most often associated with RSV, enterovirus, and rhinovirus infections.
cord-323009-frej2qmb	2013	FINDINGS: A prospective study was conducted in the Central African Republic (CAR) between January and December 2010 among infants and children aged 0–15 years attending sentinel sites for influenza-like illness or acute respiratory illness. The aim of the study reported here was to determine the circulation of 2009 pandemic influenza A/H1N1 virus (H1N1pdm09) by molecular methods and to identify the causative viruses, the incidence and the clinical features of acute respiratory illness among infants and young children at sentinel sites in Bangui and three rural areas. All infants and children aged between 0-15 years who attended sentinel sites in Bangui and three rural areas ( Figure 1 ) for influenza-like illness (ILI) or severe acute respiratory illness between January and December 2010 were included in the study (Figure 2A ). Abbreviations CAR: Central African Republic; ILI: Influenza-like illness; HRSV: Human respiratory syncytial virus; PIV: Parainfluenza viruses.
cord-323066-tvguutak	2018	METHODS: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). 10 The objective of our study was to ascertain demographic characteristics, clinical findings and presumptive aetiologic agents (respiratory viruses demonstrated in nasopharyngeal swab) associated with bronchiolitis severity defined as length of hospitalization for >24 hours. Electronic medical records of patients included in the study were reviewed, and statistical analysis was performed for the following clinical and laboratory data: gender, chronological age at admission, prematurity (defined as birth before 37 weeks of gestation), birthweight, history of allergies, number of previous bronchiolitis episodes, clinical manifestations of bronchiolitis using the Wang Respiratory Score, 9 comorbidities (chronic lung disease, congenital heart disease, immune deficiency or neuromuscular diseases), body temperature at admission, treatment with bronchodilators, antibiotics or supplemental oxygen and respiratory virus detected in the nasopharyngeal swab.
cord-323112-e78zpa9c	2009	This review will focus on the human, pathogen and environmental factors that contribute to the continued global burden or respiratory diseases with a particular focus on areas where we might hope to see some progress in the coming decades. 14 While it is clear that strict infection control can reduce nosocomial infection rates, 15 the practical necessity of pooling vulnerable hosts together combined with the inevitable ageing of health-care facilities will ensure that nosocomial outbreaks continue to be a problem. In recent years the marked increase in tumour necrosis factor antagonists and monoclonal antibodies targeting specific lymphoid populations in patients with inflammatory arthritis (and especially rheumatoid disease) has significantly over taken patients on immunosuppressant therapy after solid organ transplantation as the major cause of iatrogenic immunosuppression. New therapeutic and diagnostic approaches coupled with clinical vigilance, strict infection control and solid public health measures are the hopes for reducing the burden of pulmonary infectious disease over the coming decades.
cord-323551-22v2hn3v	2019	We enrolled 214 individuals at multiple New York City locations and tested weekly for respiratory viral pathogens, irrespective of symptom status, from fall 2016 to spring 2018. Here, we document rates of asymptomatic respiratory virus infection through a large-scale community study across multiple age groups. For the entire duration of the study, participants provided a daily report rating nine respiratory illness-related symptoms (fever, chills, muscle pain, watery eyes, runny nose, sneezing, sore throat, cough, chest pain), which were recorded on a Likert scale (0 = none, 1 = mild, 2 = moderate, 3 = severe). Pairwise comparisons between single infections and coinfections across all eight definitions showed that testing positive for multiple viruses was not associated with more severe symptoms. Figure 3 shows that while children were most frequently infected with a respiratory virus (they presented with the highest number of viral shedding events per season), they recorded (as reported by their parents) the lowest symptom scores on average.
cord-324217-secnz2ta	2016	The present chapter reviews natural traditional remedies used in the treatment of respiratory infections with the emphasis on antibacterial, antiviral, and antiinflammation activities of the volatile natural compounds (essential oils, etc.), and provides a brief view in some of structural activity relationships between antibacterial potencies and chemical structures of the essential oil''s constituents. 10 Besides the antimicrobial activity of the essential oils in natural products, other characteristics such as high vapor pressure, low toxicity, and antiinflammatory potential create a worthwhile theme for using of these natural compounds for new drug development in respiratory infections. As a member of the phytochemicals, terpenoids have been observed as a model of lipid soluble agents, which have an impact on the activities of membrane catalyzed enzymes; for 3 SCREENING OF THE ANTIbACTERIAL EFFECTS OF ESSENTIAL OILS example, enzymes involved in respiratory pathways. 98 Among the natural chemical compounds, significant antiinflammatory activities of plant-based essential oil have been reported by many researchers, which showed the basis for folk and traditional uses of these herbs for treatment of inflammatory diseases.
cord-324432-k0g3r1lw	2018	PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. The community cohort was derived from the Mobile Surveillance for Acute Respiratory Infections (ARIs) and Influenza-like Illness (ILI) in the Community (MoSAIC) study, a 5-year community-based surveillance ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. epidemiology, parainfluenza, respiratory, seasonality, viruses F I G U R E 1 Flowcharts depicting the overall number of respiratory viral panel (RVP) tests ordered which yielded the final number of human parainfluenza virus (HPIV) types in the community cohort (1A) and in hospitalized patients (1B) study in New York City (NYC) that includes 250 households annually.
cord-324601-s3rgxtg6	2019	title: Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study We therefore studied the prevalence of respiratory pathogens in TB patients and household contact controls, and assessed the associations between both respiratory viruses and bacterial pathogens and the clinical presentation of TB patients who were prospectively recruited in an area of Dar es Salaam (Tanzania) with a high TB burden. Logistic regression models adjusting for age, sex, and HIV infection were used to assess the associations between respiratory pathogens and clinical presentations of TB at the time of recruitment among TB patients, with the following outcome variables: severe TB score (score of 6) versus mild (score of 1e5), high sputum bacterial load (sputum AFB smear microscopy of 2þ) versus low bacterial load, and presence versus absence of lung infiltrations and cavitations (chest x-ray findings).
cord-324775-3x5os79m	2008	Respiratory syncytial virus (RSV) is the most common pathogen, with hMPV, PIV-3, influenza viruses, and rhinoviruses accounting for the majority of the remainder of acute viral respiratory infections. Respiratory syncytial virus (RSV), parainfluenza viruses (PIVs), adenoviruses, and influenza viruses were identified initially as the most common causes of serious lower respiratory tract disease in infants and children. These patients also suffer more frequent and more severe disease including mortality with common respiratory viruses, including RSV, hMPV, PIV, influenza viruses, rhinoviruses, and adenoviruses. Enterovirus infections occur most commonly in the summer months in temperate areas, which differs from the season of many of the other most common respiratory viruses such as paramyxoviruses and influenza virus. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease. Humans generally do not develop lifelong immunity to reinfection with these viruses; rather, specific immunity protects against severe and lower respiratory tract disease.
cord-324786-8k81jetq	2012	Our study tests the hypothesis that both oral azithromycin and amoxicillin-clavulanic acid are superior to placebo at improving resolution rates of respiratory exacerbations by day 14 in children with bronchiectasis unrelated to cystic fibrosis. Our multicentre, double-blind RCT is designed to determine if azithromycin and amoxicillin-clavulanic acid, compared with placebo, improve symptom resolution on day 14 in children with acute respiratory exacerbations. Early and effective management of bronchiectasis exacerbations in children may lead to reduced hospitalisations, better quality of life (QOL) and improved future adult lung function. Our study tests the primary hypothesis that both oral azithromycin and amoxicillin-clavulanic acid are superior to placebo in improving the resolution rate of respiratory exacerbations by day 14 in children with non-CF bronchiectasis. We are conducting a multicentre, parallel group, double-blind placebo RCT (with concealed allocation) to assess the impact of treatment with antibiotics (azithromycin or amoxicillinclavulanic acid) in children with an exacerbation of bronchiectasis.
cord-324843-r43u7sld	2019	OBJECTIVES: To analyze the course of seasonal viral infections of respiratory tract in patients hospitalized in pediatric intensive care units (PICU) of 16 centers in Turkey. The critical pH value related with mortality was ≤7.10, and critical PCO(2) ≥60 mm Hg. CONCLUSION: Our findings demonstrate that patients with neurological symptoms, tachycardia, hypoxia, hypotension, acidosis, impaired liver, and renal function at the time of admission exhibit more severe mortal progressions. By presenting the analyzed data of 302 PICU admissions, current study reveals severity of viral respiratory tract infections and release tips for handling them. 7 This retrospective observational study was conducted in order to analyze the course of seasonal viral infections of respiratory tract in patients hospitalized in PICUs of 16 centers representing the whole country. Viral respiratory tract infections constitute significant proportion of patients admitted to PICUs in winter, and these patients require advanced intensive care support with high mortality and morbidity rates.
cord-324898-bjxpuqhr	2020	Where present, respiratory physiotherapists (RPh) made a great contribution by working together with other health professionals in assisting patients, providing "quick basic training sessions" about respiratory care for non-specialist healthcare professionals, locating and assessing all kinds of equipment (ventilators, interfaces, oxygen delivery systems, among others) to assist patients with respiratory failure and implementing early intervention with those patients in healthier conditions. Despite the absolute novelty of the pathology and the lack of scientific evidence, based on the available knowledge of physiopathology and respiratory care strategies, in collaboration with other scientific societies (Associazione Italiana Fisioterapisti -AIFI-, Associazione Italiana Pneumologi Ospedalieri -AIPO-, Società Italiana Pneumologia -SIP-, European Respiratory Society-ERS-), documents have been published in open-access journals and platform aimed to promote safe use of personal protective equipment (PPE) and to support the decision process in the management of COVID-19 patients in the acute and postacute phases [1] [2] [3] [4] .
cord-324950-ux7shvji	2020	In pigs, the term "Porcine Respiratory Disease Complex" (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The outcome of any coinfection or superinfection can be affected by the interactions taking place between the infectious agents, the nature of the cell/host, adverse environmental and management conditions, intestinal and respiratory microbiomes, and the triggered immune response-innate and adaptive-developed afterwards [2, 3] . It is well-known that viral infections can induce an ideal environment for a bacterial superinfection through different mechanisms such as the destruction of the epithelial barrier, the over-expression of the receptors involved in the bacterial adhesion to the cells, and the alteration of the host immune response [1, 2, 94, 95] .
cord-325353-tx6s4ggu	2018	The goals of this review are (1) to outline the differences between the neonatal and adult immune systems and (2) to present murine and human data that support the hypothesis that early-life interactions between the immune system and respiratory viruses can create a lung environment conducive to the development of asthma. Because RSV, influenza, and RVs cause a large proportion of respiratorytract infections in neonates, we will focus primarily on these three pathogens as models to better understand how early-life infection and antiviral immune responses might contribute to the subsequent development of asthma. The addition of RSV infection of airway epithelial cells with production of the type-2 innate cytokines, IL-33 (138) , TSLP (123) , and IL-25 (128) , would, therefore, be predicted to create an even more exaggerated type-2-biased microenvironment in the lung with activation of other immune cells (e.g., M2 macrophages, DCs, and/or ILC2 cells) and the development of AHR.
cord-325611-tu1bn4hu	2019	We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. In this report, we performed a systematic study of respiratory specimens collected from a carefully characterized and highly representative, prospective cohort of pediatric cases suffering unexplained ARI, and we compared the rate of detection of pathogens by utilizing validated molecular assays, and a comprehensive sequence-independent, high-throughput sequencing-based analysis. In order to assess for the clinical relevance of the viral identifications made by HTS in the specimens collected from the unexplained cases of respiratory infections, a second cohort of age-matched healthy individuals from the same epidemiologic environment was also studied with the same methodology. Respiratory viral pathogens identified by target-agnostic HTS analysis and confirmed by contig-specific molecular assays in the respiratory specimens from the cases of respiratory infection and from the control group.
cord-325635-don9qjpz	2013	Using global population data for 2005, for children under the age of five years, it was estimated that RSV was responsible for over 30 million episodes of lower respiratory tract infections (LRTI), with~3 million of these requiring hospital admission, and 66,000-199,000 deaths [7] . In 2007, the US Centers for Disease Control and Prevention (CDC) and the Shoklo Malaria Research Unit (SMRU) established a respiratory virus surveillance programme in the Burmese refugee population living in Maela camp, Northwest Thailand. Laboratory-enhanced surveillance has documented the contribution of respiratory viruses to 708 hospitalised clinical pneumonia episodes occurring in a crowded refugee camp on the Thailand-Myanmar border during April 2009 to September 2011. The results are broadly consistent with a similar surveillance programme conducted in two Kenyan refugee camps [22] , where 51.3% patients with severe acute respiratory infection (SARI) had at least one of adenovirus, hMPV, influenza A/B, parainfluenza virus 1-3, or RSV detected.
cord-325783-pqonn0as	2003	Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Methods Post-mortem tissue samples from six patients who died from SARS in February and March, 2003 , and an open lung biopsy from one of these patients were studied by histology and virology. Since Nov 1, 2002 , an outbreak of severe acute respiratory syndrome (SARS) has affected 33 countries in five continents, with 7053 reported cases and 506 deaths at the time of writing. The case definition was fever (temperature 38°C or higher), cough or shortness of breath, new pulmonary infiltrates on chest radiograph, and either a history of exposure to a patient with SARS or a lack of response to empirical antimicrobial coverage for typical and atypical pneumonia (beta-lactams and macrolides, fluoroquinolones or tetracyclines).
cord-325830-mrtpihc7	2020	In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings. In this review, we summarize recently published characteristics of POCTs and discuss their implications for the treatment of RTIs. The second key aspect of this work is a description of new and innovative diagnostic techniques, ranging from biosensors to novel portable and current lab-based nucleic acid amplification methods with the potential future use in point-of-care settings.
cord-326004-wg47sd06	2018	A recently conducted prospective randomized controlled trial at 2 district-level hospitals in Ghana revealed that the use of continuous positive airway pressure (CPAP) reduces the allcause mortality rate in children <1 year old who presented with undifferentiated acute respiratory distress [3] . In that study, nasopharyngeal swabs were collected from the children at the time of presentation and tested for common pediatric respiratory pathogens; the goal was to decrease the knowledge gap regarding the incidence of respiratory pathogens that affect children <5 years of age in low-and middle-income countries. In this report, we describe the respiratory pathogens detected in children aged 1 month to 5 years who presented to 1 of 2 district-level hospitals in Ghana with undifferentiated acute respiratory distress. Despite the limitations of this study, our results show that viral respiratory pathogens were frequent among children aged 1 month to 5 years who presented with acute respiratory distress to 1 of 2 district-level hospitals in Ghana.
cord-326122-5m1727m1	2014	The Pediatric Infectious Disease Society (PIDS) and the Infectious Diseases Society of America (IDSA) recommend in their guideline ''Community-Acquired Pneumonia (CAP) in Infants and Children'' the use of sensitive and specific tests for the rapid diagnosis of influenza virus and other respiratory viruses in the evaluation of children older than three months of age with CAP [19] . In another recent retrospective study of 177 children with ARI in a general hospital, antibiotic management was not influenced after detecting a viral respiratory pathogen, although the authors state that routine testing of common respiratory pathogens could lead to a better understanding of their role in disease in children with respiratory symptoms [38] . Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children
cord-326163-u8nh8cr3	2003	The aim of this study was to investigate potential differences in the local nasal immune response between bronchiolitis and upper respiratory tract infection induced by respiratory syncytial virus (RSV). This study investigated whether differences could be observed on the cellular level between the nasal immune responses of infants with RSV-induced bronchiolitis and RSV-induced upper respiratory tract infection. During the acute phase of bronchiolitis as well as during upper respiratory tract infection, there was a marked increase in the numbers of macrophages (CD68positive cells) in nasal brush samples compared with convalescent samples (Fig. 1A) . Most importantly, this study showed a striking difference in cytokine responses between both types of infection, i.e., an increase in the number of IL-18 positive cells in nasal brush samples during bronchiolitis.
cord-327264-j0efi5vc	2017	Lower respiratory tract infections remain the number one cause of death in the developing world. 1 In the developed world, lower respiratory tract infections are still the fifth leading cause of death. As well as host factors, it is the speed of adaptation of the pathogens that makes it most likely that we will not conquer death from respiratory infection any time soon. While some progress has been made in reducing pneumococcal disease with the newer conjugate vaccines, 2 there is evidence that the speed of adaptation (as measured by the proportion of strains not covered by the vaccines) is increasing. In this series on respiratory infections in Respirology, many of the above-mentioned challenges will be covered including the burden of disease due to respiratory pathogens (both acute and long-term), drug-resistant pathogens and newly emerging pathogens.
cord-327493-v2iatbol	2013	BACKGROUND: The objective of our study was to understand the epidemiological and clinical features of respiratory adenoviral infections among children at a single institution over the course of several years. CONCLUSION: Our study demonstrates that respiratory adenovirus infections are an important cause of hospitalization in young children, and contribute to a significant morbidity. The study was performed to more fully characterize the epidemiological pattern, clinical features and complications associated with hospitalization for adenoviral infection in Korean children. Adenovirus was associated with a wide variety of diagnoses, ranging from upper respiratory tract infections (URTI) to severe pneumonia and encephalitis ( Table 1 ). 22 reported that 70% of hospitalized children with adenoviral infection had pneumonia, while our results revealed a significant proportion of patients (45.4%) with URTI. Lower respiratory tract infections due to adenovirus in hospitalized Korean children: epidemiology, clinical features, and prognosis
cord-327685-fymfqvp3	2017	In contrast, highly pathogenic hCoVs such as severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV) predominantly infect lower airways and cause fatal pneumonia. Severe pneumonia caused by pathogenic hCoVs is often associated with rapid virus replication, massive inflammatory cell infiltration and elevated pro-inflammatory cytokine/chemokine responses resulting in acute lung injury (ALI), and acute respiratory distress syndrome (ARDS). Although there is no direct evidence for the involvement of pro-inflammatory cytokines and chemokines in lung pathology during SARS and MERS, correlative evidence from patients with severe disease suggests a role for hyper-inflammatory responses in hCoV pathogenesis. Infection of non-human primates (NHPs) with SARS-CoV induced a dysregulated immune response resulting in increased disease severity in aged but not young NHPs, despite similar viral titers in the airways [67] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice
cord-328086-ji2emajn	2018	BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). Clinical disease and viral load in children infected with respiratory syncytial virus or human metapneumovirus Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection High viral load of human bocavirus correlates with duration of wheezing in children with severe lower respiratory tract infection High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical significance of different virus load of human bocavirus in patients with lower respiratory tract infection
cord-328501-mbwgi56x	2015	title: Risk factors for febrile respiratory illness and mono-viral infections in a semi-closed military environment: a case-control study CONCLUSION: Increasing age, smoker, recruit-camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military environment. Previous documented risk factors of FRI in other countries included body mass index equal or greater than 25 kg/m 2 , previous respiratory tract infections [30] , overcrowding and closed units [29, [31] [32] [33] , presence of sand and dust storms, extreme temperature changes [34, 35] , smoking [36] , female, Navy service, poor latrine facilities, increasing age and higher rank [37] . Increasing age, smokers, recruit camp, stay-out personnel with ill household members and stay-in personnel with ill bunkmates were independent risk factors of FRI in a semi-closed military setting. Outbreak of febrile respiratory illness associated with adenovirus 11a infection in a Singapore military training cAMP
cord-328742-r4ht266w	2018	During January 2013–April 2014, we subjected nasopharyngeal specimens collected from patients with acute febrile respiratory illness in a military hospital to PCR testing to detect 12 respiratory viruses and sequence a partial hexon gene for human adenovirus (HAdV) molecular typing. During January 2013-April 2014, we subjected nasopharyngeal specimens collected from patients with acute febrile respiratory illness in a military hospital to PCR testing to detect 12 respiratory viruses and sequence a partial hexon gene for human adenovirus (HAdV) molecular typing. HAdV is most prevalent in patients with acute lower respiratory tract infection and is the most common cause of pneumonia among military personnel in South Korea (12) . Thus, our study aimed to investigate the epidemiology of HAdV infections and to compare the clinical characteristics by type of HAdVs in soldiers in South Korea via hospital-based surveillance on viral respiratory infections.
cord-328829-yywxmioq	2012	title: Microbiological study of patients hospitalized for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) and the usefulness of analytical and clinical parameters in its identification (VIRAE study) The etiology of the respiratory infection was studied by conventional sputum, paired serology tests for atypical bacteria, and viral diagnostic techniques (immunochromatography, immunofluorescence, cell culture, and molecular biology techniques). The aims of our study were to identify the etiology of respiratory infections in patients hospitalized for AE-COPD using different diagnostic tests and to evaluate the usefulness of the clinical and analytical parameters of the diagnostic process. Identification was made based on the respiratory infection and dyspnea admission diagnoses from the International Statistical Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) 19,20 (491, 492, 493, 496, 518.81, 464, 465, 466, 519.11, 786 .0), excluding the patients who had a known cause of respiratory failure that was different from infectious exacerbation (heart failure, pulmonary thromboembolism, pneumonia).
cord-329263-o5e2go23	2007	title: Molecular epidemiology and disease severity of respiratory syncytial virus in relation to other potential pathogens in children hospitalized with acute respiratory infection in Jordan Human respiratory syncytial virus (HRSV) is the major viral cause of acute lower respiratory tract infections in children. Human respiratory syncytial virus (HRSV) is the leading viral cause of acute respiratory infection in infants and young children in terms of prevalence and effect [Shay et al., 2001] . We also compared the disease severity of HRSV subgroups A and B and their associated genotypes in hospitalized Jordanian children set in the context of other potential respiratory pathogens. A total of 72/326 (22%) patients had no pathogens detected by PCR (Table I) , but 254 (78%) had at least one potential respiratory pathogen detected which consisted of 140/ 326 (43%) HRSV, 116/312 (37%) adenoviruses, 57/312 (18%) HBoV, 36/325 (11%) rhinovirus, 14/312 (4.5%) Chlamydia spp., 8/326 (2.5%) HMPV, 4/325 (1.2%) human coronavirus NL63, and 2/323 (0.6%) influenza A virus.
cord-329306-p5wmqmvj	2014	Rhinovirus infection is typically associated with the common cold and has rarely been reported as a cause of severe pneumonia in immunocompetent adults. Rhinovirus infection can extend to lower respiratory tract in children [4] [5] [6] or immunocompromised hosts 7, 8 , but is generally not concerned as singular cause of severe pneumonia, especially in immunocompetent adults. Although technical advances have allowed for increased detection of viral pneumonia, viral infections other than influenza are generally not considered as causes of severe respiratory tract infection in immunocompetent hosts, because viral clearance usually occurs rapidly in healthy individuals. Therefore, it is still believed that severe viral pneumonia caused by frequently exposed rhinovirus could hardly occurs in immunocompetent adults. On the contrary, our relatively young immunocompetent patient suffered severe rhinovirus pneumonia without bacterial co-infection, which was confirmed by BAL fluid analysis, and not by the nasopharyngeal specimen. Rhinovirus associated with severe lower respiratory tract infections in children
cord-329877-vish6v8e	2003	BACKGROUND: Severe acute respiratory syndrome (SARS) is a contagious viral illness first recognized in late 2002. Severe acute respiratory syndrome (SARS) is a viral illness characterized by a syndrome of fever and respiratory symptoms that can progress to respiratory failure and death. This review describes the current state of knowledge of SARS, with particular reference to the management of the critically ill patient and the safety and protection of the ICU staff. Case definitions of SARS are currently based on the presence of epidemiological risk factors (close contact with SARS cases or travel to SARS "affected" areas) along with a combination of fever and respiratory symptoms, with or without hypoxia and/or chest radiographic changes [3] . Other high-risk procedures include obtaining nasopharyngeal swabs, bag-mask ventilation, intubation, suctioning, chest physiotherapy in nonintubated patients, nebulized drug therapy, noninvasive ventilation, and extubation (see Table 1 ).
cord-330079-pdaowkop	2012	To investigate the epidemiological and genetic variation of HBoV in Guangzhou, South China, we screened 3460 throat swab samples from 1686 children and 1774 adults with acute respiratory infection symptoms for HBoV between March 2010 and February 2011, and analyzed the complete genome sequence of 2 HBoV strains. In our current study, we screened throat swab specimens from patients with acute respiratory tract infection symptoms for HBoV and other common respiratory viruses over a 12-month period using polymerase chain reaction (PCR) methods, and in addition, the molecular phylogeny and complete genome sequences of 2 HBoV strains were also analyzed. Of the 3460 samples collected from patients with respiratory tract infection symptoms and signs enrolled in the study during the period between March 2010 and February 2011, detection for 7 viruses, namely, Influenza, PIV, RSV, HMPV, HCoV, AdV and HBoV, showed that 1275 (36.8%) were found positive for one single virus and 112 (3.2%) were infected by more than one virus.
cord-330343-p7a8chn4	2019	► Diagnostic research and development (R&D) needs to include point-of-care testing options, syndromic panels for differential diagnosis, a greater understanding of viral and antibody kinetics, improved access to clinical specimens, and establishment of international reference standards. Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation.
cord-330919-dep3v1pt	2020	The global pandemic of coronavirus disease 2019 (COVID‐19) is associated with the development of acute respiratory distress syndrome (ARDS), which requires ventilation in critically ill patients. Tissue factor (TF) is exposed on damaged alveolar endothelial cells and on the surface of leukocytes promoting fibrin deposition, while significantly elevated levels of plasminogen activator inhibitor 1 (PAI‐1) from lung epithelium and endothelial cells create a hypofibrinolytic state. In severe cases, patients with COVID-19 develop a type of acute respiratory distress syndrome (ARDS), sepsis and multiorgan failure. However, the principal fibrinolytic inhibitor described in the pathogenesis of ARDS is plasminogen activator inhibitor 1 (PAI-1), which is known to be elevated in severe acute respiratory syndrome coronavirus (SARS-CoV) and ALI [11, 61] . Tissue Plasminogen Activator (tPA) as a Novel Treatment for Refractory COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS)? Activator (tPA) Treatment for COVID-19 Associated Acute Respiratory Distress Syndrome (ARDS): A Case Series
cord-331228-wbd0s4fo	2016	authors: Shehata, Mahmoud M.; Gomaa, Mokhtar R.; Ali, Mohamed A.; Kayali, Ghazi Role of the spike glycoprotein of human Middle East respiratory syndrome coronavirus (MERS-CoV) in virus entry and syncytia formation Middle East respiratory syndrome coronavirus (MERS-CoV)-Saudi Arabia Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study First cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-to-human transmission Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia
cord-331288-elnwn7l5	2017	This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human‐great ape interface, the Taï Chimpanzee Project (TCP) in Côte d''Ivoire, and consequently, the effectiveness of a 5‐day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human-great ape interface, the Taï Chimpanzee Project (TCP) in Côte d''Ivoire, and consequently, the effectiveness of a 5-day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. Furthermore, the risk of potential exposure to human pathogens is assessed by testing sick humans to detect common human respiratory viruses they brought to the habituation site, and by randomly testing apparently healthy humans in the beginning and at the end of quarantine to assess the possibility of excreting HRSV and HMPV, the two most relevant viruses for wild great apes.
cord-331520-o9e4qqn4	2020	The winter respiratory virus season always poses challenges for long-term care settings; this winter, SARS-CoV-2 will compound the usual viral infection challenges. This special article discusses unique considerations that COVID-19 brings to the health and well-being of residents and staff in nursing homes and other long-term care settings this winter. Before the COVID-19 pandemic, influenza was the most concerning viral respiratory infection 27 for nursing home (NH) residents, with outbreaks requiring both treatment and prophylaxis, and 28 even causing some buildings to close to outsiders for brief periods of time. In 39 this special article, we discuss unique challenges that COVID-19 will bring to the health and 40 well-being of residents and staff in long-term care settings this winter. The winter respiratory virus season always poses challenges for long-term care settings, and 307 those challenges will be exacerbated with the second wave of COVID-19; as such, they present 308 numerous implications for practice, policy, and research.
cord-331973-avjw4kx1	2018	Serological tests can successfully identify antibodies to most respiratory pathogens such as RSV, adenovirus, influenza A and B, parainfluenza 1-3 virus, etc., and can detect mixed infections from hospitalized children suffering from acute respiratory infections, with the exception of infants for whom an antibody response is usually undetected (Hall et al., 1991; Chkhaidze et al., 2006) . FA testing, in addition to RT-PCR, is useful for epidemiological studies as it increases the probability of identifying acute viral infections and has been used for accurate assessment of respiratory viruses other than influenza in children (Sawatwong et al., 2012; Feikin et al., 2013; Zhang et al., 2017) . Most of the studies evaluating the clinical performance of these assays have reported high sensitivity (87-100%) and specificity (>98%) for detecting influenza A/B and RSV in pediatric and adult patients (Bell et al., 2014; Nie et al., 2014; Popowitch and Miller, 2015; Gibson et al., 2017; Ling et al., 2018) .
cord-332055-lrpfzsog	2015	National and world organizations define asthma "by the history of respiratory symptoms such as wheeze, shortness of breath, chest tightness and cough that vary over time and in intensity, together with variable expiratory airflow limitation." 12 The reversibility of airflow obstruction is the hallmark distinguishing asthma from other obstructive respiratory disorders. In contrast, chronic obstructive pulmonary disease (COPD)/ emphysema is defined as "persistent airflow limitation that is usually progressive and associated with enhanced chronic inflammatory responses in the airways and the lungs." 12 These patients also frequently wheeze, but may have a different course of acute and chronic disease. Rapid evaluation by lung-cardiac inferior vena cava (LCI) integrated ultrasound for differentiating heart failure from pulmonary disease as the cause of acute dyspnea in the emergency setting Clinical policy: critical issues in the evaluation and management of adult patients presenting to the emergency department with acute heart failure syndromes
cord-332361-pdoln3nr	2012	title: Epidemiology and seasonality of respiratory viral infections in hospitalized children in Kuala Lumpur, Malaysia: a retrospective study of 27 years CONCLUSION: Viral RTIs, particularly due to RSV, are commonly detected in respiratory samples from hospitalized children in Kuala Lumpur, Malaysia. In this study, we describe etiological agents, demographic details of patients, and seasonality (including association with meteorological factors) due to viral RTIs in a teaching hospital in Kuala Lumpur, over the last 27 years. Our findings support a previous local study carried out over a year, which showed that RSV was the most commonly detected respiratory virus, followed by parainfluenza viruses, influenza viruses and adenovirus [7] . Respiratory viral infections due to RSV, parainfluenza viruses, influenza viruses and adenovirus are significant causes of morbidity in hospitalized children in Kuala Lumpur, and are likely to be underdiagnosed.
cord-332926-8hdkpkgz	2017	During seasonal outbreaks of bronchiolitis from November through March in North America, respiratory syncytial virus (RSV) is identified as the etiologic agent in up to 80% of hospitalized children 7 (Table 33 .1). Unlike other respiratory viral infections, exposure to passive household tobacco smoke has not been associated with an increased risk of RSV hospitalization on a consistent basis. Most infants with bronchiolitis can be managed at home with supportive care, but concerns regarding increasing respiratory effort, apnea, or inability to feed adequately may precipitate hospitalization of a young child. Approximately 30% to 40% of RSV-infected infants experience progression of disease to the lower respiratory tract. Technical report: updated guidance for palivizumab prophylaxis among infants and young children at increased risk of hospitalization for respiratory syncytial virus infection Technical report: updated guidance for palivizumab prophylaxis among infants and young children at increased risk of hospitalization for respiratory syncytial virus infection
cord-333026-9f6ecg30	2017	Blood samples were simultaneously examined by the enzyme-linked immunosorbent assay (ELISA) and by the FilmArray Respiratory Panel for eight different pathogens in a total of 15 tests performed in nasopharyngeal swabs. Nonetheless, since most repiratory tract infections are viral in origin and there is no treatment available, the diagnosis provided by the FilmArray Panel does not provide any additional clinical benefit and thus should be used only whenever necessary on the individual basis. This method allows for identification of 21 different respiratory pathogens from a nasopharyngeal swab, 18 of viral etiology and three of bacterial origin (Idaho Technology 2007). The laboratory costs to run one examination with different methods showed that the FilmArray multiplex PCR respiratory panel is more expensive than the ELISA, HIT, and the cultivation. Since most URIs are viral in origin and there is no treatment available, the diagnosis provided by the FilmArray panel is not always necessary and the method should be used on an individual basis when clinically justified.
cord-333286-lr32e0w4	2020	We searched PubMed, Google Scholar, and Web of Knowledge for pre-clinical and clinical studies investigating the effect of probiotics on respiratory virus infections, immune response, and the course of upper and lower respiratory tract illness. Similar effects have been demonstrated in several mouse studies with the ability to reduce virus titers in lung tissues and modulation of antiviral and pro-inflammatory gene expression before and after viral infection. The upregulation of IFN response seems to prime cells for better resistance against virus infection as probiotics were shown effective in inhibiting the replication of various respiratory viruses, including influenza viruses and RSV. Similar effects have been demonstrated in mice with the ability of the probiotics to reduce virus titers in lung tissues and to modulate antiviral and pro-inflammatory gene expression before and after viral infection. Similar effects have been demonstrated in mice with the ability of the probiotics to reduce virus titers in lung tissues and to modulate antiviral and pro-inflammatory gene expression before and after viral infection.
cord-333355-ykmp4ven	2015	In this article we discuss the pathophysiology of common symptoms of acute viral respiratory infections (e.g., sneezing, nasal discharge, sore throat, cough, muscle pains, malaise, and mood changes). The development of sneezing before coughing in patients with a common cold may be partly explained by the involvement of the upper airways first and the infection subsequent spread to the lower respiratory tract (Eccles 2005) . We focused on the most significant symptoms of acute viral respiratory infections: sneezing, nasal discharge and obstruction, sore throat, coughing, muscle pains, malaise and mood changes, fever, and febrile seizures in children. Macrophages play a key role in triggering an acute phase response with the production of cytokines (Beutler 2003) , while the release of proinflammatory cytokines and other mediators cause upper respiratory tract infection symptoms (Eccles 2000a, b) .
cord-333868-qrnsmhws	2006	These agents are relatively uncommon, however, in most US EDs, and as recently as 2003, the Centers for Disease Control and Prevention (CDC) reported that health care facility environments are rarely implicated in respiratory pathogen transmission (except in cases of immunocompromised patients). All health care facilities should have policies and procedures in place for respiratory infection control practice with specific operational plans for handling a large influx of potentially infectious patients in the event of a significant outbreak. 3, 5, 16, 17, 39 Underscoring this is the findings from one epidemiologic outbreak of SARS in Toronto that found that 36% of new infections in the hospital occurred in health care workers, with the highest rates in those working in EDs and ICUs. 5 Both the World Health Organization and the CDC provide general recommendations for handling of patients with suspected respiratory infections that include having triage staff adhere to proper hand hygiene procedures and donning face masks and eye protection.
cord-335055-gzuug3p5	2020	title: Patterns of viral pathogens causing upper respiratory tract infections among symptomatic children in Mwanza, Tanzania Therefore, there is a paramount need to establish information on the common etiologies of RTIs in Tanzania, the information that can stimulate further studies and possible control interventions including introduction of cheap and reliable methods to detect these pathogens in clinical settings. In addition due to increased use of antibiotic without a support of a diagnostic test in the treatment of URTI as observed in number of previous studies [11] [12] [13] , make the availability of epidemiological data on the patterns of etiology of URTI of paramount important. A cross sectional hospital based study involving 339 children aged 1-59 months presenting with RTI symptoms was conducted from October 2017 to February 2018 in the city of Mwanza, Tanzania. A previous study 33 , documented Rhinovirus to cause up to 25-85% of the upper respiratory tract infections.
cord-335116-c83xyev5	2014	Methods: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. Methods: The fluctuations of respiratory virus detection were compared to the major climatic variables during a two-year period using adenoids and palatine tonsils from 172 children with adenotonsillar hypertrophy and clinical evidence of obstructive sleep apnoea syndrome or recurrent adenotonsillitis, without symptoms of acute respiratory infection (ARI), by TaqMan real-time PCR. We have previously reported high rates of detection of respiratory virus genomes in tonsils and adenoids from patients with chronic adenotonsillar diseases, suggesting a significant association of viruses, particularly picornaviruses, with severe tonsillar hypertrophy [3] .
cord-335505-s013j5ex	2013	BACKGROUND: No comprehensive analysis is available on the viral etiology and clinical characterization among children with severe acute respiratory infection (SARI) in China during 2009 H1N1 pandemic and post-pandemic period. The RVP Fast assay simultaneously detects the following viruses: respiratory syncytial virus (RSV); influenza(IFV) A (H1, H3, and H5) and B viruses; parainfluenza viruse (PIV) 1, 2, 3, and 4; human metapneumovirus (hMPV); adenovirus(ADV); piconavirus(PIC) which includes enterovirus (EV) and rhinovirus (RV); human coronaviruse(HCoV) NL63, HKU1, 229E, and OC43; and human bocavirus(BoCA). To find the reason that causes severe infection, we performed complete comparison between VSARI patients and the SARI, including clinical signs, number of viral target, gender, and age(Table 3, Figure 2B ). To find the association between virus infection and clinical signs in SARI, binary logistic regression was performed between 4 commonly diagnosed respiratory abnormality, including anhelation, respiratory failure, heart failure and pleural effusion, and the viral target detected by xTAG® RVP FAST.
cord-335567-ssnvr6nj	2015	In 2001, this led to the discovery of human metapneumovirus (hMPV) and soon following that the outbreak of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) promoted an increased interest in coronavirology and the latter discovery of human coronavirus (HCoV) NL63 and HCoV-HKU1. Middle East Respiratory Syndrome coronavirus (MERS-CoV) represents the most recent outbreak of a completely novel respiratory virus, which occurred in Saudi Arabia in 2012 and presents a significant threat to human health. In recent years six new human respiratory viruses have been reported including human metapneumovirus (hMPV) [16] , bocavirus and four new human coronaviruses including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), HCoV-HKU1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV). Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients
cord-336335-spap39b7	2013	OBJECTIVES: The objectives of this study were to determine the number of emergency visits for influenza-like illness (ILI) and severe acute respiratory infection (SARI) and to evaluate the association between ILI/SARI, RVI prevalence, and meteorological factors/air pollution, in the city of Porto Alegre, Brazil, from November 2008 to October 2010. The correlations among meteorological variables, air pollution, ILI/SARI cases, and respiratory viruses demonstrated the relevance of climate factors as significant underlying contributors to the prevalence of RVI. The aims of this study were to determine the number of emergency room visits for influenza-like illness (ILI) and severe acute respiratory infection (SARI) and to evaluate the association between ILI/SARI frequency, respiratory virus prevalence, and meteorological factors/air pollution, especially in adult population, in a humid subtropical climate. The data were analyzed using time-series analysis, through a generalized linear model (GLM) to examine the association between ILI or SARI and air pollution/meteorological variables, using logistic regression.
cord-336420-1a2u9p4t	2016	title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia A Prospective Follow-Up Study Advances in molecular methods have increased the sensitivity of viral diagnostics tests, with recent studies reporting the detection of respiratory viruses in the nasopharynx in 44-57% of childhood febrile neutropenia episodes using real-time polymerase chain reaction (PCR) [3] [4] [5] 12] . Viral nucleic acids were extracted from the NPA with a MagAttract Virus Mini M48 kit (Qiagen, Sollentuna, Sweden) and analyzed with in-house real-time PCRs for the following 16 viruses: adenovirus (HAdV); bocavirus (HBoV); coronaviruses NL63/OC43/229E/HKU1 (HCoV); enterovirus (EV); influenza virus A, including A(H1N1)pdm09 and B (Flu); metapneumovirus (HMPV); parainfluenza viruses 1-3 (PIV); respiratory syncytial virus (RSV) and rhinovirus (RV) [19] . These results support the theory holding that there is a causal relationship between respiratory viral infections and episodes of febrile neutropenia, but proving this theory will require more longitudinal studies with asymptomatic neutropenic control cohorts.
cord-336562-5qmzne98	2017	The ability to obtain tidal breathing measurements may lead to new insights into changes in chest and abdominal motion in pediatric respiratory disease. 47 Acute viral bronchiolitis, due to RSV and other pathogens, continues to have a major impact worldwide on childhood mortality and hospital admissions, 51 is associated with subsequent asthma and allergy risk, 52 and could be increasing in incidence. 57 Flores et al 58 conducted a randomized clinical trial comparing 3% hypertonic saline to normal saline in previously healthy infants hospitalized with mild-to-moderate acute viral bronchiolitis. Thus, the study does not support the use of nebulized hypertonic saline over normal saline in therapy of hospitalized children with mild-to-moderate acute viral bronchiolitis. Association between trafficrelated air pollution and asthma in preschool children in a national Japanese nested case-control study Changes in lung function measured by spirometry and the forced oscillation technique in cystic fibrosis patients undergoing treatment for respiratory tract exacerbation
cord-336743-udokbcki	2020	Setting the level of ventilator assist in everyday practice relies mostly on the clinical estimation of inspiratory effort, as indicated by the breathing pattern -tidal volume (VT) and respiratory rate (RR)-and clinical signs of respiratory distress (Boles et al., 2007; Hansen-Flaschen, 2000; Hess, 2001; Ray et al., 2006) . The aim of this study was to 1) characterize the responses of respiratory drive, respiratory effort, and breathing pattern to changing levels of ventilatory assist in critically ill patients and 2) assess if changes in respiratory rate may indicate changes in respiratory drive and effort. To this end, during proportional assist ventilation with adjustable gain factors (PAV+), noninvasive measurements of respiratory drive, effort (as indicated by inspiratory muscle pressure) were obtained at different levels of assist, using a validated prototype monitor (PVI) (Kondili et al., 2010; Younes et al., 2007) .
cord-337137-0ey40gzw	2005	Published by John Wiley & Sons, Ltd. Severe acute respiratory syndrome (SARS) is a new viral disease caused by a novel coronavirus, SARS-CoV ( Figure 1 ) [1, 2] . Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Tissue and cellular tropism of the coronavirus associated with severe acute respiratory syndrome: an in-situ hybridization study of fatal cases Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung Immunohistochemical, in situ hybridization, and ultrastructural localization of SARS-associated coronavirus in lung of a fatal case of severe acute respiratory syndrome in Taiwan Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells Autoantibodies against human epithelial cells and endothelial cells after severe acute respiratory syndrome (SARS)-associated coronavirus infection
cord-337562-pkejb0a9	2009	Merkel cell polyomavirus (MCPyV) DNA was detected in 7 (1.3%) of 526 respiratory tract samples from patients in Australia with upper or lower respiratory tract symptoms. Merkel cell polyomavirus (MCPyV) DNA was detected in 7 (1.3%) of 526 respiratory tract samples from patients in Australia with upper or lower respiratory tract symptoms. I n the past 2 years, several previously unknown human polyomaviruses (PyVs) have been identifi ed: KI virus (KIPyV) (1) and WU virus (WUPyV) (2) from respiratory samples, and more recently, Merkel cell polyomavirus (MCPyV), most commonly from Merkel cell carcinoma tissue (3) . The presence of MCPyV in samples positive by real-time PCR was then confi rmed by using partial large T antigen (LT3) and major capsid protein (VP1) conventional MCPyV detection PCR assays of Feng et al. Sequence data from positive specimens indicate that MCPyV found in respiratory secretions is similar to the viruses identifi ed within Merkel cell carcinomas.
cord-337747-7sb03moe	2019	title: Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital‐based observational study in Niamey, Niger This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger''s capital city, and the reported clinical procedures. 14 This study aims to describe the viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals of Niamey, the capital city of Niger, and the reported clinical procedures. In this 1-year prospective study, both viral and bacterial pathogens were detected in high proportion among hospitalized children aged younger than 5 years with febrile ARI in Niamey, Niger. Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger
cord-339009-wcoch07b	2012	Because the causative agent of SARS is • one or more clinical findings of respiratory illness (e.g. cough, contagious, preventative measures focus on avoidance of exposhortness of breath, difficulty in breathing, or hypoxia) sure, and infection control strategies for suspected patients and • travel within 10 days of onset of symptoms to an area with contacts. [12] Of the reported cases was updated to include laboratory criteria for evidence of infection 64% were from China, 19% from Hong Kong, 8% from Taiwan, with the SARS-associated coronavirus (SARS-CoV). Algorithm for evaluating and managing patients requiring hospitalization for radiographically confirmed pneumonia, in the absence of person-toperson transmission of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) anywhere in the world.
cord-339039-6gyo9rya	2018	The purpose of this review is to describe the most frequent and relevant nosocomial viral respiratory infections, their mechanisms of transmission and the infection control measures to prevent their spread in the healthcare setting. RECENT FINDINGS: Although most mechanisms of transmission and control measures of nosocomial viral infections are already known, improved diagnostic tools allow better characterization of these infections and also lead to the discovery of new viruses such as the coronavirus, which is the cause of the Middle East Respiratory Syndrome, or the human bocavirus. Influenza virus can be transmitted through infectious droplets eliminated by patients when coughing or sneezing, or through direct contact with surfaces contaminated by respiratory secretions from symptomatic infected subjects (Table 1 ) [32] . Preventive measures to avoid adenovirus nosocomial infections include patient cohorting, reduction of visitors and contact and droplet precautions, along with the exclusion of infected healthcare workers from clinical duties (Table 2 ) [13, 36] .
cord-339386-sxyeuiw1	2015	The virus was quickly identified as a new CoV most closely related to several bat CoVs. 6 This report was followed by a number of other reports identifying a total of 537 infected individuals, all of whom had acute respiratory symptoms, severe in most, and fatal in 145 (as of May 11, 2014) . 6 Between then and May 2014, a total of 537 cases occurred, all infected by this virus, now termed the Middle East respiratory syndrome coronavirus (MERS-CoV). In response to the global spread and associated severe disease, the World Health Organization coordinated a rapid and effective control program that included isolation of cases, careful attention to contact, droplet and airborne infection control procedures, quarantine of exposed persons in some settings, and efforts to control spread between countries through travel advisories and travel alerts.
cord-339852-9rq7zzqs	2006	In addition, we performed this study in order to delineate the prevalence, the potential clinical impacts and evaluation of the genetic characterization of this pathogen in young children who presented with acute lower respiratory tract infections (ALRI). In this study we applied molecular biology techniques to identify hCoV in nasopharyngeal secretions (NPs) for the study on the prevalence of molecular characterization and clinical correlation of coronavirus infections in hospitalized infants and young children with acute lower respiratory tract infection (ALRI). In this study, we have identifi ed human coronavirus hCoV-OC43 and hCoV-229E infection in infants and young children presenting with ALRI. hCoV-229E and hCoV-OC43 have previously been proven responsible for infecting people of all age groups and causing severe lower respiratory tract infection primarily in frail patients such as young children and elderly individuals [17] [18] [19] . The clinical features associated with coronavirus infection appear to be similar to those observed with other respiratory viruses, such as RSV, parainfl uenza virus and human metapneumovirus.
cord-339869-euikj8fv	2016	However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory Introduction Molecular techniques including polymerase chain reaction (PCR) have increased the sensitivity of detection for common and emerging respiratory viruses, and often reveal the presence of more than one pathogen in respiratory patients. Our study aims to analyze the relationship between viral or bacterial co-infection detected by molecular methods, and the clinical phenotype of children admitted to hospital with lower tract acute respiratory infections (LT-ARI). PICU admission, disease severity according to different scales, need for respiratory support, and length of hospital stay followed a similar pattern in viral mono-versus co-infected children.
cord-340104-6n0sn5lk	2016	This large study population determined the burden of respiratory viruses associated with ARI in children over a 2-year period a multiplex molecular testing platform. With over 60% of 2235 children testing positive for respiratory viruses, more infections were detected than previous studies [Akhter et al., 2009; Al Hajjar et al., 2011; Alanazi et al., 2013; Bukhari and Elhazmi, 2013] . This high rate was significantly different from that obtained in the present 2-year study (23% detection for RSV in children positive for respiratory viruses), as well as others [Alanazi et al., 2013; Amer et al., 2015] . Viruses associated with respiratory tract infections in children attending to the emergency room, king abdulaziz medical city, riyadh, Saudi Arabia Viral agents causing acute lower respiratory tract infections in hospitalized children at a tertiary care center in Saudi Arabia
cord-340280-m1j6v33y	2019	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). 1, 5, 9 Contrary to the accumulating knowledge of ARIs in temperate regions, epidemiological research on acute respiratory viral illness in tropical and subtropical areas is limited, although the epidemiological diversity, according to local climate and latitude, has been well studied. 14 Our study was designed to describe the molecular epidemiology of ARI-related respiratory viruses, including the seasonality of the viruses in the northern UAE for over 2 years. 2, 24, 25 FLU was the most common respiratory virus in all age groups, and the positivity rate was 20.0%, which is similar to previous data reported from studies in Oman. 7,34 However, our data suggest that in the UAE, like in other temperate countries, a diverse set of respiratory viruses contribute to the ARI cases that compel patients to visit medical facilities, because of their severity.
cord-340811-w4x4falm	2020	Search terms include novel coronavirus pneumonia, severe acute respiratory syndrome coronavirus 2, coronavirus and ventilation. Interestingly, patients with COVID-19 pneumonia may present an atypical form of ARDS characterized by a dissociation between their relatively preserved lung mechanics and the severity of hypoxemia (23) . Oxygen therapy should be considered immediately when patients affected by severe acute respiratory infection have the following conditions: hypoxemia (PaO2 <60 mmHg or SpO 2 <93% when breathing air); respiratory distress (respiratory frequency> 24 times/min); hypotension (systolic blood pressure <100 mmHg) (24) . Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study
cord-341765-ml6eo8r3	2020	title: Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In this study, throat swab specimens were collected from patients with respiratory symptoms to identify viral etiological agents of ARTI. Singleplex PCR assays were used for detection of a panel of respiratory viruses using family-level primers for Paramyxoviridae, Herpesviridae, Coronaviridae, Hantaviridae, Adenoviridae, Arenaviridae; genus-level primers for Enterovirus, Henipavirus, Influenza A virus, Bocavirus; and Pneumovirinae sub-family primer including respiratory syncytial virus (RSV) and human metapneumovirus (HMPV). In addition to the influenza virus routinely screened in ARTI studies, other viral agents associated with severity like Herpesviridae, Enterovirus and RSV should be screened in respiratory illnesses.
cord-342133-khrljehj	2015	To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (2009–2010, 2011–2012, and 2013–2014). To evaluate the circulation of the different hBoV types and the possible relationships between viral load, virus genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children attending the emergency room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection arising between November 1 and March 31 during 3 winters (2009-2010, 2011-2012, and 2013-2014) . Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children
cord-342314-nx0a3nvd	2017	title: Aerobic bacteriological studies on the respiratory tracts of apparently healthy and pneumonic camels (Camelus dromedaries) in selected districts of Afar Region, Ethiopia A cross-sectional study was conducted to isolate and identify bacterial species from the respiratory tract of apparently healthy and pneumonic camels in Asayita and Dubti woredas in the Afar Region, Ethiopia. There was a statistically significant association between the health status of the camels as well as the anatomical site studied with the isolation rates of the major respiratory pathogens (p < 0.05). Therefore, the present study was conducted to determine comparatively the bacterial species associated with camels with and without pneumonic lungs, identify the Streptococci spp. Besides, there was a statistically significant difference between pneumonic and apparently healthy camels with the isolation rate of the major respiratory pathogens (except B. The pathogenic bacteria isolated during the present study period are comparable to those previously reported from the respiratory tract of apparently healthy camels (Ahmed and Musa 2015) .
cord-342476-0rupk21u	2019	The sensitivity, specificity and predictive values of mNGS were calculated based on 24 PCR positive and 1120 PCR negative target results of 88 samples and the normalized read counts (Table 5 ). The following markers were tested for potential associations with clinical severity of exacerbation (exacerbation severity, self-reported exacerbation severity), length of exacerbation and a decrease/increase in FEV 1 (control visit compared to baseline): mNGS pathogen positive versus negative exacerbation (qPCR targets), the number of normalized reads (log, cutoff of �5normalized reads) for the different target viruses (species level). The Shannon diversity scores for bacteriophages (normalized reads, cut-off of �5normalized reads) were comparable for COPD exacerbations of viral aetiology in PCR positive versus negative patients (Fig 5) . In this study, the respiratory virome in patients with COPD exacerbations was analysed with both mNGS and qPCR, and combined with clinical data.
cord-342649-ysossker	2012	The relationship between viral load, disease severity and antiviral immune activation in infants suffering from respiratory syncytial virus (RSV)-associated bronchiolitis has not been well identified. The main objective of this study was to determine the existence of a correlation between RSV load and disease severity and also between different clinical markers and mRNA levels of the interferon stimulated gene (ISG)56 in infants hospitalized for bronchiolitis. Results indicated that viral load was positively related to the clinical severity of bronchiolitis, the length of hospital stay, the levels of glycemia and the relative gene expression of ISG56, whereas an inverse correlation was observed with the levels of hemoglobin. In the framework of a study aimed at understanding the pathogenesis of RSV infection and at further characterizing viral and host factors involved in determining the severity of bronchiolitis, we addressed whether any diVerences in RSV-RNA levels in the airway tracts of infants with bronchiolitis might explain the broad clinical spectrum of RSVassociated bronchiolitis.
cord-342853-n3e6yawi	2007	Human bocavirus (HBoV), a virus discovered in Sweden in 2005, has been associated with acute respiratory infections in young children and subsequent reports suggest that HBoV may have a worldwide distribution. This report describes the frequency and clinical presentation of HBoV in 261 Iranian children<5 years old with acute respiratory infections attending two regional hospitals in Rasht, Iran in the winter of 2003–2004. Human bocavirus (HBoV) was first described in 2005 [Allander et al., 2005] and it was suggested that the virus might be a cause of acute respiratory infections. Children less than 5 years of age with acute respiratory infections of less than 7 days duration attending the outpatient department or being admitted to hospital from Saturday to Thursday were enrolled after informed parental consent. Given the high frequency of HBoV in Iran, this virus might play a significant role as a cause of acute respiratory infections in children.
cord-342915-r9kv67we	2013	Most of the treatment data regarding antivirals for non-influenza respiratory viruses have been derived from observational studies in immunocompromised hosts, and sometimes, infants, but recent randomized, controlled trials in specific target populations have helped to address the potential value of antiviral interventions. 12, [17] [18] [19] In addition, systematic reviews of the observational reports concluded that the common use of multiple agents in combination, varying dose regimens, paucity of studies with systematic data collection, complications from immunosuppressive therapy, and the lack of randomized, controlled trials meant that existing data were inconclusive with regard to putative antivirals and thus inadequate to determine appropriate management of SARS infections. In addition, one approved agent for selected parasitic infections, oral nitazoxanide, may have interferon-inducing properties, is inhibitory for various respiratory viruses including influenza and a canine CoV in vitro, 32 and has shown promising dose-related activity in a phase 2, placebo-controlled, randomized trial in treating uncomplicated influenza 33 Consequently, nitazoxanide would be an interesting agent to test alone and in combination with other antivirals for CoV infections.
cord-342993-deuytbml	2010	3 Various viral agents, including the respiratory syncytial virus (HRSV), influenza A and B (FLUAV and FLUBV), parainfluenza (HPIV), adenovirus (HAdV), rhinovirus (HRV), enterovirus (HEV), coronavirus (HCoV), and the recently described metapneumovirus (HMPV) 4 and bocavirus (HBoV) 5 have been detected in patients presenting with asthma exacerbation. [10] [11] We performed a cross-sectional study to determine by means of immunofluorescence assay (IFA) and molecular techniques the prevalence of traditional and newly described respiratory viruses and atypical bacteria in children hospitalized due to an acute asthma exacerbation in Buenos Aires, a temperate southern hemisphere city. [30] [31] In conclusion, the present study confirms the high prevalence of respiratory viruses in hospitalized children with an acute asthma exacerbation, highlights the importance both of HRSV and HRV in all age groups, and describes their seasonal pattern in a temperate Southern Hemisphere location.
cord-343042-9mue4eiv	2020	Following these complaints, the autopsy was performed, and subsequent histological examinations revealed the presence of typical and pathognomonic histological findings of acute viral bronchiolitis, whose morphological appearance is poorly reported in the literature. For all these reasons, the autopsy, either clinical or medicolegal, is mandatory in cases of sudden unexpected infant death to manage claim requests because only the histological examinations performed on samples collected during the autopsy can reveal the real cause of death. In fact, in the reported case studies, histopathologic diagnostics identified pathognomonic signs of acute bronchiolitis characterized by edema, congestion, leukocytic infiltration in the bronchiolar wall, leukocytes in the peribronchial interstitial pulmonary space, allowing the identification of the exact cause of death. The analysis of the presented cases shows that the autopsy is mandatory in SUID occurrence, in which the absence of anamnestic data and/or acute clinical signs does not allow to identify the cause of death.
cord-343050-1pfqgvie	2015	The results during the first 2 years (2012-2013) provided scientific evidence to (a) support a change to NZ''s vaccination policy for young children due to high influenza hospitalizations in these children; (b) contribute to the revision of the World Health Organization''s case definition for severe acute respiratory illness for global influenza surveillance; and (c) contribute in part to vaccine strain selection using vaccine effectiveness assessment in the prevention of influenza-related consultations and hospitalizations. Over 5 years, we hope this project will shed more light on the burden of influenza and other respiratory pathogens in our study population and subgroups and estimate key epidemiologic parameters such as relative rates of infection, clinical disease, general practice visits and hospitalizations as well as risk factors for illness, effectiveness of vaccination, mechanisms of immunity and monitoring for new influenza viruses with pandemic potential such as A(H7N9) and other emerging viruses (e.g. MERS-CoV) and provide a framework for timely assessment of severity which is essential in an event of emergence of these pathogens.
cord-343074-dsubeaso	2014	title: Molecular epidemiology of a post‐influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3 An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. To determine the principal cause of the outbreak, direct polymerase chain reaction (PCR) amplification followed by sequence analysis targeting parts of the hexon gene of HAdV was performed. Serotypes of 1,007 PCR‐diagnosed HAdV‐positive samples from patients with an acute upper respiratory tract illness were determined and epidemiological characteristics including major aged group and clinical symptoms were analyzed. Epidemiological and molecular data presented in this study confirmed that the outbreak in 2010 was not associated with genetic alterations causing a change in the pathology of the major causative agent, HAdV-3, nor with multiple infections with other respiratory viruses.
cord-343325-cbrly7f5	2020	title: A proposed lung ultrasound and phenotypic algorithm for the care of COVID-19 patients with acute respiratory failure We propose a management algorithm that combines the respiratory rate and oxygenation index with bedside lung ultrasound examination and monitoring that could help determine earlier the requirement for intubation and other surveillance of COVID-19 patients with respiratory failure. His phenotype changed from an H-type to an (D) L-type (courtesy of Dr. Emmanuel Charbonney and Dr. Lawrence Leroux) Lung ultrasound in COVID-19 respiratory failure therapy with a high-flow nasal cannula (HFNC) with an increased fraction of inspired oxygen (F I O 2 ). 51 Lung ultrasound can also impact clinical decision-making in patients with acute respiratory failure 52, 53 and provide comprehensive monitoring of regional lung aeration changes that could be used to predict response to prone positioning with improved right (Figs 6 and 7) [54] [55] [56] or higher positive end-expiratory pressure strategy.
cord-343365-4y9fedcr	2013	The promise of gene therapy as a cure for the disease has fizzled out, and while new antimicrobials and other pharmaceuticals promise improved longevity and better quality of life, the average life span of a patient with cystic fibrosis is still at about 35 years. Several significant challenge areas include the diagnosis and treatment of certain specific infectious lung diseases, including viral lower respiratory infections caused by respiratory syncytial virus, rhinovirus, metapneumovirus, coronovirus, and enterovirus. The search for a vaccine for respiratory syncytial virus (RSV) has been ongoing for many years, but like the previous case of gene therapy in cystic fibrosis, this also has been a challenge to achieve. The current global strategies for the development of an RSV vaccine now target four areas: infants <6 months of age; infants >6 months of age and young children; pregnant women for whom passive immunization can be implemented; and the elderly, in whom RSV can also have significant morbidity [52] [53] [54] .
cord-343390-y903mxcj	2018	title: Bovine respiratory syncytial virus seroprevalence and risk factors in non-vaccinated dairy cattle herds in Brazil This study aimed to characterize the epidemiology of BRSV infection in dairy cattle herds of São Paulo State, Brazil, using serological and risk factors analyses. The analysis of risk factors indicated that the age group and the occurrence of coinfection with bovine herpesvirus 1 (BoHV-1) and bovine viral diarrhea virus 1 (BVDV-1) should be associated with a higher prevalence of BRSV, while natural suckling was considered a protective factor. Due to this, the current study aimed to determine antibody prevalence against BRSV and investigate some risk factors associated with BRSV seroprevalence in herds of an important milk producing region in São Paulo State, Brazil. Bovine respiratory syncytial virus seroprevalence and risk factors in endemic dairy cattle herds Prevalence of and risk factors for bovine respiratory syncytial virus (BRSV) infection in non-vaccinated dairy and dual-purpose cattle herds in Ecuador
cord-344271-5aynmdsk	2007	title: Spectrum of Viruses and Atypical Bacteria in Intercontinental Air Travelers with Symptoms of Acute Respiratory Infection Using sensitive polymerase chain reactions, we studied the spectrum of atypical bacteria and respiratory viruses in travelers fulfilling the case definition of severe acute respiratory syndrome. These assays were used to determine a point prevalence of the full spectrum of respiratory viruses and atypical bacteria in SARS-compatible patients. Inf and PIV were clearly the most prevalent agents in flight patients, at 14.2% and 15.5%, respectively, without significant differences between age groups (1-way analysis of variance [ANOVA], 95% significance level). Baseline data on the prevalence of respiratory viruses and atypical bacteria after air travel are not currently available. It cannot be told whether the high prevalence and diversity of respiratory viruses seen in our study is specific to patients with recent intercontinental air travel.
cord-344889-1y4ieamp	2006	OBJECTIVES: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Abstract Objectives: We aimed to characterise and quantify the incidence of common infectious agents in acute exacerbations of chronic obstructive pulmonary disease (COPD) requiring ventilation, with a focus on respiratory viruses. Of these, influenza types A and B (Inf A, B), parainfluenza types 1, 2 and 3 (Para 1, 2, 3), rhinovirus (RV), adenovirus (AV), respiratory syncytial virus (RSV), coronavirus (CoV) [11, 12] and, less commonly, human metapneumovirus (hMPV) [13] , and enterovirus (EV) [14, 15] have been shown to play significant roles in airway infections. A probable virus pathogen was found in 46 cases (43%) and a probable bacterial aetiology was found in 25 cases (23%) in this study of ventilated COPD exacerbation patients.
cord-345211-4ivqlsgt	2016	Guidelines for the management of community-acquired pneumonia in children are even more restrictive, again recommending that tests should mainly be used on patients with severe disease, with a focus on blood cultures and detection of respiratory viruses [11, 12] . While not exactly new (polymerase chain reaction (PCR) assays for respiratory pathogens have been around for over 20 years), the widespread adoption of nucleic acid detection tests (NATs) by diagnostic laboratories has been relatively slow. The NATs that are most widely used in diagnostic laboratories are those that detect potential pneumonia pathogens that are not part of the normal flora, namely respiratory viruses and selected non-colonizing bacteria. Quantitative multiplex PCR has been used to determine the etiology of community-acquired pneumonia in adults using cutoffs developed for interpretation of culture results from lower respiratory tract specimens [85, 86] .
cord-345472-qrddwebe	2020	A vaccine against respiratory syncytial virus (RSV), the leading cause of viral bronchiolitis in infancy, remains elusive, and hence new therapeutic modalities are needed to limit disease severity. (1), degranulation (2), respiratory oxygen species (ROS) production (3), and the release of neutrophil extracellular traps (NETosis) (4) are associated with increased lung inflammation, systemic fever, mucus hypersecretion, airway obstruction, and epithelial cell death. Excessive neutrophil-derived inflammatory cytokine production (1), degranulation (2), respiratory oxygen species (ROS) production (3), and the release of neutrophil extracellular traps (NETosis) (4) are associated with increased lung inflammation, systemic fever, mucus hypersecretion, airway obstruction, and epithelial cell death. Unlike wild-type (WT) control mice, plasmacytoid dendritic cell (pDC)-depleted, Toll-like receptor (TLR)7-deficient, or interferon regulatory factor (IRF)7-deficient neonatal mice develop severe pathology, characterised by increased neutrophilia and lung inflammation in response to acute PVM infection [80] [81] [82] .
cord-346096-aml84iv1	2018	These results suggest the feasibility of employing bioaerosol surveillance techniques in public transportation areas, such as airports, as a noninvasive way to detect and characterize novel respiratory viruses. In this pilot study, we studied bioaerosol samples collected in Raleigh Durham International Airport for molecular evidence of respiratory viruses. Although not the focus of our study, we did not detect viable viruses using culture analysis associated with positive aerosol samples at RDU airport. In this pilot aerosol study, we conducted surveillance for human and zoonotic respiratory viruses in an airport setting over a period of nine weeks from January to March 2018. Despite these limitations, the results of this study suggest that aerosol sampling is a useful technique for respiratory virus surveillance in high traffic and crowded areas such as airports.
cord-346253-0mnsm6s4	2012	HRV are the most common viral agents [33] ; Other respiratory tract viruses detected in children with an asthma exacerbation include RSV, influenza, coronavirus, hMPV, parainfluenza virus, adenovirus, and bocavirus [34] [35] [36] . Beside importance for bone health, vitamin D plays an important role in adequate function of both the innate and adaptive immune systems including development of dendritic cells and regulatory T lymphocytes [151, 152] production of antimicrobial proteins by airway epithelium [153] , modifying the effect of intestinal flora on inflammatory disorders [107] , and modulation of the inflammatory response to viral infections [154] . In a recent study of 48 children from five to 18 years of age, with newly diagnosed asthma, vitamin D supplementation during the northern hemisphere winter months (September to July) prevented declining serum concentrations of 25(OH) D and reduced the risk of asthma exacerbation triggered by acute respiratory tract infections [161] .
cord-346290-my8ow5ee	2020	Respiratory viruses are responsible for a variety of clinical syndromes including the common cold, acute otitis media, laryngitis, sinusitis, pneumonia, bronchiolitis, influenza-like illness, and exacerbations of asthma and chronic obstructive pulmonary disease. Treatment modalities include over-the-counter and non-specific remedies along with a small number of specific antiviral medications such as the influenza neuraminidase inhibitors or palivizumab against respiratory syncytial virus. Viruses of the family of Pneumoviridae form enveloped, spherical or filamentous virions with 100-200 nm in diameter, which contain a single, linear, negative-sense RNA genome. Human bocavirus 1 (HBoV1), a member of the species Primate bocaparvovirus 1, in the genus Bocaparvovirus and the subfamily of Parvovirinae, is strongly associated with upper and lower respiratory tract infections in young children. The common cold is a rather benign clinical entity, which may however be complicated by secondary bacterial infections, otitis media, sinusitis, pneumonia, and asthma exacerbations; severe courses of disease and death may occur in young children and immunocompromised patients.
cord-346539-kxnrf5g5	2020	This paper answers pressing questions, formulated by young clinicians and scientists, on SARS‐CoV‐2, COVID‐19 and allergy, focusing on the following topics: virology, immunology, diagnosis, management of patients with allergic disease and asthma, treatment, clinical trials, drug discovery, vaccine development and epidemiology. The first cases of the coronavirus disease 2019 (COVID19) , caused by the novel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), were reported in China in December 2019 1 and rapidly led to pandemic. 40, 41 A seroconversion study in COVID-19 patients has found and association between disease severity and SARS-CoV-2-specific IgA levels. Mesenchymal stem cell therapy may potentiate the low IFN-I and -III levels and moderate IFN-stimulated gene response reported in SARS-CoV-2-infected ferrets and COVID-19 patients. Effect of High vs Low Doses of Chloroquine Diphosphate as Adjunctive Therapy for Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: A Randomized Clinical Trial
cord-346673-kyc1wks5	2016	In particular, our study shows that (i) human coronavirus infections are more common during influenza seasons and in co-infections than previously recognized, (ii) factors associated with co-infection differ from those associated with viral infection overall, (iii) virus prevalence has increased over time especially in infants aged <1 year, and (iv) viral infection risk is greater in the post-2009 pandemic era, likely reflecting a widespread change in the viral population that warrants further investigation. We analysed diagnostic data generated by NHSGGC using multiplex PCR from 2005 to 2013 with the following objectives: (i) to describe testing and virus prevalence trends, (ii) to examine temporal and patient subgroup distributions for each individual virus, and (iii) to compare factors associated with overall viral infection and co-infection using statistical modelling, in order to provide robust and timely estimates of who is most at risk of viral-associated respiratory illness, and when, within a major urban UK population.
cord-346887-dl0wc4u2	2012	The aims of this study were to determine the overall distribution of respiratory viruses in neonates hospitalized with acute lower respiratory tract infectiosns (ALRI) and to describe the clinical characteristics of RSV infections in these neonates. In addition to respiratory syncytial virus (RSV), human rhinovirus (hRV), human parainfluenza virus (hPIV), and human metapneumovirus (hMPV) have been found to be major causes of acute lower respiratory tract infections (ALRI) in infants and young children. 1, 13 One study based on hospitalized children with ALRI in Korea reported that RSV (33.2%) was the most common virus among 13 respiratory viruses and was followed by hRV (19.1%), influenza virus (16.9%), hMPV (15.4%), and hPIV (8.3%). In the present study a significantly higher proportion of the RSV group obtained infections from neonatal day-care centers. FLIP-2 Study: Risk factors linked to respiratory syncytial virus infection requiring hospitalization in premature infants born in Spain at a gestational age of 32 to 35 weeks
cord-347246-0vofftmj	1990	This paper reviews several important infectious diseases of the upper airway of rats and mice and discusses the potential influence of these conditions on the results of toxicology studies. All three agents cause significant rodent respiratory disease, with lesions in the upper airways, including the nasal passages. Although there are many excellent descriptive studies ofthe histogenesis of Sendai virus-induced lesions within the lower respiratory tract, few pathology reports include a description of lesions in the nasal cavity and upper airway. Although numerous bacteria can infect the upper airway of the rat and mouse, they are not generally prevalent in well-conducted toxicology studies begun with animals free of adventitious murine pathogens and maintained with modern methods of laboratory animal husbandry. A variety of important microbial pathogens including viruses, mycoplasmas, bacteria, and fungi infect the upper respiratory tract of the mouse and rat and result in significant pathologic alterations.
cord-347255-fl9lur4h	2019	Secondary outcomes included the proportion of patients with a respiratory pathogen identified by the FilmArray Respiratory Panel test or any other upper respiratory pathogen diagnostic test ordered by the physician; the proportion of patients with a laboratory-confirmed influenza diagnosis; the proportion of patients receiving appropriate anti-influenza treatment or prescription in the ED by an emergency medicine clinician (composite rate of anti-influenza treatment in positive patients and nonuse of anti-influenza treatment in negative patients); the proportion of patients discharged home from the ED vs hospital admission; the proportion of patients with all-cause or respiratory illness-related repeat ED visit, hospital or ICU admission, or death within 30 days; clinician adherence to guidelines for the treatment of patients with influenza (recommendations for use of antivirals only); length of ED stay; length of hospital stay; time to influenza test results; and time to other respiratory pathogen test results. Thus, we conducted a randomized clinical trial of the FilmArray RP vs usual care in ED patients with signs or symptoms of upper respiratory infection or influenza-like illness.
cord-347262-q88g1561	2020	Whilst none of these were anaesthetists or intensivists, 53/1718 (3.1%) healthcare workers performing or involved in tracheal intubation of patients with confirmed or suspected COVID-19 subsequently reported laboratory-confirmed SARS-CoV-2 infection [4] . Here, we review the evidence from SARS and contemporaneous data from COVID-19 to inform assessment and management of the risk of SARS-CoV-2 transmission to healthcare workers involved in elective peri-operative care. The WHO list of aerosol-generating procedures is based on epidemiological evidence of transmission to healthcare workers caring for SARS patients [30, [36] [37] [38] [39] [40] [41] [42] [43] [44] . The studies upon which the WHO list of aerosol-generating procedures is based do not provide any direct evidence that tracheal intubation itself increases the risk of SARS transmission. Aerosol Generating Procedures and Risk of Transmission of Acute Respiratory Infections to Healthcare Workers: A Systematic Review
cord-347465-yu6oj30v	2018	METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. In conclusion, in our study we investigated the etiological structure of acute respiratory viral infections in hospitalized children in Novosibirsk, Russia, and evaluated age and seasonal distribution of the various respiratory viruses.
cord-347509-2ysw9a0a	2016	1, 2 Susceptibility to respiratory viral infections may be important especially in older age, but the viral etiology and clinical significance of respiratory illnesses in elderly adults is poorly documented. [2] [3] [4] The aims of this study were to investigate the presence of viruses in elderly adults and to assess the association between viral infection and respiratory illness and between viral infection and chronic illness in individuals with an illness that requires hospitalization. 10 The current study shows that there is an association between respiratory virus detection and weight in elderly adults. 3, 4 The objective of the current study was to assess what older adults with cancer know about their diagnosis and treatment and to identify factors associated with the completeness of this information.
cord-348490-dqabq6d8	2016	title: Sickle-cell disease in febrile children living in a rural village of Madagascar and association with malaria and respiratory infections From May 2011 to November 2013, a cross-sectional study was conducted in the rural village of Ampasimanjeva in the south east cost of Madagascar aiming to identify blood-borne protein biomarkers that can differentiate the causes of unexplained acute febrile illness in children. Our study shows that prevalence of SCD was 2.4% and that of SCT 23.8% among children aged 2-59 months presenting with fever and living in high endemic area for malaria. However, among the 23 viral and atypical bacteria pathogens studied, there was no statistical difference in prevalence between the three groups for 20 of them and include HRV the most common respiratory virus detected or influenza virus A (H1N1)/ pdm09 known to increase disease severity in children with SCD [29] .
cord-349226-xzlc1pni	2020	To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. The COVID-19 disease is caused by a virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China at the end of 2019 [4] . The COVID-19 disease begins with the invasion of lungs by SARS-CoV-2 virus, and the major complications that develop subsequently are related to lung infection and immune response generation, therefore, lung microbiome might play an important role from initiation to the progression of this disease [16] . The SARS-CoV-2 viral infection occurs amid the local environment of diverse microbiota; therefore, it is apparent that lung microbiota can have an impact on the initiation, development, and progression of the COVID-19 disease.
cord-349279-wbb7h2zu	2019	The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. The most commonly detected viruses in samples collected during ARI were HRV (52.8%), HCoV (11.0%), parainfluenza virus (PIF) (6.0%), IFV (4.5%), RSV (3.8%), and HMPV (3.5%). Detection of any virus and codetection of viruses were both significantly associated with swabs collected during ARI episodes. While their corresponding risk ratios are not considered significant, the number of detections of these viruses is relatively small, and a larger analysis would be required to rule out the clinical significance of detecting HRV-B, AdV and HBoV in ARIs. The effect of viral coinfection on respiratory disease severity in children has not been well established. New molecular virus detection methods and their clinical value in lower respiratory tract infections in children Viruses associated with acute respiratory infection in a community-based cohort of healthy New Zealand children
cord-349287-mwj2qby4	2015	The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20 % of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Since asymptomatic zoonoses have been posited [72] , an absence of antibodies to MERS-CoV among some humans who have regular and close contact with camels may reflect the rarity of actively infected animals at butcheries, a limited transmission risk associated with slaughtering DCs [70] , a pre-existing cross-protective immune status or some other factor(s) resulting in a low risk of disease and concurrent seroconversion developing after exposure in this group. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-tohuman transmission
cord-349560-8n65rgfz	2009	The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Creer and co-workers [1] identified at least one potential pathogen in 69% of specimens from adults suffering from lower respiratory tract infections (LRTI, 63% contained viruses, 26% contained bacteria) still leaving a significant diagnostic gap to be filled with so far unidentified pathogenic microorganisms. For this reason, detection of virus-specific antibodies by complement fixation assays, enzyme linked immunosorbent assays (ELISA), or immunofluorescence assays (IFA), all of which are available for established respiratory viruses, is inappropriate for the identification of the etiologic agent causing an acute respiratory tract infection, but useful for retrospective or epidemiological studies. Following the discovery of WUPyV in Australia, the virus was detected in specimens from patients with respiratory tract disease on all continents suggesting a worldwide distribution [10, [29] [30] [31] .
cord-349606-lup6tm2s	2014	Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using real-time polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Methods A prospective observational study was conducted in 36 patients under 12 years of age with upper airway lymphoid hypertrophy who were undergoing adenoidectomy, in which various respiratory viruses were investigated using realtime polymerase chain reaction in adenoid tissue and nasopharyngeal secretions collected preoperatively and 30 days postoperatively. Several respiratory viruses (influenza A and B; parainfluenza 1, 2, 3, and 4; rhinovirus; respiratory syncytial virus; human bocavirus; coronaviruses; and metapneumovirus) were investigated by quantitative real-time polymerase chain reaction (q-PCR) in adenoid tissue removed surgically and nasal swab specimens collected preoperatively and at 1 month postoperative follow-up visit.
cord-349956-h4i2t2cr	2019	We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. showed that human rhinovirus (HRV) and influenza viruses were the most common viral respiratory pathogens isolated from ill Hajj pilgrims [6] . Unadjusted associations between respiratory pathogen carriage with multiples factors: sociodemographic characteristics (gender, ≥60 years), chronic respiratory disease, BMI classification, smoking status; individual preventive measures (vaccination against influenza, vaccination against IPD, use of a face mask, hand washing, disinfectant gel and disposable handkerchiefs); antibiotic intake 10 days before each sample; respiratory virus or bacteria and dual carriage were analysed by univariable analysis. aureus carriage increase and the initial wave of respiratory symptoms, suggests that this pathogen association was responsible for the RTIs that affected most pilgrims soon after arriving in Mecca.
cord-350928-vj5qlzpj	2012	Objectives To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. In patients where HBoV is the only virus detected, the clinical symptoms reported are similar to those occurring as a result of infection with respiratory syncytial virus (RSV) and human metapneumovirus (HMPV), including bronchiolitis, bronchitis, pneumonia and exacerbation of asthma. 20 Here, we report the findings of the first study investigating the prevalence, seasonality, clinical characteristics and the molecular epidemiology of HBoV in amongst an all-ages population of patients hospitalized for acute lower respiratory illness (ALRI) in Cambodia over 3 consecutive years. 5 In this study, ALRI patient samples were screened for HBoV infection using a highly sensitive multiplex PCR assay previously shown to have a lower limit of detection of 4 copies of HBoV DNA ⁄ ll of viral transport medium.
cord-351008-p0n1fdxw	2020	We evaluated whether ambulance dispatch calls of highest urgency reflect the circulation of influenza A virus, influenza B virus, respiratory syncytial virus (RSV), rhinovirus, adenovirus, coronavirus, parainfluenzavirus and human metapneumovirus (hMPV). Specifically, we evaluated the association of syndromes compatible with respiratory infections in ambulance dispatches with trends in detections of influenza A, influenza B, RSV, rhinovirus, adenovirus, coronavirus, parainfluenza and human metapneumovirus (hMPV). Calls with triage codes that were potentially compatible with respiratory infections (Table 1) year, and hMPV (4%) and influenza A (1%) mainly during the winter peaks. Because of its ability to capture variations in respiratory virus circulation, ambulance dispatch data might be useful to signal events and to monitor the respiratory season as a whole, specifically reflecting severe infections and thus complementing existing surveillance systems. Use of ambulance dispatch calls for surveillance of severe acute respiratory infections Ambulance dispatch calls attributable to influenza A and other common respiratory viruses in the Netherlands
cord-351046-yq7287k9	2019	There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. There is a broad differential for a patient with respiratory failure, and careful physical examination and history are imperative to reduce morbidity and prevent mortality. The initial vital signs on his third ED presentation were as follows: temperature 36.7°C, heart rate 130 beats per minute, respiratory rate 30 breaths per minute, pulse oximetry 99%, and blood pressure of 113/81 mm Hg. On examination, the patient was awake and calm in his mother''s arms with no acute distress. The differential for a patient presenting to the ED with acute respiratory distress is broad and includes infection, ingestion, trauma, envenomation, muscular disorders, and autoimmune etiologies. Scorpion envenomation often presents with respiratory distress along with increased drooling, abnormal eye movements, muscle twitching, and agitation. 13, 14 The treatment for myasthenia gravis begins with respiratory support including intubation or noninvasive ventilation.
cord-351323-cbejbm5v	2013	The samples were tested further for influenza C virus, parainfluenza viruses 1–4, human rhinovirus, metapneumovirus and respiratory syncytial virus by conventional RT‐ PCR. Hence the information on epidemiology and clinical features of respiratory virus infection in India is based entirely on research studies and the disease burden or seasonal prevalence of respiratory viruses remains largely undefined. This study initiated to complete the information on circulating respiratory viruses among patients attending the outpatients departments of different hospitals with acute respiratory infections in the eastern region of India during 2010 through 2011. Comparative evaluation of real-time PCR and conventional RT-PCR during 2 year surveillance for influenza and respiratory syncytial virus among children with acute respiratory infections in Kolkata, India, reveals a distinct seasonality of infection Prevalence of respiratory syncytial virus group B genotype BA-IV strains among children with acute respiratory tract infection in Kolkata, Eastern India
cord-351990-aham72b9	2014	METHODS: Febrile respiratory illness (FRI) and severe acute respiratory infection (SARI) surveillance was conducted from October 2011 through March 2013 among three US populations: civilians near the US–Mexico border, Department of Defense (DoD) beneficiaries, and military recruits. Recruits with rhinovirus had higher percentages of pneumonia, cough, shortness of breath, congestion, cough, less fever and longer time to seeking care and were more likely to be male compared to those in the no/unknown pathogen group. This study aimed to describe characteristics associated with specific respiratory pathogens, as well as the etiology, seasonality, and coinfection rates among three US populations: military recruits, Department of Defense (DoD) beneficiaries, and civilians living near the US-Mexico border. Additionally, the following demographic and clinical signs and symptoms were collected from each FRI and SARI case: sex, age, study population, month of illness, pneumonia, sore throat, cough, nausea, shortness of breath, congestion, pink eye, body ache, headache, temperature, number of days of symptoms before seeking care, and date of seeking care.
cord-352222-zq9o66i4	2013	BACKGROUND: Acute respiratory infections are a leading cause of infectious disease-related morbidity, hospitalisation and mortality among children worldwide, and particularly in developing countries. MATERIALS AND METHODS: We conducted a prospective study in a paediatric ward in Antananarivo from November 2010 to July 2012 including patients under 5 years old suffering from respiratory infections. CONCLUSION: Co-mordidity, low-income and age under 6 months increase the risk of severe outcome for children infected by numerous respiratory pathogens. Our study aimed to evaluate the risk factors associated with the evolution and outcome of respiratory illnesses in patients aged under 5 years old hospitalised in one of the four main public hospitals in Antananarivo. In our study, Streptococcus pneumoniae was the most common bacterial pathogen as in other studies of hospitalised patients with acute respiratory illness, and Haemophilus influenzae type B was the next most frequent [16] [17] [18] [19] .
cord-352684-4o623x3n	2016	We report HBoV infection in a child post‐liver transplantation, who presented with persistent fever and mild tachypnea, 3 weeks after a successful transplant. She had episodes of prolonged fever even after her collections were drained, and a respiratory multiplex (PCR-based test) to look for viruses, from nasopharyngeal aspirates, was negative (3 weeks prior to transplant). 4 However, in recent years, it has been emerged that HBoV alone is pathogenic and can cause disease in immunocompetent children, most commonly presenting with respiratory symptoms, such as wheeze and bronchiolitis. 8 There are a few reports of HBoV infections in immunocompromised hosts wherein they have caused respiratory or diarrhoeal illness, and rarely even life-threatening conditions in the stem cell transplant population. 9 HBoV has also been shown to cause disseminated illness in a child, post-stem cell transplant. 11 There are no reports of HBoV-associated respiratory infections in children after liver transplantation.
cord-352837-a29d5dkv	2019	Given the technical and bioinformatic advances as well as the declining laboratory costs, the application of deep sequencing to identify etiologic agents in clinical samples has been approached in different pathologies, including those caused by community-acquired respiratory viruses (CARVs). With these caveats in mind, and given the significant global burden of viral respiratory tract disease in the very young and the very old [10] [11] [12] oropharyngeal (NP/OP) samples of SARI cases were identified through a national surveillance study conducted by the Uganda Virus Research Institute from 2010 through 2015. Taken together, this report from resource-limiting settings is also of relevance for resource-rich countries and raises the question about how to best expand current first-or second-line testing for respiratory viral pathogens including CMV, parvovirus B19, and measles, and how to move to more deep sequencing virome analysis and comprehensive metagenomics in the near future.
cord-353308-e4s8el0s	2004	This dramatic chain of transmission brought to the world''s attention this new respiratory disease, called severe acute respiratory syndrome (SARS), and clearly illustrated the potential for SARS to spread extensively from a single infected person and to rapidly disseminate globally through air travel. Diarrhoea has been reported at presentation in approximately 25% of patients, although this symptom was observed in as many as 73% of all patients affected by an outbreak at an apartment complex in Hong Kong that is believed to have resulted from fecal-oral/respiratory transmission of SARS-CoV. [53] [54] [55] [56] Given that profuse watery diarrhoea is seen in a significant proportion of patients and SARS-CoV can be shed in large quantities in stool, faeces remain a possible source of virus and fecal-oral or fecal-respiratory spread are the leading hypotheses for a large outbreak affecting more than 300 people at an apartment complex in Hong Kong. Fatal severe acute respiratory syndrome is associated with multiorgan involvement by coronavirus (SARS-CoV)
cord-353698-gj8sx3zy	2020	title: Adapted Diving Mask (ADM) device as respiratory support with oxygen output during COVID-19 pandemic The most extended therapeutic approach for COVID-19 is based on two main strategies [10] [11] [12] [13] : pharmacological treatment directed toward several physiological targets (viremia, immunological reactions, prothrombotic reactions) and hemodynamic and respiratory support with positive end-expiratory pressure (PEEP) in addition to mechanical ventilation. A descriptive case series study of twenty-five patients with acute respiratory syndrome secondary to SARS-CoV2 infection was performed at a Spanish center, Hospital Universitario Infanta Leonor of Madrid, between March 30 and April 18, 2020. Table 4 shows the different variables used to analyze the improvement in the intervention and the mean value of all oxygen saturation measurements for all days that ADM therapy was used in those patients who prolonged its time of use.
cord-353786-284qn075	2020	title: Diagnosis and treatment recommendations for pediatric respiratory infection caused by the 2019 novel coronavirus At the onset of the disease, infected children mainly present with fever, fatigue and cough, which may be accompanied by nasal congestion, runny nose, expectoration, diarrhea, headache, etc. 2. Children with a history of contacting patients with fever or respiratory symptoms who have a travel or residence history in Wuhan City and neighboring areas, or in other areas with persistent local transmission within 14 days prior to disease onset. 3. Children with a history of contacting confirmed or suspected cases infected with 2019-nCoV within 14 days prior to disease onset. 4. Children who are related with a cluster outbreak: in addition to this patient, there are other patients with fever or respiratory symptoms, including suspected or confirmed cases infected with 2019-nCoV. Most of the cases have normal or decreased white blood cell counts, while severely infected children show reduced level of lymphocyte count.
cord-354918-129inbwq	2007	A few home truths (i) Viral infections are an important cause of respiratory infection and yet a specific diagnosis is rarely made, (ii) few antiviral therapies exist and when they do -such as in the case of influenza -they are either underused or overused because of diagnostic inefficiencies, (iii) our approach to using antibacterial agents is guided by ''what should reasonably be covered'' or ''what organisms are being missed'' rather than a treatment regimen targeted for a particular organism, (iv) in association with diagnostic uncertainty, we do not make sufficient allowances for immunocompromised states or overexuberant immune responses to respiratory infectious disease (RID) and (v) current antibiotic guidelines encourage an approach of increasingly covering all potential organisms depending on the severity of illness. Our current reliance on empirical antibiotic strategies to cover ''likely bacterial pathogens'' as set out in numerous guidelines is unavoidable in the short term given the current diagnostic limitations for respiratory infection syndromes.
cord-355165-xc6ythgp	2008	We defi ned syndrome data as data in health-related registries that refl ect infectious disease activity without identifying causative pathogen(s) or focusing on pathogenspecifi c symptoms (such as routine surveillance data for infl uenza-like illness [11] or surveillance of acute fl accid paralysis for polio [12] ). Six registries were selected ( Table 1 ) that collected data on work absenteeism, general practice (GP) consultations, prescription medications dispensed by pharmacies, diagnostic test requests (laboratory submissions) (13), hospital diagnoses, and deaths. As a reference for the syndrome data, we included specifi c pathogen counts for 1999-2004 from the following sources: 1) Weekly Sentinel Surveillance System of the Dutch Working Group on Clinical Virology (which covers 38%-73% of the population of the Netherlands [14] respiratory disease-related counts of Streptococcus pneumoniae (data in 2003-2004 were interpolated for 2 laboratories during short periods of missing data; total coverage 24%); and 3) national mandatory notifi cations of pertussis.