Observational research in childhood respiratory diseases

Viral respiratory tract infections and asthma: The course ahead

Background: Viral acute respiratory infections (ARIs) are the commonest illnesses experienced by all age groups, especially in infants where infection rates are highest. Nevertheless, during the molecular era, outside of hospital-based studies, little is known about the current aetiology and community burden of viral ARIs in infants and young children. The observational research in childhood infectious disease (ORChID) project is a prospective community-based birth-cohort study of healthy Australian infants and children. It began in 2010 to investigate respiratory virus infections until two-years of age. My PhD established laboratory quality control techniques for studies of this nature and describes the respiratory viruses and molecular epidemiology of human rhinoviruses (RV) during the first year of life in a nested subgroup of this cohort. The hypotheses were: I. During the first year of life and in otherwise healthy infants, RV is the most commonly detected respiratory virus in respiratory secretions. II. Various factors impact upon successful viral detection, including the ability of parents to collect appropriate samples and other laboratory-based technical issues. III. Repeated detection of RV-RNA in respiratory secretions over periods of more than 4-weeks results from genotype replacement and new infection events rather than from prolonged shedding of the same genotype. IV. Many RV genotypes circulate in a single location in 1 year period. Methods The ongoing ORChID study completed sample collection at the end of 2014. Parents were approached antenatally and asked to collect weekly anterior nasal swabs from the time of their child’s birth until their second birthday. Swabs were mailed to the laboratory where they were stored at -80oC until analysis. Parents also completed a daily symptom diary, which was submitted monthly. My PhD focused on samples collected from an infant subgroup within this cohort and the first two-years of the ORChID study. Samples were extracted using an automated robotic system after spiking each sample with equid herpes virus (EHV-1). The extraction quality and presence of human DNA in extracts were assessed by real-time PCR for EHV-1 and endogenous retrovirus 3 (ERV-3) respectively. Respiratory virus PCR testing included: RV, influenza viruses (IFVs: A/B), parainfluenza viruses (PIV: 1-3), respiratory syncytial virus (RSV; A/B), human metapneumovirus (hMPV); human coronaviruses (hCoV; NL63, 229E, OC43 and HKU); human polyomaviruses (PyV: WU and KI), adenovirus (AdV), and human bocavirus (hBoV). In a subset of 3366 nasal swab samples, the impact of ERV-3 load upon respiratory virus detection was determined. Mould was observed incidentally in some samples reaching the laboratory. The impact of different mould levels upon ERV-3 and respiratory virus detection was therefore investigated. The influence of sequence variation upon target sequences was assessed for HAdV detection. Two new HAdV real-time PCR assays utilising combinations of degenerate oligonucleotides were tested in parallel with a previously designed and well established real-time PCR assay. ORChID (n=8800) and routine clinical (n=779) samples were then tested and the results compared. The nature and shedding patterns of respiratory viruses, including the molecular epidemiology of RV was investigated in the nested infant cohort. Viral protein regions 4 and 2 were targeted to investigate RV-genotypes. Simple descriptive statistics and regression models analysed associations and outcomes of interest. Results My nested subgroup of 72 infants provided 3446 swabs. Of these, RV (19.1%) had the highest detection rates followed by PyV-KIV (1.7%), hBoV (1.6%), AdV (1.1%), PyV-WUV (0.9%), RSV-A (0.6%), hCoV-OC43 (0.3%), PIV-3 (0.3%), hCoV-NL63 (0.3%), RSV-B (0.2%), hMPV (0.2%), PIV-1 (0.1%), IFV-A (0.09%), IFV-B (0.06%), hCoV-229E (0.06%), PIV-2 (0.03%) and hCoV-HKU1 (0.03 %). Failure to detect ERV-3 was associated with 60% reduction in virus detection rates in nasal swabs. Mould was observed in 23% of samples and associated with delays in transportation, season and reduced ERV-3 and respiratory virus detection. Degenerate oligonucleotides may overcome season-to-season variation in viral gene targets. Compared with the established assay, the new HAdV assays provided similar qualitative, but superior quantitative results. Serial RV-detection for more than 3-4 weeks was from genotype replacement rather than prolonged shedding. Although detected in asymptomatic infants, an association was found between RV and respiratory symptoms, especially for the RV-C species. Conclusions Longitudinal studies help further understand respiratory virus detection, viral shedding and disease burden in the community. The quality of nasal swab collection and transportation can be monitored in real-time using the human DNA marker ERV-3. Gene target variation is a potential problem for longitudinal studies and was addressed successfully in HAdV real-time PCR assays by using combinations of degenerate oligonucleotides. This developmental work allowed me to show that in otherwise healthy Australian infants RVs were the dominant respiratory pathogens, followed by the DNA respiratory viruses. The apparent prolonged shedding of RVs over more than 3-4 weeks was from genotype replacement rather than persistent infection. RV-C appeared more pathogenic than the other RV-species and if confirmed this will help identify a viral target for future novel therapeutic and public health

Infections, Immunity & their Effects on Asthma

1. Asif Noor, MD* 2. Theresa Fiorito, MD* 3. Leonard R. Krilov, MD*,† 1. *Department of Pediatrics, Children's Medical Center, NYU Winthrop Hospital, Mineola, NY 2. †Department of Pediatrics, State University of New York, Stony Brook School of Medicine, Stony Brook, NY * Abbreviations: AAP: : American Academy of Pediatrics Adv: : adenovirus CDC: : Centers for Disease Control and Prevention FDA: : Food and Drug Administration hMPV: : human metapneumovirus PCR: : polymerase chain reaction PIV: : parainfluenza virus RSV: : respiratory syncytial virus RV: : rhinovirus Clinicians must learn to identify viral infections in children during the winter months and must practice caution with the use of unnecessary medications in such cases. Recognition of the clinical pattern of viral infection (eg, bronchiolitis) in conjunction with judicious use of viral tests (either office-based immunoassays or newer molecular tests) may assist in epidemiological monitoring, cohorting patients in the hospital, withholding unnecessary therapies, and providing a definitive diagnosis. After completing this article, readers should be able to: 1. Review the epidemiological aspects and clinical signs and symptoms of common cold weather viruses. 2. Recognize situations in which viral testing is indicated. 3. Recognize situations in which treatment is indicated. In early November you are evaluating a 9-month-old boy born at 33 weeks of gestation. The infant presents with 2 days of fevers (101°F–102°F [38.3°C–38.8°C]), copious rhinorrhea, and 1 day of coughing with difficulty breathing. He is otherwise feeding well and has had adequate urination. His 4-year-older sister has an upper respiratory tract infection. On physical examination, the infant has a respiratory rate of 45 breaths/min without chest wall retractions. On auscultation there is good air entry with scattered rhonchi bilaterally. What is the most appropriate next step in management? 1. Obtain respiratory syncytial virus (RSV) and influenza antigen testing. 2. Obtain a chest radiograph to look for focal infiltrate. 3. Provide supportive care with nasal …

Community-acquired respiratory viruses

Respiratory syncytial virus: co-infection and paediatric lower respiratory tract infections

New Aspects on Human Rhinovirus Infections

Rhinoviruses in the pathogenesis of asthma: The bronchial epithelium as a major disease target

Information about viral acute respiratory infections (ARIs) is essential for prevention, diagnosis and treatment, but it is limited in tropical developing countries. This study described the clinical and epidemiological characteristics of ARIs in children hospitalized in Vietnam. Nasopharyngeal samples were collected from children with ARIs at Ho Chi Minh City Children's Hospital 2 between April 2010 and May 2011 in order to detect respiratory viruses by polymerase chain reaction. Viruses were found in 64% of 1082 patients, with 12% being co-infections. The leading detected viruses were human rhinovirus (HRV; 30%), respiratory syncytial virus (RSV; 23·8%), and human bocavirus (HBoV; 7·2%). HRV was detected all year round, while RSV epidemics occurred mainly in the rainy season. Influenza A (FluA) was found in both seasons. The other viruses were predominant in the dry season. HRV was identified in children of all age groups. RSV, parainfluenza virus (PIV) 1, PIV3 and HBoV, and FluA were detected predominantly in children aged 24 months, respectively. Significant associations were found between PIV1 with croup (P < 0·005) and RSV with bronchiolitis (P < 0·005). HBoV and HRV were associated with hypoxia (P < 0·05) and RSV with retraction (P < 0·05). HRV, RSV, and HBoV were detected most frequently and they may increase the severity of ARIs in children.

The aim of this study was to investigate the prevalence and seasonal distribution of respiratory viruses in pediatric and adult outpatients and inpatients who were admitted to hospital with the symptoms of upper and lower respiratory tract infections, during a 12-year period. A total of 5102 clinical samples (4372 nasopharyngeal swabs, 316 bronchoalveolar lavages, 219 transtracheal aspirates, 163 nasopharyngeal aspirates, 20 sputum, 10 nasal swabs) examined in our laboratory between January 1st 2002 and July 17th 2014, were evaluated retrospectively. Of the specimens, 1107 (21.7%) were obtained from outpatients and 3995 (78.3%) from hospitalized patients. Of the patients, 2851 (55.9%) were male and 2251 (44.1%) were female, while 1233 (24.2%) were adults and 3869 (75.8%) were children (age range: 1 day - 93 years; median: 3 years). Respiratory samples were investigated for the presence of respiratory syncytial virus (RSV), influenza virus type A and B (INF-A, INF-B), adenovirus (AdV), parainfluenza viruses (PIV types 1-4), human rhinoviruses (HRV), human coronaviruses (HCoV), human metapneumovirus (HMPV) and human bocavirus (HBoV). All specimens were tested by both direct immunofluorescence antibody (DFA) and shell vial cell culture (SVCC) methods. In DFA assay the samples were initially screened by fluorescent-labeled polyclonal antibodies, and the positive ones were typed by using monoclonal antibodies (Light Diagnostics, Merck Millipore, USA). In SVCC, HEp-2, MDCK, A-549 and Vero cell lines were used for the isolation of viruses. In addition to these methods, real-time multiplex PCR methods (RealAccurate®, Respiratory RT PCR, PathoFinder, Netherlands and Seeplex® RV15 ACE Detection, Seegene, South Korea) were used for the detection of respiratory viruses in samples (n= 2104) obtained from 2007 to 2014. Respiratory viruses were detected in a total of 1705 (33.4%) patients, of them 967 (19%) were male and 738 (14.4%) were female. Three hundred and eighteen (18.6%) of the 1705 patients were infected with multiple respiratory viruses. The most frequently observed co-infections were RSV+INF-A (40/318; 12.6%), and RSV+PIV (33/318; 10.4%). The rate of positivity for the respiratory viruses in pediatric and adult groups were 35.4% (1369/3869) and 27.3% (336/1233), respectively (p< 0.000). The most frequently detected virus in pediatric group was RSV (336/1369; 24.5%), followed by influenza viruses (314/1369; 22.9%), PIV (197/1369; 14.4%), HRV (118/1369; 8.6%), AdV (75/1369; 5.5%) and the others (49/1369; 3.6%). On the other hand the most frequently detected virus in adult group was influenza viruses (181/336; 53.8%) followed by AdV (37/336; 11%), RSV (24/336; 7.1%), PIV (24/336; 7.1%), HRV (23/336; 6.8%) and the others (9/336; 2.7%). The rate of multiple virus infections in pediatric and adult groups were 7.2% (280/3869) and 3% (38/1233), respectively. Most of the coinfections (280/318; 88%) were detected in children. Respiratory viruses were detected positive in 40.2% (445/1107) of outpatients, and in 31.5% (1260/3995) of inpatients (p< 0.000). The most frequent viruses detected in pediatric outpatients and inpatients were HRV and RSV, respectively, while influenza viruses were the first in line among both adult outpatients and inpatients. During the study period, a PIV-3 outbreak (n= 96) have emerged between December 2004-April 2005, and an influenza A (H1N1)pdm09 outbreak (n= 207) between November 2009-January 2010. When the seasonal distribution was considered, the isolation rates of 1705 respiratory viruses in winter, spring, summer and autumn were 44.4%, 27%, 8.3% and 20.3%, respectively. RSV was most frequently detected from December to March, influenza viruses from November to March, HRV from December to June, and mixed infections from January to February. In conclusion, the data of our study obtained in about 12-year period indicated that the prevalence of respiratory viruses in acute respiratory infections is 33.4%, and they typically active during the months of winter and early spring in our region.

Acute viral respiratory infections are common causes of febrile episodes in children. There are still limited data about distribution of acute viral respiratory infections in children with cancer. The first aim of this study was to evaluate the viral etiology and seasonality of acute viral respiratory infection in pediatric patients with cancer in a 3-year study. Our second aim was to evaluate the impact of viral infections on delaying the patients' chemotherapy or radiotherapy. This cross-sectional study was conducted from January 2014 to July 2017. Nasopharyngeal aspirates were analyzed in patients younger than 21 years with acute respiratory infections. Patients were treated in the Pediatric Hematology and Oncology Department of Dr. Behçet Uz Children's Hospital with real-time multiplex polymerase chain reaction. Data were analyzed to determine the frequency and seasonality of infections. The χ or the Fisher exact tests were used. A total of 219 samples of nasopharyngeal aspirates and blood were analyzed. The mean patient age was 76.8±59.3 months, with 46.3% female and 53.7% male children in a total of 108 patients. Of this total, 55% (60/108 cases) had multiple acute respiratory infections. Acute lymphoblastic leukemia (48.1%) was the most prevalent disease. The 3 most prevalent viruses were human rhinovirus (HRV) (33.1%), parainfluenza (PI) (18.7%), and coronavirus (CoV) (14.8%). In terms of the seasonal distribution of viruses, PI was most common in winter 2014, HRV in spring 2014, HRV in fall 2014, PI in winter 2015 and summer 2015, CoV in spring 2015, HRV in fall 2015, both influenza and HRV in winter 2016, both human metapneumovirus and bocavirus in spring 2016, HRV in summer 2016, both HRV and PI in fall 2016, both respiratory syncytial virus and influenza in winter 2017, HRV in spring 2017, and both HRV and adenovirus in summer 2017. The mean duration of neutropenia for patients with viral respiratory infection was 17.1±13.8 (range: 2 to 90) days. The mean duration of symptoms of viral respiratory infection was 6.8±4.2 (range: 2 to 31) days. A delay in chemotherapy treatment owing to viral respiratory infection was detected in 73 (33.3%) patients. The mean duration of delay in chemotherapy treatment was 9.6±5.4 (range: 3 to 31) days. In conclusion, we report our 3-year experience about the frequency and seasonality of respiratory viruses in children with cancer.

Objective To study etiological characteristics of common respiratory viruses infection in children under 7 years old in Dongguan city of Guangdong province.Methods The total RNA were extracted from 340 specimens which had been collected from children under 7 years old during February 2007 to October 2007 in Shijie hospital.During the study the respiratory viruses including respiratory syncytial virus A and B(RSV-A and B), influenza A and B(FLU-A and B), parainfluenza 1, 2, 3(PIV-1, 2 and 3) and Human metapneumo virus (hMPV) were detected by reverse transcription-polymerase chain reaction(RT-PCR).Results The common respiratory viruses were demonstrated in 340 children as the positive 50.29%(171/340),including 69 cases (20.29%) with RSV-A infection, 39 cases(11.47%) with FLU-A, 32 cases (9.41%) with hMPV, 22 cases (6. 47%) with PIV-3,9 cases (2.65%) with RSV-A, and 16 cases (9.36% of all viral infection positive cases) with the mixed infection.In these respiratory viruses mixed infection cases,there were 5 hMPV cases coinfected with RSV-A, 4 RSV-A cases with PIV-3, 2 hMPV eases with PIV-3, 2 hMPV cases with FLU-B, 2 cases FLU-A with PIV-3, and 1 ease RSV-A with FLU-A, FLU-B, PIV-1, PIV-2, and multiple mixed infections haven't been detected in this study.Conclusions The data show common respiratory viruses are significant pathogens in acute respiratory infection of paediatric patients under 7 years old in Dongguan city.RSV is still the leading causes of acute respiratory infection in children, the next pathogens respectively are FLU-A and hMPV. Key words: Children; Acute respiratory infection; Respiratory virus; Etiology

The prevalence of eight respiratory viruses detected in patients with acute respiratory infections (ARIs) in Korea was investigated through analysis of data recorded by the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS) from 2013 to 2015. Nasal aspirate and throat swabs specimens were collected from 36 915 patients with ARIs, and viral nucleic acids were detected by real‐time (reverse‐transcription) polymerase chain reaction for eight respiratory viruses, including human respiratory syncytial viruses (HRSVs), influenza viruses (IFVs), human parainfluenza viruses (HPIVs), human coronaviruses (HCoVs), human rhinovirus (HRV), human adenovirus (HAdV), human bocavirus (HBoV), and human metapneumovirus (HMPV). The overall positive rate of patient specimens was 49.4% (18 236/36 915), 5% of which carried two or more viruses simultaneously. HRV (15.6%) was the most predominantly detected virus, followed by IFVs (14.6%), HAdV (7.5%), HPIVs (5.8%), HCoVs (4.2%), HRSVs (3.6%), HBoV (1.9%), and HMPV (1.6%). Most of the ARIs were significantly correlated with clinical symptoms of fever, cough, and runny nose. Although HRV and HAdV were frequently detected throughout the year in patients, other respiratory viruses showed apparent seasonality. HRSVs and IFVs were the major causative agents of acute respiratory diseases in infants and young children. Overall, this study demonstrates a meaningful relationship between viral infection and typical manifestations of known clinical features as well as seasonality, age distribution, and co‐infection among respiratory viruses. Therefore, these data could provide useful information for public health management and to enhance patient care for primary clinicians.

BACKGROUND AND OBJECTIVES:Human metapneumovirus (hMPV) and the Netherlands human coronavirus (HCoV-NL63) have been isolated from children with respiratory tract infection. The prevalence of these viruses has not been reported from Saudi Arabia. We sought to determine whether hMPV and HCoV-NL63 are responsible for acute respiratory illness and also to determine clinical features and severity of illness in the hospitalized pediatric patient population.DESIGN AND SETTING:Prospective hospital-based study from July 2007 to November 2008.PATIENTS AND METHODS:Nasopharyngeal specimens from children less than 16 years old who were suffering from acute respiratory diseases were tested for hMPV and HCoV-NL63 by reverse transcriptase–polymerase chain reaction. Samples were collected from July 2007 to November 2008.RESULTS:Both viruses were found among Saudi children with upper and lower respiratory tract diseases during the autumn and winter of 2007 and 2008, contributing to 11.1% of all viral diagnoses, with individual incidences of 8.3% (hMPV) and 2.8% (HCoV-NL63) among 489 specimens. Initial symptoms included fever, cough, and nasal congestion. Lower respiratory tract disease occurs in immunocompromised individuals and those with underlying conditions. Clinical findings of respiratory failure and culture-negative shock were established in 7 children infected with hMPV and having hematologic malignancies, myelofibrosis, Gaucher disease, and congenital immunodeficiency; 2 of the 7 patients died with acute respiratory failure. All children infected with HCoV-NL63 had underlying conditions; 1 of the 4 patients developed respiratory failure.CONCLUSION:hMPV and HCoV-NL63 are important causes of acute respiratory illness among hospitalized Saudi children. hMPV infection in the lower respiratory tract is associated with morbidity and mortality in immunocompromised children. HCoV-NL63 may cause severe lower respiratory disease with underlying conditions.

Alterations in Pulmonary Function Following Respiratory Viral Infection