# ent

id: cord-103657-php6aj1r
type: ORG
entity:
  Bipolar Disorder The Clinical Evaluation of QT QTc Interval Prolongation and Proarrhythmic Potential for Non Antiarrhythmic Drugs Akathisia


id: cord-103657-php6aj1r
type: DISEASE
entity:
  cardiovascular palpitations gastrointestinal constipation nausea vomiting hyposalivation hypersalivation


id: cord-316217-ynh8d853
type: ORG
entity:
  the Joint Usage Research Center on Tropical Disease Institute of Tropical Medicine Nagasaki University


id: cord-001045-jm60nxc2
type: ORG
entity:
  Infectious Diseases Society of America Infectious Diseases Society of America American Thoracic Society


id: cord-303845-y6ws3u6x
type: DISEASE
entity:
  ARI clarithromycin erythromycin azithromycin clindamycin amoxicillin clavulanate amoxicillin penicillin V gatifloxacin levofloxacin cefaclor tetracycline


id: cord-016499-5iqpl23p
type: PROTEIN
entity:
  cytokine protein NK natural killer PBMC peripheral blood mononuclear cells IL interleukin TNF tissue necrosis factor TSLP


id: cord-016499-5iqpl23p
type: DISEASE
entity:
  human rhinoviruses paramyxoviruses coronaviruses and bocavirus during acute respiratory tract infections


id: cord-257248-aii0tj9x
type: PROTEIN
entity:
  Streptococcus pneumoniae nontypeable Haemophilus influenzae NTHi Moraxella catarrhalis Staphylococcus aureus Bordetella


id: cord-257248-aii0tj9x
type: TAXON
entity:
  adenovirus human metapneumovirus human coronaviruses OC43 229E NL63 HKU1 human bocavirus enterovirus


id: cord-305473-w30hsr4m
type: DISEASE
entity:
  influenza A H1N1 pdm09 21 and a lack of association between days post onset and Ct values for adenovirus human metapneumovirus parainfluenza virus 1 3 22 PCR based assays may thus retain greater value


id: cord-305473-w30hsr4m
type: DISEASE
entity:
  influenza A H1N1 pdm09 based on epidemiological risk factors like travel and contact history Ethics approvals


id: cord-283946-ts2lyy4p
type: DNA
entity:
  cat named Ria The samples were xed in formol saline and hematoxylin and eosin stained tissue sections prepared


id: cord-283946-ts2lyy4p
type: PROTEIN
entity:
  feline calicivirus Cat Group 1 2 3 4 5 6 b 7 8 9 1 0 98 382 Vaccinate À c À À À À À À À À À 98 394 Vaccinate À À À À À À À À 98 431 Vaccinate À À À À À À À 98 444 Vaccinate À À À À À À À À À À 98 516 Nonvaccinate À À À À À À À À À À À À À À À 98 537 Nonvaccinate À À À À À À À À À À À À À À À À


id: cord-283946-ts2lyy4p
type: ORG
entity:
  the Clinical Pathology Service of the Veterinary Medical Teaching Hospital VMTH School of Veterinary Medicine


id: cord-288821-nalulzfo
type: DNA
entity:
  1b gene primers repSZ 1f 15973 5 GTGATGCATA TGCTAATTTG 3 repSZ 3r 16210 5 CTCTTGCAGGTAT AATCCTA 3 repSZ 2f 16012 5 TTGGTAAACAAAAGAT AACT 3


id: cord-288821-nalulzfo
type: CHEMICAL
entity:
  NM_006413 5 AGATT TGGACCTGCGAGCG 3 forward primer and 5 GAGCGG CTGTCTCCACAAGT 3 reverse primer Viral


id: cord-330819-vfagxsdz
type: ORG
entity:
  the US National Oceanic and Atmospheric Administration National Oceanic and Atmospheric Administration


id: cord-292948-1n5ej08f
type: ORG
entity:
  the Detection of SARS CoV 2 Institut Pasteur Paris Coronavirus Infections in Children Including COVID 19


id: cord-300019-8vxqr3mc
type: GGP
entity:
  HMPV OR 9 8 95 CI 2 3 41 0 AFE 90 AdV OR not available AFE approximately 100 RV OR 7 1 95 CI 3 7 13 6 AFE 86 and CoV OR 2 8 95 CI 2 0 4 1 AFE


id: cord-102515-ch6prsf3
type: WORK_OF_ART
entity:
  The Relationship Between In Home Water Service and the Risk of Respiratory Tract Skin and Gastrointestinal Tract Infections Among Rural Alaska Natives Subjective


id: cord-262773-mfta0emi
type: PROTEIN
entity:
  V Laaksi I Lee M T Loeb M Maguire J Mauger D T Majak P Manaseki Holland S Murdoch D Nakashima A Neale R E Rake C Rees J Rosendahl J Scragg R Shah D Shimizu Y Simpson Yap S Trilok Kumar G Urashima M Martineau A R title Vitamin D


id: cord-262773-mfta0emi
type: ORG
entity:
  Upper Respiratory Infection in Patients With Inflammatory Bowel Disease Effect of Vitamin D Supplementation on Recurrent Wheezing in Black Infants


id: cord-265257-p9f0pl3y
type: ORG
entity:
  Diagnosis Prevention and Treatment of Human Respiratory Syncytial Virus Developing New Antiviral Agents


id: cord-281051-i229xv0o
type: GGP
entity:
  Rev DOI 10 1186 s13643 016 0399 x sha b516e53a03a6dc4df9eb13c85d0a57ef71452125 doc_id 281051 cord_uid i229xv0o BACKGROUND Acute respiratory infections ARI


id: cord-349279-wbb7h2zu
type: DISEASE
entity:
  human rhinovirus coronavirus parainfluenza viruses influenzavirus respiratory syncytial virus and human metapneumovirus


id: cord-326122-5m1727m1
type: ORG
entity:
  the Infectious Diseases Society of America American Academy of Pediatrics Subcommittee on Diagnosis and Management of Bronchiolitis Diagnosis


id: cord-326122-5m1727m1
type: DISEASE
entity:
  hematologic malignancies hematopoietic stem cell transplantation solid organ transplantation premature


id: cord-326122-5m1727m1
type: DISEASE
entity:
  acute respiratory tract infections Illness severity viral shedding and antibody responses in infants hospitalized


id: cord-268977-hcg2rrhl
type: GGP
entity:
  Parainfluenza 1 1 34 3 1 3 6 2 28 3 4 2 5 2 Parainfluenza virus 3 46 6 17 4 6 5 69 6 1 1 14 4 55 7 9 5 13 5


id: cord-268977-hcg2rrhl
type: WORK_OF_ART
entity:
  M100 S19 Manual for the Laboratory Identification of Bacterial Pathogens of Public Health Importance


# bib

id: cord-001045-jm60nxc2
author: DeLisle, Sylvain
date: 2013-08-13
txt: ./txt/cord-001045-jm60nxc2.txt
cache: ./cache/cord-001045-jm60nxc2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742728/
doi: 10.1371/journal.pone.0070944
summary:
  METHODS: A manual EMR review of 2747 outpatient ARI visits with associated chest imaging identified x-ray reports that could support the diagnosis of pneumonia (kappa score = 0.88 (95% CI 0.82∶0.93)), along with attendant cases with Possible Pneumonia (adds either cough, sputum, fever/chills/night sweats, dyspnea or pleuritic chest pain) or with Pneumonia-in-Plan (adds pneumonia stated as a likely diagnosis by the provider). The ARI CDA flagged an outpatient visit if the provider assigned it an ARI-related International Disease Classification, 9 th Revision, Clinical Modification (ICD-9) diagnostic code OR issued a prescription for a cough remedy OR documented at least two symptoms from the above ARI case definition in his/her clinical note, as retrieved by computerized text analysis [10] . Discussion Automated text analyses of chest imaging reports improved the performance of EMR-based CDAs that included structured data elements and free-text search for ARI symptoms.

title:
  Using the Electronic Medical Record to Identify Community-Acquired Pneumonia: Toward a Replicable Automated Strategy

abstract:
  BACKGROUND: Timely information about disease severity can be central to the detection and management of outbreaks of acute respiratory infections (ARI), including influenza. We asked if two resources: 1) free text, and 2) structured data from an electronic medical record (EMR) could complement each other to identify patients with pneumonia, an ARI severity landmark. METHODS: A manual EMR review of 2747 outpatient ARI visits with associated chest imaging identified x-ray reports that could support the diagnosis of pneumonia (kappa score = 0.88 (95% CI 0.82∶0.93)), along with attendant cases with Possible Pneumonia (adds either cough, sputum, fever/chills/night sweats, dyspnea or pleuritic chest pain) or with Pneumonia-in-Plan (adds pneumonia stated as a likely diagnosis by the provider). The x-ray reports served as a reference to develop a text classifier using machine-learning software that did not require custom coding. To identify pneumonia cases, the classifier was combined with EMR-based structured data and with text analyses aimed at ARI symptoms in clinical notes. RESULTS: 370 reference cases with Possible Pneumonia and 250 with Pneumonia-in-Plan were identified. The x-ray report text classifier increased the positive predictive value of otherwise identical EMR-based case-detection algorithms by 20–70%, while retaining sensitivities of 58–75%. These performance gains were independent of the case definitions and of whether patients were admitted to the hospital or sent home. Text analyses seeking ARI symptoms in clinical notes did not add further value. CONCLUSION: Specialized software development is not required for automated text analyses to help identify pneumonia patients. These results begin to map an efficient, replicable strategy through which EMR data can be used to stratify ARI severity.


id: cord-010170-rwf52bly
author: Sutrisna, B.
date: 1991-08-24
txt: ./txt/cord-010170-rwf52bly.txt
cache: ./cache/cord-010170-rwf52bly.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172283/
doi: 10.1016/0140-6736(91)90544-y
summary:
  The recommended treatment for mild acute respiratory infections (ARI) in children is supportive care only, but many physicians, especially in developing countries, continue to prescribe antibiotic treatment because they believe it prevents progression to more severe ARI. The recommended treatment for mild acute respiratory infections (ARI) in children is supportive care only, but many physicians, especially in developing countries, continue to prescribe antibiotic treatment because they believe it prevents progression to more severe ARI. In our previous work on ARI in Indonesia (unpublished), we observed that many children with mild ARI were being treated with ampicillin by physicians at Government clinics despite the Ministry of Health guidelines (which accord with WHO recommendations) that only supportive care is required.14 In our discussions with physicians, it became clear that many believed antibiotics were effective at preventing the progression of mild ARI to pneumonia or other forms of severe ARI, which are frequently bacterial in origin.

title:
  Randomised, controlled trial of effectiveness of ampicillin in mild acute respiratory infections in Indonesian children

abstract:
  The recommended treatment for mild acute respiratory infections (ARI) in children is supportive care only, but many physicians, especially in developing countries, continue to prescribe antibiotic treatment because they believe it prevents progression to more severe ARI. To find out whether ampicillin treatment conferred any benefit over supportive care alone, a randomised, controlled trial was carried out among 889 children (under 5 years) with mild ARI in Indonesia. 447 were randomly allocated ampicillin (25-30 mg/kg body weight three times daily for 5 days) plus supportive care (continued breastfeeding, clearing of the nose, and paracetamol to control fever); 442 were allocated supportive care only. The treatment groups were almost identical after randomisation in terms of age, sex, level of parental education, history of measles immunisation, and fever. After 1 week the percentages cured were nearly identical (204 [46%] ampicillin; 209 [47%] control), as were the percentages of cases progressing to moderate ARI (56 [13%] vs 53 [12%]). The effect of treatment was not modified by age, sex, measles immunisation status, or the educational level of the parents. At the 2-week follow-up, the percentages cured were 62% (277) in the ampicillin group and 58% (256) in the control group; 14% of both groups had progressed to moderate ARI; and 24% (107) and 28% (123), respectively, still had mild ARI. None of the differences in outcome between the ampicillin and control groups was statistically significant. Thus, ampicillin plus supportive care offers no benefit over supportive care alone for treatment of mild ARI in young Indonesian children.


id: cord-016499-5iqpl23p
title: Rhinoviruses
author: Mackay, Ian M.
date: 2014-02-27
txt: ./txt/cord-016499-5iqpl23p.txt
cache: ./cache/cord-016499-5iqpl23p.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120790/
doi: 10.1007/978-1-4899-7448-8_29
summary:
  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

abstract:
  Picornaviruses, which include the human rhinoviruses (HRVs) and enteroviruses (EVs), are the most frequent cause of acute human illness worldwide. HRVs are the most prevalent cause of acute respiratory tract illnesses (ARIs) which usually commence in the upper respiratory tract (URT). ARIs are the leading cause of morbidity in children under 5 years and occur in all seasons. ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing and with significant direct and indirect healthcare expenditure. ARI incidence is highest in the first 2 years of life, with up to thirteen episodes per year including up to six positive for an HRV, and it is not uncommon to average one infection per child-month.


id: cord-102515-ch6prsf3
author: Moran, Elizabeth
date: 2020-04-26
txt: ./txt/cord-102515-ch6prsf3.txt
cache: ./cache/cord-102515-ch6prsf3.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.04.22.20069781v1?rss=1
doi: 10.1101/2020.04.22.20069781
summary:
  The health disparities query identifies articles evaluating disparities in health outcomes and healthcare access with inequities in dimensions of race/ethnicity, SES, gender identity and sexual orientation, insurance status, and other populations described as "vulnerable." We then screened studies using title and abstract review to identify articles with a specific focus on all-cause ARI, ILI, RSV, and influenza. In 2009, a number of studies documented social race/ethnic outcome disparities [36] [37] [38] [39] [40] [41] , with lower SES 41 associated with increased exposure risk 36 , as well as overall incidence 37 , hospitalization 38, 39, 41 , complications 36 , and death 39,40 due to pandemic H1N1. The evidence turned up by our review, as well as the issues of racially and socioeconomic disparate exposure risks, coupled with unequal access to testing and treatment made clear by the COVID-19 pandemic, demonstrate that the principles underlying Link & Phelan''s theory of SES and race as fundamental causes of health and illness apply to ARIs as much as many non-communicable diseases as well as infections more classically understood has having social antecedents, such as tuberculosis and diarrheal disease.

title:
  Inequality in acute respiratory infection outcomes in the United States: A review of the literature and its implications for public health policy and practice.

abstract:
  Seasonal and pandemic respiratory viruses such as influenza and the novel coronavirus (SARS-COV-2) currently sweeping the globe have often been described as 'equal opportunity infectors', implying little socioeconomic disparity in susceptibility. However, early data from the COVID-19 pandemic has underscored that the burden of respiratory viruses actually reflect and magnify existing socioeconomic inequalities. We review the literature on socioeconomic and racial disparities in acute respiratory infection (ARI), as well as ARI-associated hospitalization and mortality. Our goal is to identify key principles of the relationship between socioeconomic inequality and ARI outcomes, as well as highlighting poorly understood areas that need to be addressed by research and policy in the wake of the COVID-19 pandemic. We find that there has been descriptive work in this area, but that there is a distinct lack of cohesive methodology in the literature exploring social determinants and ARI. We propose the fundamental cause theory is a useful framework for guiding future research of disparities in ARI and for the design of interventions to alleviate these disparities.


id: cord-103657-php6aj1r
author: Koller, D.
date: 2020-08-07
txt: ./txt/cord-103657-php6aj1r.txt
cache: ./cache/cord-103657-php6aj1r.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.08.03.20167502v1?rss=1
doi: 10.1101/2020.08.03.20167502
summary:
  On the contrary, the most common ADRs to OLA in schizophrenic patients are constipation, weight gain, dizziness, personality disorder, akathisia, postural hypotension, sedation, headache, increased appetite, fatigue, dry mouth and abdominal pain (R. ADRs were classified using system organ class allocation as general (asthenia, fatigue, tiredness and gait alterations), cardiovascular (palpitations), gastrointestinal (constipation, nausea, vomiting, hyposalivation, hypersalivation, dry mouth and diarrhea), nervous system (akathisia, headache, difficulties with concentration, dizziness, paraesthesia, presyncope, syncope, tremor, somnolence and restless legs), psychiatric (restlessness, insomnia, anxiety, abnormal orgasm and nightmares), respiratory (epistaxis, hiccups, cough and sore throat), endocrine (galactorrhea), metabolic (lack of appetite, increased appetite and hyporexia), reproductive (dysmenorrhea, mastalgia and menstrual irregularity), skin (hair loss, pruritus, rash and sweating), musculoskeletal (shoulder pain, knee pain, neck pain, upper limb weakness, lumbalgia, cramps, back pain and leg pain), infections (cold), eye (photophobia) and

title:
  Safety and cardiovascular effects of multiple-dose administration of aripiprazole and olanzapine in a randomised clinical trial

abstract:
  Objective: To assess adverse events and safety of aripiprazole and olanzapine treatment. Methods: Twenty-four healthy volunteers receiving 5 daily oral doses of 10 mg aripiprazole and 5 mg olanzapine in a crossover clinical trial were genotyped for 46 polymorphisms in 14 genes by qPCR. Drug plasma concentrations were measured by HPLC-MS/MS. Blood pressure and 12-lead ECG were measured in supine position. Adverse events were also recorded. Results: Aripiprazole decreased diastolic blood pressure on the first day and decreased QTc on the third and fifth day. Olanzapine had a systolic and diastolic blood pressure, heart rate and QTc lowering effect on the first day. Polymorphisms in ADRA2A, COMT, DRD3 and HTR2A genes were significantly associated to these changes. The most frequent adverse drug reactions to aripiprazole were somnolence, headache, insomnia, dizziness, restlessness, palpitations, akathisia and nausea while were somnolence, dizziness, asthenia, constipation, dry mouth, headache and nausea to olanzapine. Additionally, HTR2A, HTR2C, DRD2, DRD3, OPRM1, UGT1A1 and CYP1A2 polymorphisms had a role in the development of adverse drug reactions. Conclusions: Olanzapine induced more cardiovascular changes; however, more adverse drug reactions were registered to aripiprazole. In addition, some polymorphisms may explain the difference in the incidence of these effects among subjects.


id: cord-252012-hdjbxah8
author: McErlean, Peter
date: 2010-11-01
txt: ./txt/cord-252012-hdjbxah8.txt
cache: ./cache/cord-252012-hdjbxah8.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0889856110000652
doi: 10.1016/j.iac.2010.08.001
summary:
  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.

title:
  Viral diversity in asthma: Immunology and Allergy Clinics of North America: Asthma and Infectious Disease

abstract:
  Asthma exacerbations are precipitated primarily by respiratory virus infection and frequently require immediate medical intervention. Studies of childhood and adult asthma have implicated a wide variety of respiratory viruses in exacerbations. By focusing on both RNA and DNA respiratory viruses and some newly identified viruses, this review illustrates the diversity and highlights some of the uncertainties that exist in our understanding of virus-related asthma exacerbations.


id: cord-257248-aii0tj9x
author: O''Grady, K.F.
date: 2016-02-22
txt: ./txt/cord-257248-aii0tj9x.txt
cache: ./cache/cord-257248-aii0tj9x.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1198743X16001129
doi: 10.1016/j.cmi.2016.02.004
summary:
  Most studies exploring the role of upper airway viruses and bacteria in paediatric acute respiratory infections (ARI) focus on specific clinical diagnoses and/or do not account for virus–bacteria interactions. Bilateral nasal swabs, demographic, clinical and risk factor data were collected at enrollment in children aged <15 years presenting to an emergency department with an ARI and where cough was a symptom. While upper airway specimens (nasopharyngeal swabs) are controversial because they cannot reliably distinguish between carriage and disease [8] , they continue to be widely used in observational and experimental studies of ARI in children, including those attempting to identify associations between organisms and clinical symptoms and/or severity. In 817 children presenting to a tertiary paediatric ED with an ARI and cough, at least one virus or bacterium was detected in nasal swab specimens from 90.6% of cases, while viruses and bacteria were codetected in 51.8%.

title:
  Prevalence, codetection and seasonal distribution of upper airway viruses and bacteria in children with acute respiratory illnesses with cough as a symptom

abstract:
  Most studies exploring the role of upper airway viruses and bacteria in paediatric acute respiratory infections (ARI) focus on specific clinical diagnoses and/or do not account for virus–bacteria interactions. We aimed to describe the frequency and predictors of virus and bacteria codetection in children with ARI and cough, irrespective of clinical diagnosis. Bilateral nasal swabs, demographic, clinical and risk factor data were collected at enrollment in children aged <15 years presenting to an emergency department with an ARI and where cough was a symptom. Swabs were tested by polymerase chain reaction for 17 respiratory viruses and seven respiratory bacteria. Logistic regression was used to investigate associations between child characteristics and codetection of the organisms of interest. Between December 2011 and August 2014, swabs were collected from 817 (93.3%) of 876 enrolled children, median age 27.7 months (interquartile range 13.9–60.3 months). Overall, 740 (90.6%) of 817 specimens were positive for any organism. Both viruses and bacteria were detected in 423 specimens (51.8%). Factors associated with codetection were age (adjusted odds ratio (aOR) for age <12 months = 4.9, 95% confidence interval (CI) 3.0, 7.9; age 12 to <24 months = 6.0, 95% CI 3.7, 9.8; age 24 to <60 months = 2.4, 95% CI 1.5, 3.9), male gender (aOR 1.46; 95% CI 1.1, 2.0), child care attendance (aOR 2.0; 95% CI 1.4, 2.8) and winter enrollment (aOR 2.0; 95% CI 1.3, 3.0). Haemophilus influenzae dominated the virus–bacteria pairs. Virus–H. influenzae interactions in ARI should be investigated further, especially as the contribution of nontypeable H. influenzae to acute and chronic respiratory diseases is being increasingly recognized.


id: cord-259338-q3kw6n9o
author: Jean, Sim Xiang Ying
date: 2020-11-04
txt: ./txt/cord-259338-q3kw6n9o.txt
cache: ./cache/cord-259338-q3kw6n9o.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0196655320309718
doi: 10.1016/j.ajic.2020.11.003
summary:
  We aimed to create a prototype staff surveillance system for the detection of acute respiratory infection (ARI) clusters amongst our healthcare workers (HCWs) and describe its effectiveness. Conclusion The use of syndromic surveillance to detect ARI clusters amongst HCWs in the COVID-19 pandemic may enable early case detection and prevent onward transmission. Utilizing the electronic health records, we have created a prototypic surveillance system in the detection of acute respiratory infection (ARI) clusters amongst staff and aim to describe its effectiveness in this study. The aim of this descriptive analytic study is to describe the effectiveness of a prototypic staff syndromic surveillance system in identifying acute respiratory infection (ARI) clusters amongst the staff population in the hospital. This initial feasibility study shows that the use of a syndromic surveillance system has the ability to identify ARI clusters amongst staff populations that would initiate downstream investigation and active screening.

title:
  Utilizing the Electronic Health Records to Create a Syndromic Staff Surveillance System During the COVID-19 outbreak

abstract:
  Objectives Since December 2019, COVID-19 has caused a worldwide pandemic and Singapore has seen escalating cases with community spread. Aggressive contact tracing and identification of suspects has helped to identify local community clusters, surveillance being the key to early intervention. Healthcare workers have contracted COVID-19 infection both at the workplace and community. We aimed to create a prototype staff surveillance system for the detection of acute respiratory infection (ARI) clusters amongst our healthcare workers (HCWs) and describe its effectiveness. Methods/Results A prototypical surveillance system was built on existing electronic health record infrastructure. Over a 10-week period, we investigated 10 ARI clusters amongst 7 departments. One of the ARI clusters was later determined to be related to COVID-19 infection. We demonstrate the feasibility of syndromic surveillance to detect ARI clusters during the COVID-19 outbreak. Conclusion The use of syndromic surveillance to detect ARI clusters amongst HCWs in the COVID-19 pandemic may enable early case detection and prevent onward transmission. It could be an important tool in infection prevention within healthcare institutions.


id: cord-262773-mfta0emi
author: Jolliffe, D.
date: 2020-07-17
txt: ./txt/cord-262773-mfta0emi.txt
cache: ./cache/cord-262773-mfta0emi.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.07.14.20152728
doi: 10.1101/2020.07.14.20152728
summary:
  title: Vitamin D supplementation to prevent acute respiratory infections: systematic review and meta-analysis of aggregate data from randomised controlled trials Design: We conducted a systematic review and meta-analysis of data from randomised controlled trials (RCTs) of vitamin D for ARI prevention using a random effects model. We previously meta-analysed individual participant data from 25 RCTs and showed a protective overall effect that was stronger in those with lower baseline 25(OH)D levels, and in trials where vitamin D was administered daily or weekly rather than in more widely spaced bolus doses. Randomised, double-blind, trials of supplementation with vitamin D 3 , vitamin D 2 or 25(OH)D of any duration, with a placebo or low-dose vitamin D control, were eligible for inclusion if they had been approved by a Research Ethics Committee and if data on incidence of ARI were collected prospectively and pre-specified as an efficacy outcome.

title:
  Vitamin D supplementation to prevent acute respiratory infections: systematic review and meta-analysis of aggregate data from randomised controlled trials

abstract:
  Objectives: To assess the overall effect of vitamin D supplementation on risk of acute respiratory infection (ARI), and to identify factors modifying this effect. Design: We conducted a systematic review and meta-analysis of data from randomised controlled trials (RCTs) of vitamin D for ARI prevention using a random effects model. Pre-specified sub-group analyses were done to determine whether effects of vitamin D on risk of ARI varied according to baseline 25-hydroxyvitamin D (25[OH]D) concentration or dosing regimen. Data Sources: MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), Web of Science, ClinicalTrials.gov and the International Standard RCT Number (ISRCTN) registry from inception to May 2020. Eligibility Criteria for Selecting Studies: Double-blind RCTs of supplementation with vitamin D or calcidiol, of any duration, were eligible if they were approved by a Research Ethics Committee and if ARI incidence was collected prospectively and pre-specified as an efficacy outcome. Results: We identified 40 eligible RCTs (total 30,956 participants, aged 0 to 95 years). Data were obtained for 29,841 (96.5%) of 30,909 participants in 39 studies. For the primary comparison of vitamin D supplementation vs. placebo, the intervention reduced risk of ARI overall (Odds Ratio [OR] 0.89, 95% CI 0.81 to 0.98; P for heterogeneity 0.009). No statistically significant effect of vitamin D was seen for any of the sub-groups defined by baseline 25(OH)D concentration. However, protective effects were seen for trials in which vitamin D was given using a daily dosing regimen (OR 0.75, 95% CI 0.61 to 0.93); at daily dose equivalents of 400-1000 IU (OR 0.70, 95% CI 0.55 to 0.89); and for a duration of [≤]12 months (OR 0.82, 95% CI 0.72 to 0.94). Vitamin D did not influence the proportion of participants experiencing at least one serious adverse event (OR 0.94, 95% CI 0.81 to 1.08). Risk of bias within individual studies was assessed as being low for all but two trials. A funnel plot showed asymmetry, suggesting that small trials showing non-protective effects of vitamin D may have been omitted from the meta-analysis. Conclusions: Vitamin D supplementation was safe and reduced risk of ARI, despite evidence of significant heterogeneity across trials. The overall effect size may have been over-estimated due to publication bias. Protection was associated with administration of daily doses of 400-1000 IU vitamin D for up to 12 months. The relevance of these findings to COVID-19 is not known and requires investigation.


id: cord-265257-p9f0pl3y
title: Viral Etiology of Acute Respiratory Infections in Pediatric Patients in Lebanon
author: Masoud, Khaldoun
date: 2019-11-01
txt: ./txt/cord-265257-p9f0pl3y.txt
cache: ./cache/cord-265257-p9f0pl3y.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.4084/mjhid.2019.059
doi: 10.4084/mjhid.2019.059
summary:
  title: Viral Etiology of Acute Respiratory Infections in Pediatric Patients in Lebanon estimated that 111 500 deaths in children <5 years were attributable to influenza-associated lower respiratory tract infections (LRI) in 2008, the vast majority of which occurred in developing countries. Infants and children younger than 18 years of age with symptoms of ARI disease presenting to the emergency department or the departments of pediatrics of the American University of Beirut Medical Center (AUBMC), Beirut, Lebanon were prospectively recruited between September 2009 to February 2012. In our study, CVEV infection constituted 38.8% of all viral ARI cases and was independently associated with rhinorrhea. Etiology, seasonality and clinical characterization of viral respiratory infections among hospitalized children in Beirut, Lebanon Viral etiologies of lower respiratory tract infections among Egyptian children under five years of age Viral and atypical bacterial detection in acute respiratory infection in children under five years

abstract:
  BACKGROUND: Acute respiratory infections (ARI) are the leading cause of death worldwide, especially among children. The majority of these infections in children are of viral etiology. In this study, we evaluated the incidence of viral ARI among children in Lebanon. PATIENTS AND METHODS: Children presenting with symptoms of ARI were prospectively recruited between September 2009 to February 2012. Nasopharyngeal aspirates were obtained from patients and screened for 11 respiratory viruses using a multiplex Luminex-based PCR assay. RESULTS: Two hundred twenty-one patients were recruited with a median age of 1 year (IQR: 0 – 5). Out of 221 patients, 116 (52.5%) were positive for at least one virus, the majority (103/116; 88.8%) of which were in children under 6-year of age. Overall, 188 viruses were detected. Rhinovirus (RhV) was the most common virus detected in 81 (69.8%) patients followed by coxsackie virus and echovirus (CVEV) which were detected as one target in the panel in 45 (38.8%), and parainfluenza viruses (PIV types: 1, 2, 3, 4) in 24 (20.7%) patients. Coinfection with more than one virus was detected in 49 (42.9%) patients. RhV and CVEV were the most common viruses associated with co-infections and higher risk of rhinorrhea. CONCLUSIONS: Viral pathogens account for at least half of the ARIs in Lebanon, with a high frequency of co-infections being detected.


id: cord-268977-hcg2rrhl
author: Feikin, Daniel R.
date: 2012-08-24
txt: ./txt/cord-268977-hcg2rrhl.txt
cache: ./cache/cord-268977-hcg2rrhl.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/22937071/
doi: 10.1371/journal.pone.0043656
summary:
  METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. Compared with other regions, the mortality rate among older children and adults remains several-fold higher in sub-Saharan Africa, where acute respiratory infections (ARI) are a leading cause of this high mortality, as well as associated morbidity [1] .

title:
  Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010

abstract:
  BACKGROUND: Few comprehensive data exist on disease incidence for specific etiologies of acute respiratory illness (ARI) in older children and adults in Africa. METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). We also collected swabs from asymptomatic controls, from which we calculated pathogen-attributable fractions, adjusting for age, season, and HIV-status, in logistic regression. We calculated incidence by pathogen, adjusting for health-seeking for ARI and pathogen-attributable fractions. Among 3,406 ARI patients >5 years old (adjusted annual incidence 12.0 per 100 person-years), influenza A virus was the most common virus (22% overall; 11% inpatients, 27% outpatients) and Streptococcus pneumoniae was the most common bacteria (16% overall; 23% inpatients, 14% outpatients), yielding annual incidences of 2.6 and 1.7 episodes per 100 person-years, respectively. Influenza A virus, influenza B virus, respiratory syncytial virus (RSV) and human metapneumovirus were more prevalent in swabs among cases (22%, 6%, 8% and 5%, respectively) than controls. Adenovirus, parainfluenza viruses, rhinovirus/enterovirus, parechovirus, and Mycoplasma pneumoniae were not more prevalent among cases than controls. Pneumococcus and non-typhi Salmonella were more prevalent among HIV-infected adults, but prevalence of viruses was similar among HIV-infected and HIV-negative individuals. ARI incidence was highest during peak malaria season. CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings.


id: cord-281051-i229xv0o
author: Bishop-Williams, Katherine E.
date: 2017-01-26
txt: ./txt/cord-281051-i229xv0o.txt
cache: ./cache/cord-281051-i229xv0o.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28122603/
doi: 10.1186/s13643-016-0399-x
summary:
  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

title:
  A protocol for a systematic literature review: comparing the impact of seasonal and meteorological parameters on acute respiratory infections in Indigenous and non-Indigenous peoples

abstract:
  BACKGROUND: Acute respiratory infections (ARI) are a leading cause of morbidity and mortality globally, and are often linked to seasonal and/or meteorological conditions. Globally, Indigenous peoples may experience a different burden of ARI compared to non-Indigenous peoples. 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. METHODOLOGY: A search string will be used to search PubMed(®), CAB Abstracts/CAB Direct(©), and Science Citation Index(®) aggregator databases. Articles will be screened using inclusion/exclusion criteria applied first at the title and abstract level, and then at the full article level by two independent reviewers. Articles maintained after full article screening will undergo risk of bias assessment and data will be extracted. Heterogeneity tests, meta-analysis, and forest and funnel plots will be used to synthesize the results of eligible studies. DISCUSSION AND REGISTRATION: This protocol paper describes our systematic review methods to identify and analyze relevant ARI, season, and meteorological literature with robust reporting. The results are intended to improve our understanding of potential associations between seasonal and meteorological parameters and ARI and, if identified, whether this association varies by place, population, or other characteristics. The protocol is registered in the PROSPERO database (#38051). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13643-016-0399-x) contains supplementary material, which is available to authorized users.


id: cord-283946-ts2lyy4p
author: Pedersen, N.C
date: 2000-05-11
txt: ./txt/cord-283946-ts2lyy4p.txt
cache: ./cache/cord-283946-ts2lyy4p.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0378113500001838
doi: 10.1016/s0378-1135(00)00183-8
summary:
  An isolated epizootic of a highly fatal feline calicivirus (FCV) infection, manifested in its severest form by a systemic hemorrhagic-like fever, occurred over a 1-month period among six cats owned by two different employees and a client of a private veterinary practice. The causative agent was isolated from blood and nasal swabs from two cats; the electron microscopic appearance was typical for FCV and capsid gene sequencing showed it to be genetically similar to other less pathogenic field strains. The ®fth cat in this focal epidemic was Aristotle (Ari), a 3.5-year old, neutered male, domestic, indoors-only cat and the son of Ria. There were no signi®cant past health problems; he tested negative for FeLV and FIV infections and had been parenterally vaccinated against rabies and FPHCV on 10 April 1997 Ari presented on 19 October 1998 with a history of an acute onset of lethargy and anorexia of 2 days duration.

title:
  An isolated epizootic of hemorrhagic-like fever in cats caused by a novel and highly virulent strain of feline calicivirus

abstract:
  An isolated epizootic of a highly fatal feline calicivirus (FCV) infection, manifested in its severest form by a systemic hemorrhagic-like fever, occurred over a 1-month period among six cats owned by two different employees and a client of a private veterinary practice. The infection may have started with an unowned shelter kitten that was hospitalized during this same period for a severe atypical upper respiratory infection. The causative agent was isolated from blood and nasal swabs from two cats; the electron microscopic appearance was typical for FCV and capsid gene sequencing showed it to be genetically similar to other less pathogenic field strains. An identical disease syndrome was recreated in laboratory cats through oral inoculation with tissue culture grown virus. During the course of transmission studies in experimental cats, the agent was inadvertently spread by caretakers to an adjoining room containing a group of four normal adult cats. One of the four older cats was found dead and a second was moribund within 48–72 h in spite of symptomatic treatment; lesions in these animals were similar to those of the field cats but with the added feature of severe pancreatitis. The mortality in field cats, deliberately infected laboratory cats, and inadvertently infected laboratory cats ranged from 33–50%. This new isolate of calicivirus, named FCV-Ari, was neutralized at negligible to low titer by antiserum against the universal FCV-F9 vaccine strain. Cats orally immunized with FCV-F9, and then challenge-exposed shortly thereafter with FCV-Ari, developed a milder self-limiting form of disease, indicating partial protection. However, all of the field cats, including the three that died, had been previously immunized with parenteral FCV-F9 vaccine. FCV-Ari caused a disease that was reminiscent of Rabbit Hemorrhagic Disease, a highly fatal calicivirus infection of older rabbits.


id: cord-287063-kheek4lx
title: Influence of maternal asthma on the cause and severity of infant acute respiratory tract infections
author: Carroll, Kecia N.
date: 2012-02-14
txt: ./txt/cord-287063-kheek4lx.txt
cache: ./cache/cord-287063-kheek4lx.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S009167491200139X
doi: 10.1016/j.jaci.2012.01.045
summary:
  In this investigation that included mother-infant dyads enrolled in the Tennessee Children''s Respiratory Initiative (TCRI), we tested the hypothesis that a familial atopic predisposition was associated with viral cause and increased severity of viral acute respiratory tract infection (ARI) during infancy. In our next set of analyses we examined whether having a mother with asthma (first defined by maternal self-report and then using the atopic asthma and nonatopic asthma classifications) was associated with increased severity of the infant''s HRV-or RSV-induced ARI. [5] [6] [7] 12, 22 Because of the known differential risk of early childhood asthma after RSV-and HRV-induced infant infections, we were interested in studying whether a familial predisposition to asthma and allergies was associated with the viral cause of the infant''s ARI and the severity of the ARI.

abstract:
  BACKGROUND: Respiratory syncytial virus (RSV) and rhinovirus infections are the most common significant infant respiratory tract illnesses and are associated with increased but differential risks of childhood asthma. OBJECTIVE: We sought to determine whether maternal asthma is associated with higher odds of infant respiratory tract infection with rhinovirus versus RSV and increased infection severity. METHODS: Mother-infant dyads were enrolled from 2004-2008 during an infant respiratory tract infection (104 with rhinovirus and 279 with RSV). Mothers were classified into mutually exclusive groups (atopic asthma, nonatopic asthma, and no asthma). We determined viral cause using PCR and the severity of the infant’s respiratory tract infection using the bronchiolitis severity score. Adjusted relative odds of maternal asthma with viral cause were calculated by using logistic regression. Proportional odds models assessed the association of maternal asthma and infant infection severity. RESULTS: Infants with a mother with atopic asthma compared with infants whose mothers did not have asthma were more likely to have rhinovirus versus RSV infection (adjusted odds ratio, 2.42; 95% CI, 1.19-4.90). Similarly, among infants with rhinovirus, having a mother with atopic asthma was associated with increased infection severity (adjusted odds ratio, 3.10; 95% CI, 1.21-7.98). This relationship was not seen among infants with RSV. CONCLUSIONS: Clinically significant rhinovirus infection during infancy was more strongly associated with having a mother with atopic asthma than clinically significant RSV infection. Having a mother with atopic asthma was associated with increased severity of infant rhinovirus but not RSV infections. Infants with rhinovirus were more likely to have a familial atopic predisposition, which might partly explain the subsequent increased asthma risk.


id: cord-287167-rc9a5xs5
title: Healthcare worker acute respiratory illness cluster in 2020: Could it be from COVID-19?
author: Kyaw, Win Mar
date: 2020-07-23
txt: ./txt/cord-287167-rc9a5xs5.txt
cache: ./cache/cord-287167-rc9a5xs5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1017/ice.2020.364
doi: 10.1017/ice.2020.364
abstract: nan
summary:
  To the Editor-Since the emergence of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in China, >45,000 confirmed cases including >60 healthcare workers (HCWs) have been reported in Singapore. 4 After the SARS nosocomial outbreak, web-based staff sickness surveillance systems have been established at TTSH for the early detection of HCW clusters of acute respiratory infection (ARI). 7 During the COVID-19 pandemic, a team of public healthtrained personnel maintained close monitoring of staff sickness reporting to identify ARI clusters among the 12,000 HCWs working at the 1,600-bed TTSH and its collocated 330-bed National Centre for Infectious Diseases, the national referral centre for COVID-19 response. Compared to the first 27 weeks of 2019 (n = 28), the number of ARI clusters identified among staff working in inpatient wards in 2020 (n = 39) was significantly lower: 49% versus 78%, respectively (OR, 0.26; 95% CI, 0.09-0.78; P = .016).


id: cord-288332-y15g1yak
title: Clinical and laboratory profiles of hospitalized children with acute respiratory virus infection
author: Choi, Eunjin
date: 2018-06-25
txt: ./txt/cord-288332-y15g1yak.txt
cache: ./cache/cord-288332-y15g1yak.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3345/kjp.2018.61.6.180
doi: 10.3345/kjp.2018.61.6.180
summary:
  PURPOSE: Despite the availability of molecular methods, identification of the causative virus in children with acute respiratory infections (ARIs) has proven difficult as the same viruses are often detected in asymptomatic children. METHODS: Multiplex reverse transcription polymerase chain reaction assays were performed to detect 15 common respiratory viruses in children under 15 years of age who were hospitalized with ARI between January 2013 and December 2015. Nasopharyngeal aspirates from all patients were obtained within 48 hours of admission for multiplex RT-PCR assay to detect the following 15 common respiratory viruses: influenza virus A and B (IFA, IFB), respiratory syncytial virus A and B (RSV A, RSV B), parainfluenza virus 1-4 (PIV 1, PIV 2, PIV 3, PIV 4), human coronavirus 229E and OC43 (hCV-229E, hCV-OC43), human rhinovirus (hRV), human enterovirus (hEV), adenovirus (AdV), human bocavirus (hBV), and human metapneumovirus (hMPV).

abstract:
  PURPOSE: Despite the availability of molecular methods, identification of the causative virus in children with acute respiratory infections (ARIs) has proven difficult as the same viruses are often detected in asymptomatic children. METHODS: Multiplex reverse transcription polymerase chain reaction assays were performed to detect 15 common respiratory viruses in children under 15 years of age who were hospitalized with ARI between January 2013 and December 2015. Viral epidemiology and clinical profiles of single virus infections were evaluated. RESULTS: Of 3,505 patients, viruses were identified in 2,424 (69.1%), with the assay revealing a single virus in 1,747 cases (49.8%). While major pathogens in single virus-positive cases differed according to age, human rhinovirus (hRV) was common in patients of all ages. Respiratory syncytial virus (RSV), influenza virus (IF), and human metapneumovirus (hMPV) were found to be seasonal pathogens, appearing from fall through winter and spring, whereas hRV and adenovirus (AdV) were detected in every season. Patients with ARIs caused by RSV and hRV were frequently afebrile and more commonly had wheezing compared with patients with other viral ARIs. Neutrophil-dominant inflammation was observed in ARIs caused by IF, AdV, and hRV, whereas lymphocyte-dominant inflammation was observed with RSV A, parainfluenza virus, and hMPV. Monocytosis was common with RSV and AdV, whereas eosinophilia was observed with hRV. CONCLUSION: In combination with viral identification, recognition of virus-specific clinical and laboratory patterns will expand our understanding of the epidemiology of viral ARIs and help us to establish more efficient therapeutic and preventive strategies.


id: cord-288487-hs3wfffs
author: Lambert, Stephen B
date: 2008-01-24
txt: ./txt/cord-288487-hs3wfffs.txt
cache: ./cache/cord-288487-hs3wfffs.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1465-9921-9-11
doi: 10.1186/1465-9921-9-11
summary:
  The point estimate of the mean cost of community-managed influenza illnesses in healthy preschool aged children is three times greater than those illnesses caused by RSV and other respiratory viruses. Even for influenza, the most studied of all respiratory viruses, cost-of-illness and vaccine cost-effectiveness evaluations in children have tended to rely on assumptions or use retrospectively collected estimates, often from surveys, for resource utilisation, such as carer time away from work in seeking healthcare or caring for an ill child [6] [7] [8] [9] . Despite overlapping confidence intervals, the finding of most note in this study was the dramatically higher point estimate of the mean cost of influenza A ARIs, being three times higher than illnesses caused by RSV and the other common respiratory viral infections of childhood. Further studies that collect primary, integrated epidemiologic and economic data, particularly indirect costs, directly from families about community-managed ARIs in children, are required.

title:
  The cost of community-managed viral respiratory illnesses in a cohort of healthy preschool-aged children

abstract:
  BACKGROUND: Acute respiratory illnesses (ARIs) during childhood are often caused by respiratory viruses, result in significant morbidity, and have associated costs for families and society. Despite their ubiquity, there is a lack of interdisciplinary epidemiologic and economic research that has collected primary impact data, particularly associated with indirect costs, from families during ARIs in children. METHODS: We conducted a 12-month cohort study in 234 preschool children with impact diary recording and PCR testing of nose-throat swabs for viruses during an ARI. We used applied values to estimate a virus-specific mean cost of ARIs. RESULTS: Impact diaries were available for 72% (523/725) of community-managed illnesses between January 2003 and January 2004. The mean cost of ARIs was AU$309 (95% confidence interval $263 to $354). Influenza illnesses had a mean cost of $904, compared with RSV, $304, the next most expensive single-virus illness, although confidence intervals overlapped. Mean carer time away from usual activity per day was two hours for influenza ARIs and between 30 and 45 minutes for all other ARI categories. CONCLUSION: From a societal perspective, community-managed ARIs are a significant cost burden on families and society. The point estimate of the mean cost of community-managed influenza illnesses in healthy preschool aged children is three times greater than those illnesses caused by RSV and other respiratory viruses. Indirect costs, particularly carer time away from usual activity, are the key cost drivers for ARIs in children. The use of parent-collected specimens may enhance ARI surveillance and reduce any potential Hawthorne effect caused by compliance with study procedures. These findings reinforce the need for further integrated epidemiologic and economic research of ARIs in children to allow for comprehensive cost-effectiveness assessments of preventive and therapeutic options.


id: cord-288821-nalulzfo
title: Human Coronavirus NL63 Infection in Canada
author: Bastien, Nathalie
date: 2005-02-15
txt: ./txt/cord-288821-nalulzfo.txt
cache: ./cache/cord-288821-nalulzfo.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15655772/
doi: 10.1086/426869
summary:
  Although, in a study like this one, the inclusion of a control group of healthy individuals is necessary to clearly demonstrate a causal relationship, the detection of HCoV-NL63 in respiratory-tract specimens from patients suffering from ARI of unknown causes strongly suggests that it is associated with respiratory illness. We detected the presence of HCoV-NL63 in 19 (3.6%) of the 525 analyzed specimens that were negative for (1) influenza viruses A and B; (2) PIV 1, 2, and 3; (3) adenovirus; (4) RSV; and (5) hMPV; and these results provide further evidence of the contribution of HCoV-NL63 to ARI-and of the significant burden that it therefore may present to health-care systems. Thus, the systematic detection of HCoV-NL63 in respiratory specimens may improve the understanding of the etiology of ARI; however, the possibility of dual infection cannot be excluded, because the present study utilized samples from patients with ARI who were tested-and found to be negative-for only (1) influenza viruses A and B; (2) PIV 1, 2, and 3; (3) adenovirus; (4) RSV; and (5) hMPV.

abstract:
  The isolation of human coronavirus NL63 (HCoV-NL63) in The Netherlands raised questions about its contribution to respiratory illness. In this study, a total of 525 respiratory specimens, collected in Canada primarily during the winter months of 2001–2002, were tested for HCoV-NL63; 19 tested positive for HCoV-NL63, demonstrating virus activity during January–March 2002. Patients with HCoV-NL63 were 1 month-100 years old (median age, 37 years). The main clinical presentations were fever (15/19), sore throat (5/19), and cough (9/19), and 4 patients were hospitalized. These results provide evidence for the worldwide distribution of HCoV-NL63.


id: cord-292948-1n5ej08f
author: Masse, Shirley
date: 2020-06-10
txt: ./txt/cord-292948-1n5ej08f.txt
cache: ./cache/cord-292948-1n5ej08f.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v12060630
doi: 10.3390/v12060630
summary:
  title: Epidemiology and Clinical Symptoms Related to Seasonal Coronavirus Identified in Patients with Acute Respiratory Infections Consulting in Primary Care over Six Influenza Seasons (2014–2020) in France Further studies with representative samples should be conducted to provide additional insights into the epidemiology and clinical features of HCoVs. Coronaviruses (CoVs) are an enveloped, single positive-strand RNA species of viruses belonging to the Coronaviridae family, which infect birds and mammals. Here, we document the epidemiological and clinical features of HCoV patients with acute respiratory infection (ARI) observed in general practice. To study the weekly number of HCoVs detected among ILI/ARI patients seen in general practice during the six influenza seasons, we gathered all samples collected by GPs for influenza surveillance and for the IRIIS study (Table 1 and Figure 1 ).

title:
  Epidemiology and Clinical Symptoms Related to Seasonal Coronavirus Identified in Patients with Acute Respiratory Infections Consulting in Primary Care over Six Influenza Seasons (2014–2020) in France

abstract:
  There is currently debate about human coronavirus (HCoV) seasonality and pathogenicity, as epidemiological data are scarce. Here, we provide epidemiological and clinical features of HCoV patients with acute respiratory infection (ARI) examined in primary care general practice. We also describe HCoV seasonality over six influenza surveillance seasons (week 40 to 15 of each season) from the period 2014/2015 to 2019/2020 in Corsica (France). A sample of patients of all ages presenting for consultation for influenza-like illness (ILI) or ARI was included by physicians of the French Sentinelles Network during this period. Nasopharyngeal samples were tested for the presence of 21 respiratory pathogens by real-time RT-PCR. Among the 1389 ILI/ARI patients, 105 were positive for at least one HCoV (7.5%). On an annual basis, HCoVs circulated from week 48 (November) to weeks 14–15 (May) and peaked in week 6 (February). Overall, among the HCoV-positive patients detected in this study, HCoV-OC43 was the most commonly detected virus, followed by HCoV-NL63, HCoV-HKU1, and HCoV-229E. The HCoV detection rates varied significantly with age (p = 0.00005), with the age group 0–14 years accounting for 28.6% (n = 30) of HCoV-positive patients. Fever and malaise were less frequent in HCoV patients than in influenza patients, while sore throat, dyspnoea, rhinorrhoea, and conjunctivitis were more associated with HCoV positivity. In conclusion, this study demonstrates that HCoV subtypes appear in ARI/ILI patients seen in general practice, with characteristic outbreak patterns primarily in winter. This study also identified symptoms associated with HCoVs in patients with ARI/ILI. Further studies with representative samples should be conducted to provide additional insights into the epidemiology and clinical features of HCoVs.


id: cord-300019-8vxqr3mc
author: Shi, Ting
date: 2019-03-08
txt: ./txt/cord-300019-8vxqr3mc.txt
cache: ./cache/cord-300019-8vxqr3mc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30849176/
doi: 10.1093/infdis/jiy662
summary:
  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.

title:
  The Etiological Role of Common Respiratory Viruses in Acute Respiratory Infections in Older Adults: A Systematic Review and Meta-analysis

abstract:
  Acute respiratory tract infections (ARI) constitute a substantial disease burden in adults and elderly individuals. 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. We conducted a systematic literature review (across 7 databases) of case-control studies published from 1996 to 2017 that investigated the viral profile of older adults with and those without ARI. We then computed a pooled odds ratio (OR) with a 95% confidence interval and virus-specific attributable fraction among the exposed (AFE) for 8 common viruses: respiratory syncytial virus (RSV), influenza virus (Flu), parainfluenza virus (PIV), human metapneumovirus (HMPV), adenovirus (AdV), rhinovirus (RV), bocavirus (BoV), and coronavirus (CoV). From the 16 studies included, there was strong evidence of possible causal attribution for RSV (OR, 8.5 [95% CI, 3.9–18.5]; AFE, 88%), Flu (OR, 8.3 [95% CI, 4.4–15.9]; AFE, 88%), PIV (OR, not available; AFE, approximately 100%), HMPV (OR, 9.8 [95% CI, 2.3–41.0]; AFE, 90%), AdV (OR, not available; AFE, approximately 100%), RV (OR, 7.1 [95% CI, 3.7–13.6]; AFE, 86%) and CoV (OR, 2.8 [95% CI, 2.0–4.1]; AFE, 65%) in older adults presenting with ARI, compared with those without respiratory symptoms (ie, asymptomatic individuals) or healthy older adults. However, there was no significant difference in the detection of BoV in cases and controls. 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. Disease burden estimates should take into account the appropriate AFE estimates (for older adults) that we report.


id: cord-303845-y6ws3u6x
author: DeLisle, Sylvain
date: 2010-10-14
txt: ./txt/cord-303845-y6ws3u6x.txt
cache: ./cache/cord-303845-y6ws3u6x.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0013377
doi: 10.1371/journal.pone.0013377
summary:
  Several factors, some of which have already been mentioned, may limit the generalizability of our results: 1) factors related to the performance of our study at the VA health care system: a) the veterans study population is mostly male and excludes the pediatric population, a key target for ARI surveillance [44] ; b) veterans health care utilization may differ from that observed in uninsured or privately insured individuals; c) clinical practices, documentation and coding habits by VA practitioners may differ from those observed in solo or group practices or in health systems subject to different financial or quality-control incentives; 2) factors related to our study period: optimal CDAs could differ outside the respiratory infection season, or during periods of heightened apprehension for an influenza epidemic; 3) factors related to our iterative CDA development process, which may have over adapted CDAs to VA''s particular EMR implementation and to our sample dataset in particular, this despite our efforts to maintain a separation between development and validation data subsets; 4) factors related to our text mining approach: a) we did not employ a spell checker prior to applying the NegEx algorithm.

title:
  Combining Free Text and Structured Electronic Medical Record Entries to Detect Acute Respiratory Infections

abstract:
  BACKGROUND: The electronic medical record (EMR) contains a rich source of information that could be harnessed for epidemic surveillance. We asked if structured EMR data could be coupled with computerized processing of free-text clinical entries to enhance detection of acute respiratory infections (ARI). METHODOLOGY: A manual review of EMR records related to 15,377 outpatient visits uncovered 280 reference cases of ARI. We used logistic regression with backward elimination to determine which among candidate structured EMR parameters (diagnostic codes, vital signs and orders for tests, imaging and medications) contributed to the detection of those reference cases. We also developed a computerized free-text search to identify clinical notes documenting at least two non-negated ARI symptoms. We then used heuristics to build case-detection algorithms that best combined the retained structured EMR parameters with the results of the text analysis. PRINCIPAL FINDINGS: An adjusted grouping of diagnostic codes identified reference ARI patients with a sensitivity of 79%, a specificity of 96% and a positive predictive value (PPV) of 32%. Of the 21 additional structured clinical parameters considered, two contributed significantly to ARI detection: new prescriptions for cough remedies and elevations in body temperature to at least 38°C. Together with the diagnostic codes, these parameters increased detection sensitivity to 87%, but specificity and PPV declined to 95% and 25%, respectively. Adding text analysis increased sensitivity to 99%, but PPV dropped further to 14%. Algorithms that required satisfying both a query of structured EMR parameters as well as text analysis disclosed PPVs of 52–68% and retained sensitivities of 69–73%. CONCLUSION: Structured EMR parameters and free-text analyses can be combined into algorithms that can detect ARI cases with new levels of sensitivity or precision. These results highlight potential paths by which repurposed EMR information could facilitate the discovery of epidemics before they cause mass casualties.


id: cord-305473-w30hsr4m
author: Jiang, Lili
date: 2017-02-20
txt: ./txt/cord-305473-w30hsr4m.txt
cache: ./cache/cord-305473-w30hsr4m.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/srep42963
doi: 10.1038/srep42963
summary:
  To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Our study concurrently assessed the role of routine laboratory diagnostics, and usefulness of the novel PathChip platform as well as ILI case definitions in identifying respiratory virus infection in a community cohort and hospital inpatients from a broad range of age groups (6 to 81, and 20 to 89 years respectively), to reflect what may be encountered in either community or primary care (mild-ARI) as well as tertiary care settings (severe-ARI) in a tropical environment with less distinct seasonal patterns.

title:
  Detection of viral respiratory pathogens in mild and severe acute respiratory infections in Singapore

abstract:
  To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Community-ARI and inpatient-ARI was also combined with mild and severe cases of influenza from a historical prospective study as mild-ARI and severe-ARI respectively to evaluate the performance of clinical case definitions. We analysed 130 community-ARI and 140 inpatient-ARI episodes (5 inpatient-ARI excluded because multiple pathogens were detected), involving 138 and 207 samples respectively. Detection by PCR declined with days post-onset for influenza virus; decrease was faster for community-ARI than for inpatient-ARI. No such patterns were observed for non-influenza respiratory virus infections. PathChip added substantially to viruses detected for community-ARI only. Clinical case definitions discriminated influenza from other mild-ARI but performed poorly for severe-ARI and for older participants. Rational strategies for diagnosis and surveillance of influenza and other respiratory virus must acknowledge the differences between ARIs presenting in community and hospital settings.


id: cord-316217-ynh8d853
title: Influenza B associated paediatric acute respiratory infection hospitalization in central vietnam
author: Yoshihara, Keisuke
date: 2019-02-28
txt: ./txt/cord-316217-ynh8d853.txt
cache: ./cache/cord-316217-ynh8d853.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12626
doi: 10.1111/irv.12626
summary:
  In Victoria lineage, Group1 ARI cases were clinically more severe compared to Group5, presenting a greater proportion of wheeze, tachypnea, and lower respiratory tract infection. With regard to the demographic and clinical characterization of overall paediatric ARI hospitalization cases enrolled in the current study (n = 4,429), 2,602 were male (58.8%), and the median age (in months) was 16.6 (IQR: 8.6-27.3). The demographic and clinical characteristics between influenza B (n = 133) and non-influenza B ARI groups (n = 4296) were compared ( Table 2 ). The proportion of paediatric ARI hospitalizations with chest X-ray abnormal findings was also greater in the non-influenza B ARI group ( Furthermore, in the comparison between influenza A and B, influenza B-associated ARI hospitalizations were slightly older with different age distribution pattern (P = 0.002) (Table S2) .

abstract:
  BACKGROUND: Influenza B is one of the major etiologies for acute respiratory infections (ARI) among children worldwide; however, its clinical‐epidemiological information is limited. We aimed to investigate the hospitalization incidence and clinical‐epidemiological characteristics of influenza B‐associated paediatric ARIs in central Vietnam. METHODS: We collected clinical‐epidemiological information and nasopharyngeal swabs from ARI children hospitalized at Khanh Hoa General Hospital, Nha Trang, Vietnam from February 2007 through June 2013. Nasopharyngeal samples were screened for 13 respiratory viruses using Multiplex‐PCRs. Influenza B‐confirmed cases were genotyped by Haemagglutinin gene sequencing. We analyzed the clinical‐epidemiological characteristics of influenza B Lineages (Victoria/Yamagata) and WHO Groups. RESULTS: In the pre‐A/H1N1pdm09 period, influenza B‐associated ARI hospitalization incidence among children under five was low, ranging between 14.7 and 80.7 per 100 000 population. The incidence increased to between 51.4 and 330 in the post‐A/H1N1pdm09. Influenza B ARI cases were slightly older with milder symptoms. Both Victoria and Yamagata lineages were detected before the A/H1N1pdm09 outbreak; however, Victoria lineage became predominant in 2010‐2013 (84% Victoria vs 16% Yamagata). Victoria and Yamagata lineages did not differ in demographic and clinical characteristics. In Victoria lineage, Group1 ARI cases were clinically more severe compared to Group5, presenting a greater proportion of wheeze, tachypnea, and lower respiratory tract infection. CONCLUSIONS: The current results highlight the increased incidence of influenza B‐related ARI hospitalization among children in central Vietnam in the post‐A/H1N1pdm09 era. Furthermore, the difference in clinical severity between Victoria lineage Group1 and 5 implies the importance of influenza B genetic variation on clinical presentation.


id: cord-317912-v2wovcqd
author: Akmatov, Manas K.
date: 2012-11-14
txt: ./txt/cord-317912-v2wovcqd.txt
cache: ./cache/cord-317912-v2wovcqd.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0048508
doi: 10.1371/journal.pone.0048508
summary:
  found similar detection rates for respiratory pathogens between self-and staffcollected midturbinate swabs when one staff-collected and one selfcollected swab were taken from opposite nostrils during the same visit to a campus health center [5] . In the study center, a trained staff member (A.G.) obtained a nasal swab (regular flocked swab, Copan, Brescia, Italy, product number 359C) from the participant''s left nostril and instructed him/her how to perform a self-swab. Sensitivity and specificity of self-collected swabs, obtained in the study center, to detect viral respiratory pathogens (compared to staff-collected swabs)*. The detection of a viral pathogen was independent of the amount of b-actin DNA in both staff-and self-swabs collected on day 1 (Fig. 4) . This prospective study comparing staff-and self-collected nasal swabs for the detection of ARI pathogens clearly demonstrated the validity of self-swabbing; specifically, self-swabbing was not inferior in terms of acceptance, satisfaction, sample adequacy, and viral detection rate.

title:
  Equivalence of Self- and Staff-Collected Nasal Swabs for the Detection of Viral Respiratory Pathogens

abstract:
  BACKGROUND: The need for the timely collection of diagnostic biosamples during symptomatic episodes represents a major obstacle to large-scale studies on acute respiratory infection (ARI) epidemiology. This may be circumvented by having the participants collect their own nasal swabs. We compared self- and staff-collected swabs in terms of swabbing quality and detection of viral respiratory pathogens. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a prospective study among employees of our institution during the ARI season 2010/2011 (December-March). Weekly emails were sent to the participants (n = 84), reminding them to come to the study center in case of new symptoms. The participants self-collected an anterior nasal swab from one nostril, and trained study personnel collected one from the other nostril. The participants self-collected another two swabs (one from each nostril) on a subsequent day. Human β-actin DNA concentration was determined in the swabs as a quality control. Viral respiratory pathogens were detected by multiplex RT-PCR (Seeplex RV15 kit, Seegene, Eschborn, Germany). Of 84 participants, 56 (67%) reported at least one ARI episode, 18 participants two, and one participant three. Self-swabbing was highly accepted by the participants. The amount of β-actin DNA per swab was higher in the self- than in the staff-collected swabs (p = 0.008). β-actin concentration was lower in the self-swabs collected on day 1 than in those collected on a subsequent day (p<0.0001). A respiratory viral pathogen was detected in 31% (23/75) of staff- and in 35% (26/75) of self-collected swabs (p = 0.36). With both approaches, the most frequently identified pathogens were human rhinoviruses A/B/C (12/75 swabs, 16%) and human coronavirus OC43 (4/75 swabs, 5%). There was almost perfect agreement between self- and staff-collected swabs in terms of pathogen detection (agreement = 93%, kappa = 0.85, p<0.0001). CONCLUSIONS/SIGNIFICANCE: Nasal self-swabbing for identification of viral ARI pathogens proved to be equivalent to staff-swabbing in this population in terms of acceptance and pathogen detection.


id: cord-319845-oob2ktnz
author: Proença-Modena, José Luiz
date: 2011-06-20
txt: ./txt/cord-319845-oob2ktnz.txt
cache: ./cache/cord-319845-oob2ktnz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21701591/
doi: 10.1371/journal.pone.0021083
summary:
  Therefore, in order to test whether active viral replication of human bocavirus is associated with respiratory diseases and to understand the clinical impact of this virus in patients with these diseases, we performed a 3-year retrospective hospital-based study of HBoV in outpatients and inpatients with symptoms of Acute Respiratory Infections (ARI) in Brazil. This article reports a cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, in which the shedding of VP1 mRNA in respiratory secretions was used as surrogate marker for active HBoV replication, to look for correlations with viral load, and presence of particular clinical manifestations and simultaneous detection of other respiratory viruses. The results of this cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, indicate that shedding of VP1 mRNA in respiratory secretions, as a marker of HBoV replication, correlates positively with high viral load, presence of diarrhea, and lack of co-infection by other respiratory viruses.

title:
  Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea

abstract:
  Human bocavirus (HBoV) is a parvovirus recently identified in association with acute respiratory infections (ARI). Despite its worldwide occurrence, little is known on the pathogenesis of HBoV infections. In addition, few systematic studies of HBoV in ARI have been conducted in Latin America. Therefore, in order to test whether active viral replication of human bocavirus is associated with respiratory diseases and to understand the clinical impact of this virus in patients with these diseases, we performed a 3-year retrospective hospital-based study of HBoV in outpatients and inpatients with symptoms of Acute Respiratory Infections (ARI) in Brazil. Nasopharyngeal aspirates (NPAs) from 1015 patients with respiratory symptoms were tested for HBoV DNA by PCR. All samples positive for HBoV were tested by PCR for all other respiratory viruses, had HBoV viral loads determined by quantitative real time PCR and, when possible, were tested by RT-PCR for HBoV VP1 mRNA, as evidence of active viral replication. HBoV was detected in 4.8% of patients, with annual rates of 10.0%, 3.0% and 3.0% in 2005, 2006 and 2007, respectively. The range of respiratory symptoms was similar between HBoV-positive and HBoV-negative ARI patients. However, a higher rate of diarrhea was observed in HBoV-positive patients. High HBoV viral loads (>10(8) copies/mL) and diarrhea were significantly more frequent in patients with exclusive infection by HBoV and in patients with detection of HBoV VP1 mRNA than in patients with viral co-infection, detected in 72.9% of patients with HBoV. In summary, our data demonstrated that active HBoV replication was detected in a small percentage of patients with ARI and was correlated with concurrent diarrhea and lack of other viral co-infections.


id: cord-320808-taj5swwc
author: Lu, Guilan
date: 2020-07-23
txt: ./txt/cord-320808-taj5swwc.txt
cache: ./cache/cord-320808-taj5swwc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32703176/
doi: 10.1186/s12879-020-05258-2
summary:
  title: An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55 To isolate HAdV, we inoculated Hep-2 cells with the human adenovirus (HAdV)-positive samples and then carried out sequencing and phylogenetic analysis of the hexon, fiber, and penton genes of the isolated adenoviruses. Furthermore, the clinical laboratory data from this outbreak provides important reference for the clinical diagnosis and may ultimately aid in informing the development of strategies to control and prevent respiratory tract infections caused by HAdV-B55. To help identify the causative pathogen, we collected pharyngeal swab specimens from the affected students and carried out molecular detection and typing, phylogenic analysis, and whole-genome sequencing. The hexon (2841 bp), fiber (978 bp), and penton (1674 bp) sequences from the seven HAdV isolates were 100% identical, suggesting that this outbreak was caused by a single viral strain. Genome sequence of human adenovirus type 55, a re-emergent acute respiratory disease pathogen in China

title:
  An outbreak of acute respiratory infection at a training base in Beijing, China due to human adenovirus type B55

abstract:
  BACKGROUND: Twelve students experienced symptoms of acute respiratory infection (ARI) at a training base in Beijing from August 26 to August 30, 2015. We investigated the cause of this ARI outbreak. METHODS: In partnership with the local center for disease control, we collected a total of twelve pharyngeal swab specimens as well as demographic information for the affected patients. We used multiplex real-time PCR to screen for sixteen common respiratory viruses in these samples. To isolate HAdV, we inoculated Hep-2 cells with the human adenovirus (HAdV)-positive samples and then carried out sequencing and phylogenetic analysis of the hexon, fiber, and penton genes of the isolated adenoviruses. In addition, we analyzed the entire genome of one strain isolated from the index case to identify single-nucleotide substitutions. RESULTS: We identified ten HAdV-positive students using multiplex real-time PCR. None of the students were co-infected with other viruses. We successfully isolated seven HAdV strains from the pharyngeal swab specimens. The coding sequences of the hexon, fiber, and penton genes of these seven HAdV strains were identical, suggesting that they represented seven strains from a single virus clone. One HAdV isolate obtained from the index case, BJDX-01-2015, was selected for whole genome analysis. From this isolate, we obtained a 34,774-nucleotide sequence. The genome of BJDX-01-2015 clustered with HAdV-B55 in phylogenetic analyses and had 99.97% identity with human adenovirus 55 isolate HAdV-B/CHN/BJ01/2011/55 (GenBank accession no. JX491639). CONCLUSIONS: We identified HAdV-B55 as the strain associated with the August 2015 ARI outbreak at a training base in Beijing. This was the first reported outbreak in Beijing due to HAdV-B55. Continuous surveillance of respiratory adenoviruses is urgently needed to understand the epidemiological and evolutionary features of HAdV-B55, and an epidemiological modeling approach may provide further insights into this emerging public health threat. Furthermore, the clinical laboratory data from this outbreak provides important reference for the clinical diagnosis and may ultimately aid in informing the development of strategies to control and prevent respiratory tract infections caused by HAdV-B55.


id: cord-326122-5m1727m1
title: PCR testing for Paediatric Acute Respiratory Tract Infections
author: Wishaupt, Jérôme O.
date: 2014-08-04
txt: ./txt/cord-326122-5m1727m1.txt
cache: ./cache/cord-326122-5m1727m1.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1526054214000803
doi: 10.1016/j.prrv.2014.07.002
summary:
  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

abstract:
  Acute respiratory tract infection (ARI) is a frequently occurring disease in children. It is a clinical diagnosis for which no internationally accepted diagnostic test is available. The majority of ARI is viral in origin, though diagnostic tests for viruses were rarely performed in the past. In the past 2 decades, new molecular techniques have been introduced in many hospitals. They are capable of generating a high yield of viral and bacterial diagnoses, but their impact upon clinical practices is still questionable. In this paper, we discuss the difficulties of diagnosing ARI in children, the indications for conventional and new diagnostics and their implications.


id: cord-330819-vfagxsdz
author: Althouse, Benjamin M
date: 2018-08-14
txt: ./txt/cord-330819-vfagxsdz.txt
cache: ./cache/cord-330819-vfagxsdz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.ijid.2018.08.001
doi: 10.1016/j.ijid.2018.08.001
summary:
  Using enhanced hospital based surveillance of childhood ARI we identify seasonal patterns in hospitalizations as a proxy for transmission and explore the relationship of hospitalizations associated with virus detection with rainfall, temperature, and dew point, to try and identify contributing factors to observed seasonality. To examine the relationship between monthly average rain, temperature, and dew point and incidence hospitalized childhood ARI infections, we estimated the cross-wavelet transform between the z-standardized time series (we subtracted the mean of the time series and divided by the standard deviation) of weather and viral detections (Cazelles et al., 2008) . We evaluated seasonal patterns and associations with weather of hospitalizations for several respiratory viruses using three lines of evidence: 1) Poisson regression examining the relative incidence across months of virus detections adjusted for weather covariates, 2) cross-wavelet transforms of hospitalizations with viral detections, and 3) a sensitivity analysis with a logistic regression model finding odds ratio of hospitalizations with viral detections and weather variables.

title:
  Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam

abstract:
  BACKGROUND: Acute respiratory infections (ARIs) are the most common causes of death in children under 5 years of age. While the etiology of most pneumonia and ARI episodes is undiagnosed, a broad range of ARI-causing viruses circulate widely in South East Asia. However, the patterns and drivers of the seasonal transmission dynamics are largely unknown. Here we identify the seasonal patterns of multiple circulating viruses associated with hospitalizations for ARIs in Nha Trang, Vietnam. METHODS: Hospital based enhanced surveillance of childhood ARI is ongoing at Khanh Hoa General Hospital in Nha Trang. RT-PCR was performed to detect 13 respiratory viruses in nasopharyngeal samples from enrolled patients. Seasonal patterns of childhood ARI hospital admissions of various viruses were assessed, as well as their association with rainfall, temperature, and dew point. RESULTS: Respiratory syncytial virus peaks in the late summer months, and influenza A in April to June. We find significant associations between detection of human parainfluenza 3 and human rhinovirus with the month's mean dew point. Using a cross-wavelet transform we find a significant out-of-phase relationship between human parainfluenza 3 and temperature and dew point. CONCLUSIONS: Our results are important for understanding the temporal risk associated with circulating pathogens in Southern Central Vietnam. Specifically, our results can inform timing of routing seasonal influenza vaccination and for when observed respiratory illness is likely viral, leading to judicious use of antibiotics in the region.


id: cord-337747-7sb03moe
author: Lagare, Adamou
date: 2019-10-11
txt: ./txt/cord-337747-7sb03moe.txt
cache: ./cache/cord-337747-7sb03moe.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1002/hsr2.137
doi: 10.1002/hsr2.137
summary:
  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

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

abstract:
  BACKGROUND AND AIMS: In Niger, acute respiratory infections (ARIs) are the second most common cause of death in children aged younger than 5 years. However, the etiology of ARI is poorly understood in the country. 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. METHODS: We conducted a prospective study among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals in Niamey between January and December 2015. Clinical presentation and procedures during admission were documented using a standardized case investigation form. Nasopharyngeal specimens collected from each patient were tested for a panel of respiratory viruses and bacteria using the Fast Track Diagnostic 21 Plus kit. RESULTS: We enrolled and tested 638 children aged younger than 5 years, of whom 411 (64.4%) were aged younger than 1 year, and 15 (2.4%) died during the study period. Overall, 496/638 (77.7%) specimens tested positive for at least one respiratory virus or bacterium; of these, 195 (39.3%) tested positive for respiratory viruses, 126 (25.4%) tested positive for respiratory bacteria, and 175 (35.3%) tested positive for both respiratory viruses and bacteria. The predominant viruses detected were respiratory syncytial virus (RSV) (149/638; 23.3%), human parainfluenza virus (HPIV) types 1 to 4 (78/638; 12.2%), human rhinovirus (HRV) (62/638; 9.4%), human adenovirus (HAV) (60/638; 9.4%), and influenza virus (INF) (52/638; 8.1%). Streptococcus pneumoniae (249/638; 39.0%) was the most frequently detected bacterium, followed by Staphylococcus aureus (112/638; 12.2%) and Haemophilus influenzae type B (16/638; 2.5%). Chest X‐rays were performed at the discretion of the attending physician on 301 (47.2%) case patients. Of these patients, 231 (76.7%) had abnormal radiological findings. A total of 135/638 (21.2%) and 572/638 (89.7%) children received antibiotic treatment prior to admission and during admission, respectively. CONCLUSION: A high proportion of respiratory viruses was detected among children aged younger than 5 years with febrile ARI, raising concerns about excessive use of antibiotics in Niger.


id: cord-349279-wbb7h2zu
author: Walker, Gregory J.
date: 2019-05-07
txt: ./txt/cord-349279-wbb7h2zu.txt
cache: ./cache/cord-349279-wbb7h2zu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1002/jmv.25493
doi: 10.1002/jmv.25493
summary:
  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

title:
  Viruses associated with acute respiratory infection in a community‐based cohort of healthy New Zealand children

abstract:
  Acute respiratory infections (ARIs) are a major cause of morbidity among children. Respiratory viruses are commonly detected in both symptomatic and asymptomatic periods. 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. Children otherwise healthy aged 1 to 8 years were prospectively enrolled in the study during two consecutive winters, when ARIs peak in New Zealand. Parents completed a daily symptom diary for 8 weeks, during which time they collected a nasal swab from the child for each clinical ARI episode. A further nasal swab was collected by research staff during a clinic visit at the conclusion of the study. All samples were tested for 15 respiratory viruses commonly causing ARI using molecular multiplex polymerase chain reaction assays. There were 575 ARIs identified from 301 children completing the study, at a rate of 1.04 per child‐month. Swabs collected during an ARI were positive for a respiratory virus in 76.8% (307 of 400), compared with 37.3% (79 of 212) of swabs collected during asymptomatic periods. The most common viruses detected were human rhinovirus, coronavirus, parainfluenza viruses, influenzavirus, respiratory syncytial virus, and human metapneumovirus. All of these were significantly more likely to be detected during ARIs than asymptomatic periods. Parent‐administered surveillance is a useful mechanism for understanding infectious disease in healthy children in the community. Interpretation of molecular diagnostic assays for viruses must be informed by understanding of local rates of asymptomatic infection by such viruses.


