# pos

id: cord-350928-vj5qlzpj
pos: NFP
token:
  ..............................................................................................................

lemma:
  ..............................................................................................................


# ent

id: cord-002137-j5sfiyz8
type: ORG
entity:
  Policy Directive Occupational Assessment Screening Vaccination Against Specified Infectious Diseases Royal Australian College of General Practitioners Infection Control Standards for Office Based Practices Co


id: cord-002137-j5sfiyz8
type: ORG
entity:
  General Practice Network Influenza Survey Report National Foundation of Infectious Diseases Improving Influenza Vaccination Rates


id: cord-002137-j5sfiyz8
type: ORG
entity:
  Atlanta Centre for Disease Control and Prevention Australian Institute of Health Welfare AIHW Rural Regional


id: cord-002137-j5sfiyz8
type: ORG
entity:
  the Australian Government Department of Health and Ageing the NSW Department of Health and The Children s Hospital


id: cord-002138-uywz5nqw
type: DISEASE
entity:
  influenza A H1N1 virus via global airline transportation World Health Organization Global surveillance during an influenza pandemic Modeling targeted layered


id: cord-002138-uywz5nqw
type: DISEASE
entity:
  influenza A H1N1 v in the Netherlands the first 115 cases Early transmission characteristics of influenza A H1N1 v in Australia Victorian state Pandemic potential of a strain of influenza A H1N1


id: cord-002138-uywz5nqw
type: DISEASE
entity:
  influenza A H1N1 virus and its age specificity in Japan Modelling of the influenza A H1N1 v outbreak


id: cord-002257-30s14h9j
type: DNA
entity:
  VP2 regions 18 CS07 7 A24 A A A CS09 5 A24 A A A CS09 22 A24 A A A CS09 3 A33 A A A CS09 12 A33 A A A CS09 2 A67 A branches


id: cord-002257-30s14h9j
type: PROTEIN
entity:
  HRV89 A A MS07 20 A57 A A A MS07 21 A57 A A A CS09 6 A21 A A A CS09 17 A21 A A A CS09 21 A21 A A A MS06 4 A61 A A A MS06 6 A61 A A A CS09 15 A41 A A A MS08 8 A55 A A A CS09 11 A58 A A A CS09 26 A58 A A A MS06 2 A89 A A A CS09 28 A8 A A A CS07 9 1B A A A CS07 12 1B A A A CS07 13 1B A A A CS07 14 1B A A A CS07 18 1B A A A MS08 6 A43 A A A CS09 4 A43 A A A


id: cord-269665-byuv48wi
type: PROTEIN
entity:
  adenoviruses human metapneumovirus coronavirus 229E NL63 parainfluenza viruses 1 2 or 3 influenza viruses A or B respiratory syncytial virus A or B rhinovirus A B


id: cord-263927-hnsyas9q
type: DISEASE
entity:
  influenza A influenza B enterovirus rhinovirus RSV parainfluenza adenovirus coronaviruses and metapneumovirus


id: cord-263927-hnsyas9q
type: DISEASE
entity:
  influenza A H1N1 2009 virus during the first pandemic wave in Brazil Bacterial coinfections in lung tissue


id: cord-278554-rg92gcc6
type: ORG
entity:
  World Health Organization Pandemic Influenza Preparedness and Response A WHO Guidance Document Geneva World Health Organization America s Forgotten Pandemic Estimating


id: cord-278554-rg92gcc6
type: ORG
entity:
  influenza WHO Regional Office for Europe Recommendations for Good Practice in Pandemic Preparedness Identified Through Evaluation of the Response to Pandemic


id: cord-285425-3v1bid02
type: ORG
entity:
  Risk Assessment Center for Disease Control and Prevention CDC Respiratory Syncytial Virus Infection RSV Transmission and Prevention Public Health Agency


id: cord-286096-h275nner
type: TAXON
entity:
  Legionella pneumophila Mycoplasma pneumoniae Chlamydophila psittaci Chlamydophila pneumoniae Coxiella burnetii


id: cord-292946-iggv9f0k
type: DATE
entity:
  between 1 November and 31 March of four consecutive winter seasons 2008 2009 2009 2010 2010 2011 and 2011 2012


id: cord-292946-iggv9f0k
type: ORG
entity:
  Catalonia Spain World Health Organization Pneumonia Vaccine Trial Investigators Group Standardization of Interpretation of Chest Radiographs for the Diagnosis of Pneumonia in Children WHO V


id: cord-293354-55nawxos
type: DISEASE
entity:
  influenza viruses rhinoviruses RV human parainfluenza viruses hPIV human adenoviruses hAdV human coronaviruses hCoV OC43 hCoV 229E hCoV NL63


id: cord-297609-6g39lu1y
type: TAXON
entity:
  human metapneumovirus Mycoplasma pneumoniae Chlamydophila pneumoniae Legionella pneumophila serotype 1


id: cord-306923-eujbxdqi
type: GGP
entity:
  Sameera Alghamdi Mohammed G title Factors associated with recovery delay in a sample of patients diagnosed by MERS CoV rRT PCR A Saudi Arabian multicenter retrospective study date 2018 04 25 journal Influenza Other Respir Viruses DOI 10 1111 irv 12560 sha 32ffbe671caf791831bb7516b550b4b27240a5f0 doc_id 306923 cord_uid eujbxdqi BACKGROUND


id: cord-310956-qwe4ndvb
type: DISEASE
entity:
  influenza A H1N1 pandemic in Wuxi China The surveillance data of both systems were correlated with the influenza epidemic and therefore valuable in monitoring influenza activity


id: cord-316956-nnqi0dj1
type: GGP
entity:
  Viruses DOI 10 1111 irv 12414 sha 0c2489ea506fea5ac57b464c2a99f893cc867ff3 doc_id 316956 cord_uid nnqi0dj1 BACKGROUND Respiratory syncytial virus


id: cord-307338-4nta9b6w
type: DISEASE
entity:
  influenza A H1N1 virus in Switzerland Isolation of viruses antigenically related to the swine influenza virus


id: cord-323066-tvguutak
type: DISEASE
entity:
  respiratory syncytial virus infection Respiratory syncytial virus and parainfluenza virus Evaluation


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


id: cord-336335-spap39b7
type: DISEASE
entity:
  respiratory symptoms cough coryza nasal obstruction odynophagia dyspnea chest pain dysphonia wheezing


id: cord-320592-wnrzv4hg
type: CELL_LINE
entity:
  HEp 2 cell cultures protocol 520 I National Institute for Health USA 5 Healthy individuals with similar age and sex n 10


id: cord-343050-1pfqgvie
type: DISEASE
entity:
  influenza virus respiratory syncytial virus RSV rhinovirus parainfluenza virus types 1 3 adenovirus and human metapneumovirus Figure 3 60 A


id: cord-343050-1pfqgvie
type: DISEASE
entity:
  influenza and respiratory syncytial virus in the United States Assessment of the burden of influenza in children Influenza infection


id: cord-354151-psog34u3
type: DISEASE
entity:
  influenza A H1N1 pdm09 pandemic strain appeared and the ILI epidemic threshold was reached by early October week 41 Such early occurrence may affect the circulation of other seasonal pathogens


id: cord-335948-qkfxfmxb
type: ORG
entity:
  the World Health Organization Consultation on Northern Hemisphere Influenza Vaccine Composition for Public


id: cord-350928-vj5qlzpj
type: PROTEIN
entity:
  Cam2008 E244 S R S Cam2009 P280 N S Cam2008 E374 S Cam2009 E532 N Cam2008 E446 N S Cam2008 E473 N S Cam2008


id: cord-350928-vj5qlzpj
type: PROTEIN
entity:
  N Cam2009 P280 S P Q H Cam2009 P232 H Cam2009 P231 H Cam2009 E585 Y Cam2009 E569 H Cam2009 E532 KH Cam2008 P125 Cam2008 P0202 H Cam2008 E474 H Cam2008 E473 H Cam2008 E446 H Cam2008 E374 H Cam2008 E244 Y Cam2008 E216 Y Cam2007 E141 Y 43


id: cord-001521-l36f1gp7
type: DNA
entity:
  Mongolian pandemic isolates 3 gene segments I PB2 2 gene segments II PB1 3 gene segments III PA 9 gene segments IV HA 3 gene segments V NP 4 gene segments VI NA 7 gene segments VII M and 3 gene segments


id: cord-001521-l36f1gp7
type: DNA
entity:
  CY050844 CY0533648 CY050846 CY050845 CY065987 CY065989 CY065990 CY 065988 CY065991 CY065985 CY065984 CY065986 CY052366 CY053365 CY054546 CY054547 CY055169 CY 055170 CY055171 CY056363 CY055308 CY057191 CY057083 CY065995 CY065997 CY065998 CY065996 CY 065999 CY065993 CY065992 CY065994 CY054548 CY054549 CY073448 All 8 genes


id: cord-001521-l36f1gp7
type: PROTEIN
entity:
  TAT 600 nm MUS_TLR4R AGGCCCCAGAGTTTTGTTC T 900 nm MUS_TLR5F CTGGGGACCCAGTATGCTAA 600 nm MUS_TLR5R ACAGCCGAAGTTCCAAGAGA 900 nm MUS_TLR7F GGAGCTCTGTCCTTGAGTGG 900 nm MUS_TLR7R CAAGGCATGTCCTAGGTGGT 600


id: cord-001521-l36f1gp7
type: PROTEIN
entity:
  NF kappaB nuclear factor kappaB TNFa tumor necrosis factor alpha TGFb transforming growth factor beta HO 1 heme oxygenase 1


id: cord-001521-l36f1gp7
type: PROTEIN
entity:
  Janus kinase signal transducers and activators of transcription signaling pathways 3 10 11 12 The in vivo experiments presented here showed that NF jB and AP 1 inhibitors


id: cord-001521-l36f1gp7
type: GGP
entity:
  Space 7 SVT 5 CF 9 BellKor 10 PF 11 and FWLS 12 Eventually the team BellKor s Pragmatic Chaos won this contest Their methods combines nonlinear probe blending


id: cord-001521-l36f1gp7
type: ORG
entity:
  World Health Organization WHO Influenza Collaboration Centers Centers for Disease Control and Prevention Atlanta


id: cord-001521-l36f1gp7
type: WORK_OF_ART
entity:
  Manual of Diagnostic Tests and Vaccines For Terrestrial Animals Mammals Birds and Bees An avian influenza virus


id: cord-001521-l36f1gp7
type: ORG
entity:
  New Pharmaceutical Substances Moscow Ministry of Public Health Department of Quality Effectiveness and Safety


id: cord-001521-l36f1gp7
type: ORG
entity:
  USSR Ministry of Health Planning and Performance of Clinical Study of Medicines Federal Pharmaceutical Substances


id: cord-001521-l36f1gp7
type: GPE
entity:
  the Republic of Kazakhstan National Pharmacopoeia of the Republic of Kazakhstan Planning and Performance of Clinical Study of Medicines Federal


id: cord-001521-l36f1gp7
type: ORG
entity:
  a State Key Laboratory for Infectious Disease Control and Prevention National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention


id: cord-001521-l36f1gp7
type: ORG
entity:
  the Special Coordination Funds for Promoting Science and Technology of Ministry of Education Science Sports and Culture of Japan


id: cord-001521-l36f1gp7
type: ORG
entity:
  the Ministry of Education Culture Sports Science and Technology Japan Takeda Science Foundation Terumo Life Science Foundation


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A H1N1 hemagglutinins 5 The recombinant protein was used as the antigen attached through histidine


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A H1N1 2009 Specificity and clinical sensitivity of the two one step RT PCRs Fast Set InfA InfB


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A H3N2 vaccinations 76 of which were given to adults over 55 years of age Consequently vaccine administration


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  H5N1 infected primary human macrophages and that it played a regulatory role in the H5N1hyperinduced host pro inflammatory responses 1


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A viral genotypes system 13 The work presented here is one of the first steps towards the development of a nomenclature system for influenza A virus lineages


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A H1N1 pandemic 2009 positive by real time PCR Detection of influenza virus in respiratory samples was much lower with the ResPlex II


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A virus NS1 protein A NS1 Figure 2A The splicing of influenza A virus M gene specific mRNA was also increased by co expression with C NS1 though it was inhibited by co expression with A NS1 Figure 2B


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A H3N2 viruses isolated worldwide from 1994 to 2005 a cause for concern Surveillance of resistance to adamantanes


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A H1N1 virus in the United States Isolation of oseltamivirresistant influenza A H1N1 virus of different origins


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A H1N1 virus and its age specificity in Japan The transmissibility and control of pandemic influenza A H1N1 virus Effect of clinical and virological parameters on the level of neutralizing antibody against pandemic influenza A virus H1N1


id: cord-001521-l36f1gp7
type: DISEASE
entity:
  influenza A H5N1 viruses in primary human alveolar and bronchial epithelial cells Differential onset of apoptosis


# bib

id: cord-000114-f0vud3gu
title: Ducks: The “Trojan Horses” of H5N1 influenza
author: Kim, Jeong‐Ki
date: 2009-05-31
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749972/
doi: 10.1111/j.1750-2659.2009.00084.x
abstract:
  Abstract Wild ducks are the main reservoir of influenza A viruses that can be transmitted to domestic poultry and mammals, including humans. Of the 16 hemagglutinin (HA) subtypes of influenza A viruses, only the H5 and H7 subtypes cause highly pathogenic (HP) influenza in the natural hosts. Several duck species are naturally resistant to HP Asian H5N1 influenza viruses. These duck species can shed and spread virus from both the respiratory and intestinal tracts while showing few or no disease signs. While the HP Asian H5N1 viruses are 100% lethal for chickens and other gallinaceous poultry, the absence of disease signs in some duck species has led to the concept that ducks are the “Trojan horses” of H5N1 in their surreptitious spread of virus. An important unresolved issue is whether the HP H5N1 viruses are maintained in the wild duck population of the world. Here, we review the ecology and pathobiology of ducks infected with influenza A viruses and ducks’ role in the maintenance and spread of HP H5N1 viruses. We also identify the key questions about the role of ducks that must be resolved in order to understand the emergence and control of pandemic influenza. It is generally accepted that wild duck species can spread HP H5N1 viruses, but there is insufficient evidence to show that ducks maintain these viruses and transfer them from one generation to the next.


id: cord-001521-l36f1gp7
title: Oral and Poster Manuscripts
author: nan
date: 2011-04-08
txt: ./txt/cord-001521-l36f1gp7.txt
cache: ./cache/cord-001521-l36f1gp7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313891/
doi: 10.1111/j.1750-2659.2011.00209.x
abstract: nan
summary:
  The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses.


id: cord-002136-mkl89qkt
title: An ex vivo swine tracheal organ culture for the study of influenza infection
author: Nunes, Sandro F.
date: 2009-12-09
txt: ./txt/cord-002136-mkl89qkt.txt
cache: ./cache/cord-002136-mkl89qkt.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941949/
doi: 10.1111/j.1750-2659.2009.00119.x
summary:
  Objectives We aimed to develop an air interface EVOC using pig tracheas in the study of influenza infection demonstrating that tracheal explants can be effectively maintained in organ culture and support productive influenza infection. 1, 3 Influenza infection in humans and pigs is primarily restricted to the upper and lower respiratory tract with viral replication occurring in the epithelial cells present on the surface of the respiratory mucosa. Ex vivo organ cultures (EVOC) of tracheal explants with an air interface system have been successfully developed and used in the study of both human and animal respiratory pathogens. To determine if the swine tracheal explants supported productive viral replication, explants were infected with 2AE5 · 10 2 pfu of swine influenza virus and maintained in organ culture for 5 days. Cultures of equine respiratory epithelial cells and organ explants as tools for the study of equine influenza virus infection

abstract:
  Background The threat posed by swine influenza viruses with potential to transmit from pig populations to other hosts, including humans, requires the development of new experimental systems to study different aspects of influenza infection. Ex vivo organ culture (EVOC) systems have been successfully used in the study of both human and animal respiratory pathogens. Objectives We aimed to develop an air interface EVOC using pig tracheas in the study of influenza infection demonstrating that tracheal explants can be effectively maintained in organ culture and support productive influenza infection. Methods Tracheal explants were maintained in the air interface EVOC system for 7 days. Histological characteristics were analysed with different staining protocols and co‐ordinated ciliary movement on the epithelial surface was evaluated through a bead clearance assay. Explants were infected with a swine H1N1 influenza virus. Influenza infection of epithelial cells was confirmed by immunohistochemistry and viral replication was quantified by plaque assays and real‐time RT‐PCR. Results Histological analysis and bead clearance assay showed that the tissue architecture of the explants was maintained for up to 7 days, while ciliary movement exhibited a gradual decrease after 4 days. Challenge with swine H1N1 influenza virus showed that the EVOC tracheal system shows histological changes consistent with in vivo influenza infection and supported productive viral replication over multiple cycles of infection. Conclusion The air interface EVOC system using pig trachea described here constitutes a useful biological tool with a wide range of applications in the study of influenza infection.


id: cord-002137-j5sfiyz8
title: Annual influenza vaccination: coverage and attitudes of primary care staff in Australia
author: Ward, Kirsten
date: 2010-10-12
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942009/
doi: 10.1111/j.1750-2659.2010.00158.x
abstract:
  Please cite this paper as: Ward et al. (2011) Annual influenza vaccination: coverage and attitudes of primary care staff in Australia. Influenza and Other Respiratory Viruses 5(2), 135–141. Background Annual influenza vaccination is recommended for all Australian health care workers (HCWs) including those working in primary health care. There is limited published data on coverage, workplace provision, attitudes and personal barriers to influenza vaccination amongst primary health care staff. The aim of this study was to contribute to the limited literature base in this important area by investigating these issues in the primary health care setting in New South Wales (NSW), Australia. Methods A postal survey was sent to general practitioners (GPs) and practice nurses (PNs) from inner city, semi‐urban and rural areas of NSW, Australia. There were 139 responses in total (response rate 36%) from 79 GPs (response rate 30%) and 60 PNs (response rate 46%). Results Reported influenza vaccination coverage in both 2007 and 2008 was greater than 70%, with GPs reporting higher coverage than PNs in both years. The main barriers identified were lack of awareness of vaccination recommendations for general practice staff and concern about adverse effects from the vaccine. Conclusions Rates of influenza vaccination coverage reported in this study were higher than in previous studies of hospital and institutional HCWs, though it is possible that the study design may have contributed to these higher results. Nevertheless, these findings highlight that more needs to be done to understand barriers to vaccination in this group, to inform the development of appropriate strategies to increase vaccination coverage in primary health care staff, with a special focus on PNs.


id: cord-002138-uywz5nqw
title: Transmission parameters of the A/H1N1 (2009) influenza virus pandemic: a review
author: Boëlle, Pierre‐Yves
date: 2011-03-31
txt: ./txt/cord-002138-uywz5nqw.txt
cache: ./cache/cord-002138-uywz5nqw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942041/
doi: 10.1111/j.1750-2659.2011.00234.x
summary:
  Methods We reviewed all studies presenting estimates of the serial interval or generation time and the reproduction number of the A/H1N1 (2009) virus infection. Accounting for under‐reporting in the early period of the pandemic and limiting variation because of the choice of the generation time interval, the reproduction number was between 1·2 and 2·3 with median 1·5. In the guidance document ''Global surveillance during an influenza pandemic'' released by the World Health Organization, three parameters were highlighted that should be documented quickly in this respect: the incubation period (time between infection and symptoms), the serial interval (time between symptoms onset in primary case and secondary case), and the reproduction ratio ⁄ number (average number of secondary cases per primary case). Indeed, before 2009, the two best documented values for the mean SI concerned seasonal influenza, with two estimates obtained in household-based studies: 2AE6 days (CI 95% 2AE1, 3AE0) 6 and 3AE6 days (CI 95% [2AE9, 4AE3]) 5 ; no information was available for past pandemics.

abstract:
  Please cite this paper as: Boëlle P‐Y et al. (2011) Transmission parameters of the A/H1N1 (2009) influenza virus pandemic: a review. Influenza and Other Respiratory Viruses 5(5), 306–316. Background The new influenza virus A/H1N1 (2009), identified in mid‐2009, rapidly spread over the world. Estimating the transmissibility of this new virus was a public health priority. Methods We reviewed all studies presenting estimates of the serial interval or generation time and the reproduction number of the A/H1N1 (2009) virus infection. Results Thirteen studies documented the serial interval from household or close‐contact studies, with overall mean 3 days (95% CI: 2·4, 3·6); taking into account tertiary transmission reduced this estimate to 2·6 days. Model‐based estimates were more variable, from 1·9 to 6 days. Twenty‐four studies reported reproduction numbers for community‐based epidemics at the town or country level. The range was 1·2–3·1, with larger estimates reported at the beginning of the pandemic. Accounting for under‐reporting in the early period of the pandemic and limiting variation because of the choice of the generation time interval, the reproduction number was between 1·2 and 2·3 with median 1·5. Discussion The serial interval of A/H1N1 (2009) flu was typically short, with mean value similar to the seasonal flu. The estimates of the reproduction number were more variable. Compared with past influenza pandemics, the median reproduction number was similar (1968) or slightly smaller (1889, 1918, 1957).


id: cord-002257-30s14h9j
author: Ratnamohan, Vigneswary M.
date: 2016-08-09
txt: ./txt/cord-002257-30s14h9j.txt
cache: ./cache/cord-002257-30s14h9j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5059946/
doi: 10.1111/irv.12404
summary:
  Discordant branching was seen within HRV A group: two sequences clustering as A in the VP4/VP2 tree branched within the C/A subspecies in the 5′UTR tree, and one sequence showed identity to different HRV A strains in the two genes. Human rhinoviruses are generally associated with the common cold and mild upper respiratory infections, 3 but can also cause severe respiratory infections in immunocompromised hosts (including lung and hematopoietic stem cell transplant recipients) or patients with chronic pulmonary diseases. This study aimed to identify the species and genotypes of HRV from clinical samples collected in Sydney, Australia, over four consecutive years by analysing the nucleotide homology in the 5′UTR, VP4 and part of the VP2 capsid protein coding regions. Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children

title:
  Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia

abstract:
  BACKGROUND: Human rhinoviruses (HRV) cause a wide spectrum of disease, ranging from a mild influenza‐like illness (ILI) to severe respiratory infection. Molecular epidemiological data are limited for HRV circulating in the Southern Hemisphere. OBJECTIVES: To identify the species and genotypes of HRV from clinical samples collected in Sydney, Australia, from 2006 to 2009. METHODS: Combined nose and throat swabs or nasopharyngeal aspirates collected from individuals with ILI were tested for HRV using real‐time reverse‐transcriptase polymerase chain reaction (RT‐PCR). Sequencing data of 5′UTR and VP4/VP2 coding regions on RT‐PCR‐positive specimens were analysed. RESULTS: Human rhinoviruses were detected by real‐time PCR in 20.9% (116/555) of samples tested. Phylogenetic analysis of 5′UTR and VP4/VP2 on HRV‐positive samples was concordant in the grouping of HRV A and B species but not HRV C species. Eighty per cent (16/20) of sequences that grouped as HRV C in the VP4/VP2 tree clustered as HRV A, alongside some previously described C strains as subspecies C/A. Discordant branching was seen within HRV A group: two sequences clustering as A in the VP4/VP2 tree branched within the C/A subspecies in the 5′UTR tree, and one sequence showed identity to different HRV A strains in the two genes. The prevalence of HRV C and C/A species was greater in paediatric compared to adult patients (47.9% vs 25.5%, P = .032). CONCLUSION: Human rhinoviruses are a common cause of respiratory infections, and HRV C is present in the Southern Hemisphere. Sequencing of multiple HRV regions may be necessary to determine exact phylogenetic relationships.


id: cord-002852-m4l2l2r1
title: Detection of influenza A virus in live bird markets in Kenya, 2009–2011
author: Munyua, Peninah M.
date: 2012-04-19
txt: ./txt/cord-002852-m4l2l2r1.txt
cache: ./cache/cord-002852-m4l2l2r1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780755/
doi: 10.1111/j.1750-2659.2012.00365.x
summary:
  authors: Munyua, Peninah M.; Githinji, Jane W.; Waiboci, Lilian W.; Njagi, Leonard M.; Arunga, Geoffrey; Mwasi, Lydia; Murithi Mbabu, R.; Macharia, Joseph M.; Breiman, Robert F.; Kariuki Njenga, M.; Katz, Mark A. Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs. Influenza A viruses are zoonotic pathogens that infect a variety of domestic poultry such as chickens, turkeys, ducks, and geese. 2, 4, 5 Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating influenza subtypes in the poultry population. 7, 8 Influenza viruses have also been detected in various environmental specimens collected in contaminated areas in LBMs including drinking water troughs, and surfaces in the delivery, holding and slaughter areas in markets.

abstract:
  Please cite this paper as: Munyua et al. (2013) Detection of influenza A virus in live bird markets in Kenya, 2009–2011. Influenza and Other Respiratory Viruses 7(2), 113–119. Background Surveillance for influenza viruses within live bird markets (LBMs) has been recognized as an effective tool for detecting circulating avian influenza viruses (AIVs). In Sub‐Saharan Africa, limited data exist on AIVs in animal hosts, and in Kenya the presence of influenza virus in animal hosts has not been described. Objectives This surveillance project aimed to detect influenza A virus in poultry traded in five LBMs in Kenya. Methods We visited each market monthly and collected oropharyngeal and cloacal specimens from poultry and environmental specimens for virological testing for influenza A by real time RT‐PCR. On each visit, we collected information on the number and types of birds in each market, health status of the birds, and market practices. Results During March 24, 2009–February 28, 2011, we collected 5221 cloacal and oropharyngeal swabs. Of the 5199 (99·6%) specimens tested, influenza A virus was detected in 42 (0·8%), including 35/4166 (0·8%) specimens from chickens, 3/381 (0·8%) from turkeys, and 4/335 (1·2%) from geese. None of the 317 duck specimens were positive. Influenza was more commonly detected in oropharyngeal [33 (1·3%)] than in cloacal [9 (0·4%)] specimens. None of the 485 environmental specimens were positive. Virus was detected in all five markets during most (14/22) of the months. Ducks and geese were kept longer at the market (median 30 days) than chickens (median 2 days). Conclusions Influenza A was detected in a small percentage of poultry traded in LBMs in Kenya. Efforts should be made to promote practices that could limit the maintenance and transmission of AIVs in LBMs.


id: cord-003298-vojbn0p4
title: Pandemic influenza A (H1N1) during winter influenza season in the southern hemisphere
author: Hsieh, Ying‐Hen
date: 2010-07-08
txt: ./txt/cord-003298-vojbn0p4.txt
cache: ./cache/cord-003298-vojbn0p4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225867/
doi: 10.1111/j.1750-2659.2010.00147.x
summary:
  Methods We make use of the Richards model to fit the publicly available epidemic data (confirmed cases, hospitalizations, and deaths) of six southern hemisphere countries (Argentina, Brazil, Chile, Australia, New Zealand, and South Africa) to draw useful conclusions, in terms of its reproduction numbers and outbreak turning points, regarding the new pH1N1 virus in a typical winter influenza season. We construct simple mathematical models using the epidemiologic data for these southern hemisphere countries to draw timely and useful conclusions regarding the role played by the new pH1N1 strain under the setting of a typical winter influenza season. We fit the cumulative pandemic influenza A (H1N1) 2009 case data from various southern hemisphere countries described earlier to the Richards model and its multi-wave variants. The weekly pH1N1 confirmed case and hospitalization data by onset week in Australia 8 fit the 1-wave Richards model (Table 6 and Figure 2E -F).

abstract:
  Please cite this paper as: Hsieh Ying‐Hen. (2010) Pandemic influenza A (H1N1) during winter influenza season in the southern hemisphere. Influenza and Other Respiratory Viruses 4(4), 187–197. Background Countries in the southern hemisphere experienced sizable epidemics of pandemic influenza H1N1 in their winter season during May–August, 2009. Methods We make use of the Richards model to fit the publicly available epidemic data (confirmed cases, hospitalizations, and deaths) of six southern hemisphere countries (Argentina, Brazil, Chile, Australia, New Zealand, and South Africa) to draw useful conclusions, in terms of its reproduction numbers and outbreak turning points, regarding the new pH1N1 virus in a typical winter influenza season. Results The estimates for the reproduction numbers of these six countries range from a high of 1·53 (95% CI: 1·22, 1·84) for confirmed case data of Brazil to a low of 1·16 (1·09, 1·22) for pH1N1 hospitalizations in Australia. For each country, model fits using confirmed cases, hospitalizations, or deaths data always yield similar estimates for the reproduction number. Moreover, the turning points for these closely related outbreak indicators always follow the correct chronological order, i.e., case–hospitalization–death, whenever two or more of these three indicators are available. Conclusions The results suggest that the winter pH1N1 outbreaks in the southern hemisphere were similar to the earlier spring and later winter outbreaks in North America in its severity and transmissibility, as indicated by the reproduction numbers. Therefore, the current strain has not become more severe or transmissible while circulating around the globe in 2009 as some experts had cautioned. The results will be useful for global preparedness planning of possible tertiary waves of pH1N1 infections in the fall/winter of 2010.


id: cord-255946-bcuivyku
title: Covid‐19 and Namaste
author: Kulkarni, Prashanth
date: 2020-04-21
txt: ./txt/cord-255946-bcuivyku.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/32319220/
doi: 10.1111/irv.12746
abstract: nan
summary:
  In this context, it is imperative that social distancing and good hand hygiene is practised to stem the transmission of this highly conAlternatively, other non-physical greeting forms can be explored like Namaste, which is used in Indian subcontinent since hundreds of years to greet people with folded hands, while maintaining a fair distance from each other [ Figure 1 ]. An individual in addition to saying "Namaste" presses his hands together in front of the chest and respectfully greets the other person. This form of greeting does not involve any physical touch between individuals and gives a sense of parity to all the parties. 3 In addition to following general principles of meticulous hand washing, rapid transmission of infections both in hospitals and the community can be overcome by adopting the no-touch salutation Namaste and other such forms like bowing the head as done in some Asian countries. Guidelines on Hand Hygiene in Health Care


id: cord-259368-k8t8brjy
title: Evidence for pre‐symptomatic transmission of coronavirus disease 2019 (COVID‐19) in China
author: Ren, Xiang
date: 2020-08-07
txt: ./txt/cord-259368-k8t8brjy.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12787
doi: 10.1111/irv.12787
summary:
  A novel coronavirus named "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2) was first identified in January 2020 as the pathogen responsible for a cluster of cases of atypical pneumonia in Wuhan, a large city located in Hubei province in central China. 13 Here, we retrospectively analyse data on cases identified outside of Hubei province through the Chinese Public Health Event Surveillance System at the early stage of transmission in China, in order to provide insights on the transmission dynamics of COVID-19. In these pairs of primary and secondary cases, we fitted a normal distribution to the serial intervals between illness onset dates, allowing for negative and zero serial intervals, and correcting for growth rates in the early stage of an epidemic. [22] [23] [24] [25] [26] Pre-symptomatic infectiousness is generally not thought to occur for most respiratory viruses, but measles is a well-known example of a respiratory infection that can be spread before symptom onset, 27 and viral shedding during the incubation period has also been reported for influenza.

abstract:
  BACKGROUND: Between mid‐January and early February, provinces of mainland China outside the epicentre in Hubei province were on high alert for importations and transmission of COVID‐19. Many properties of COVID‐19 infection and transmission were still not yet established. METHODS: We collated and analysed data on 449 of the earliest COVID‐19 cases detected outside Hubei province to make inferences about transmission dynamics and severity of infection. We analysed 64 clusters to make inferences on serial interval and potential role of pre‐symptomatic transmission. RESULTS: We estimated an epidemic doubling time of 5.3 days (95% confidence interval (CI): 4.3, 6.7) and a median incubation period of 4.6 days (95% CI: 4.0, 5.2). We estimated a serial interval distribution with mean 5.7 days (95% CI: 4.7, 6.8) and standard deviation 3.5 days, and effective reproductive number was 1.98 (95% CI: 1.68, 2.35). We estimated that 32/80 (40%) of transmission events were likely to have occurred prior to symptoms onset in primary cases. Secondary cases in clusters had less severe illness on average than cluster primary cases. CONCLUSIONS: The majority of transmissions are occurring around illness onset in an infected person, and pre‐symptomatic transmission does play a role. Detection of milder infections among the secondary cases may be more reflective of true disease severity.


id: cord-263927-hnsyas9q
author: Peci, Adriana
date: 2012-08-09
txt: ./txt/cord-263927-hnsyas9q.txt
cache: ./cache/cord-263927-hnsyas9q.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/j.1750-2659.2012.00418.x
doi: 10.1111/j.1750-2659.2012.00418.x
summary:
  Objectives To describe respiratory viruses, including co‐infection and associated attributes such as age, sex or comorbidity, in patients presenting with influenza‐like illness to a community sentinel network, during the pandemic A(H1N1)pdm09 in Ontario, Canada. In multinomial logistic regression analyses adjusted for age, sex, comorbidity, and timeliness of sample collection, single infection was less often detected in the elderly and co‐infection more often in patients <30 years of age. Co‐infection, but not single infection, was more likely detected in patients who had a sample collected within 2 days of symptom onset as compared to 3–7 days. [8] [9] [10] [11] [12] [13] Higher proportions of influenza A, respiratory syncytial virus (RSV), parainfluenza viruses, and rhinovirus, compared with other circulating viruses have been detected in patients with co-infections. 9, 15, 16, 20, 21 This study enrolled community patients presenting with (ILI) to a community sentinel network, during the influenza pandemic A(H1N1)pdm09 in Ontario, Canada and documented the profile of respiratory viruses causing ILI symptoms.

title:
  Community‐acquired respiratory viruses and co‐infection among patients of Ontario sentinel practices, April 2009 to February 2010

abstract:
  Please cite this paper as: Peci et al. (2012) Community‐acquired respiratory viruses and co‐infection among patients of Ontario Sentinel practices, April 2009 to February 2010. Influenza and Other Respiratory Viruses 7(4), 559–566. Background Respiratory viruses are known to cocirculate but this has not been described in detail during an influenza pandemic. Objectives To describe respiratory viruses, including co‐infection and associated attributes such as age, sex or comorbidity, in patients presenting with influenza‐like illness to a community sentinel network, during the pandemic A(H1N1)pdm09 in Ontario, Canada. Methods Respiratory samples and epidemiologic details were collected from 1018 patients with influenza‐like illness as part of respiratory virus surveillance and a multiprovincial case–control study of influenza vaccine effectiveness. Results At least one virus was detected in 668 (65·6%) of 1018 samples; 512 (50·3%) had single infections and 156 (15·3%) co‐infections. Of single infections, the most common viruses were influenza A in 304 (59·4%) samples of which 275 (90·5%) were influenza A(H1N1)pdm09, and enterovirus/rhinovirus in 149 (29·1%) samples. The most common co‐infections were influenza A and respiratory syncytial virus B, and influenza A and enterovirus/rhinovirus. In multinomial logistic regression analyses adjusted for age, sex, comorbidity, and timeliness of sample collection, single infection was less often detected in the elderly and co‐infection more often in patients <30 years of age. Co‐infection, but not single infection, was more likely detected in patients who had a sample collected within 2 days of symptom onset as compared to 3–7 days. Conclusions Respiratory viral co‐infections are commonly detected when using molecular techniques. Early sample collection increases likelihood of detection of co‐infection. Further studies are needed to better understand the clinical significance of viral co‐infection.


id: cord-267531-tqqj4cy0
author: He, Ying
date: 2014-05-14
txt: ./txt/cord-267531-tqqj4cy0.txt
cache: ./cache/cord-267531-tqqj4cy0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12257
doi: 10.1111/irv.12257
summary:
  title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China OBJECTIVES: To determine the viral etiology and seasonality of acute respiratory infections in hospitalized children, a 3-year study was conducted in Shenzhen, China. 3, 4 The most frequently reported viruses include respiratory syncytial virus (RSV), influenza viruses A and B (IAV, IBV), parainfluenza viruses (PIVs), human rhinovirus (HRV) and adenovirus (ADV), which are responsible for most episodes of ARTIs in children. The purpose of this study is to investigate the prevalence, seasonality and clinical characteristics of acute viral respiratory infections in hospitalized children in Shenzhen and to provide insights into etiologies of ARTIs in local infants and children. Most studies showed that RSV or HRV was the most prevalent viruses in children with viral respiratory tract infection. 9 In this study, due to the high detection rate and similar seasonality of RSV, HRV, IAV, PIV and HMPV, an overall spring-summer seasonality of viral respiratory infections in children was concluded.

title:
  A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China

abstract:
  BACKGROUND: The epidemiology of local viral etiologies is essential for the management of viral respiratory tract infections. Limited data are available in China to describe the epidemiology of viral respiratory infections, especially in small–medium cities and rural areas. OBJECTIVES: To determine the viral etiology and seasonality of acute respiratory infections in hospitalized children, a 3-year study was conducted in Shenzhen, China. METHODS: Nasopharyngeal aspirates from eligible children were collected. Influenza and other respiratory viruses were tested by molecular assays simultaneously. Data were analyzed to describe the frequency and seasonality. RESULTS: Of the 2025 children enrolled in the study, 971 (48·0%) were positive for at least one viral pathogen, in which 890 (91·7%) were <4 years of age. The three most prevalent viruses were influenza A (IAV; 35·8%), respiratory syncytial virus (RSV; 30·5%) and human rhinovirus (HRV; 21·5%). Co-infections were found in 302 cases (31·1%), and dual viral infection was dominant. RSV, HRV and IAV were the most frequent viral agents involved in co-infection. On the whole, the obvious seasonal peaks mainly from March to May were observed with peak strength varying from 1 year to another. CONCLUSIONS: This study provides a basic profile of the epidemiology of acute respiratory viral infection in hospitalized children in Shenzhen. The spectrum of viruses in the study site is similar to that in other places, but the seasonality is closely related to geographic position, different from that in big cities in northern China and neighboring Hong Kong.


id: cord-268105-617qcgpe
author: Refaey, Samir
date: 2016-11-11
txt: ./txt/cord-268105-617qcgpe.txt
cache: ./cache/cord-268105-617qcgpe.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27603034/
doi: 10.1111/irv.12429
summary:
  title: Cross‐sectional survey and surveillance for influenza viruses and MERS‐CoV among Egyptian pilgrims returning from Hajj during 2012‐2015 The purpose of this study was to estimate influenza virus and MERS‐CoV prevalence among Egyptian pilgrims returning from Hajj. The MOHP has additionally conducted an annual survey among pilgrims returning from Hajj to explore the risk of influenza virus transmission to the broader community. T A B L E 1 The distribution of Egyptian pilgrims surveyed by season according to gender, age group, presence of influenza-like illness (ILI), vaccination status and influenza laboratory test result Middle East respiratory syndrome coronavirus (MERS-CoV) -Saudi Arabia Risk factors for primary middle east respiratory syndrome coronavirus illness in humans, Saudi Arabia High prevalence of common respiratory viruses and no evidence of Middle East respiratory syndrome coronavirus in Hajj pilgrims returning to Ghana Cross-sectional survey and surveillance for influenza viruses and MERS-CoV among Egyptian pilgrims returning from Hajj during 2012-2015

title:
  Cross‐sectional survey and surveillance for influenza viruses and MERS‐CoV among Egyptian pilgrims returning from Hajj during 2012‐2015

abstract:
  BACKGROUND: Approximately 80 000 Egyptians participate in Hajj pilgrimage annually. The purpose of this study was to estimate influenza virus and MERS‐CoV prevalence among Egyptian pilgrims returning from Hajj. STUDY: A cross‐sectional survey among 3 364 returning Egyptian pilgrims from 2012 to 2015 was conducted. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from all participants. Sputum specimens were collected from participants with respiratory symptoms and productive cough at the time of their interview. Specimens were tested for influenza viruses, and a convenience sample of NP/OP specimens was tested for MERS‐CoV. Thirty percent of participants met the case definition for influenza‐like illness (ILI), 14% tested positive for influenza viruses, and none tested positive for MERS‐CoV. Self‐reported influenza vaccination was 20%. CONCLUSIONS: High prevalence of reported ILI during pilgrimage and confirmed influenza virus on return from pilgrimage suggest a continued need for influenza prevention strategies for Egyptian Hajj pilgrims. An evaluation of the Ministry of Health and Population's current risk communication campaigns to increase influenza vaccine use among pilgrims may help identify strategies to improve vaccine coverage.


id: cord-269644-94yrkzns
author: Cousin, Mathias
date: 2016-01-29
txt: ./txt/cord-269644-94yrkzns.txt
cache: ./cache/cord-269644-94yrkzns.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26493783/
doi: 10.1111/irv.12353
summary:
  BACKGROUND: Respiratory viral infections lead to bronchial inflammation in patients with cystic fibrosis, especially during pulmonary exacerbations. The aim of this study was to determine the impact of viral‐associated pulmonary exacerbations in children with cystic fibrosis and failure to improve forced expiratory volume in 1 s (FEV (1)) after an appropriate treatment. CONCLUSIONS: Rhinovirus infection seems to play a role in the FEV (1) recovery after pulmonary exacerbation treatment in children with cystic fibrosis. The only risk factor significantly associated with failure to improve FEV 1 above 5% after PEx was viral respiratory infection at V2 and/or V3 (OR, 2Á04; 95% CI, 1Á57-2Á67) P = 0Á0088 and especially with rhinovirus infection: (OR, 12; 95% CI, 1Á29-111Á32, P = 0Á0288). The results of this pilot study show that rhinovirus infection during PEx is significantly associated with failure to improve FEV 1 after PEx treatment in children with CF. Incidence and risk factors for pulmonary exacerbation treatment failures in patients with cystic fibrosis chronically infected with Pseudomonas aeruginosa

title:
  Rhinovirus‐associated pulmonary exacerbations show a lack of FEV (1) improvement in children with cystic fibrosis

abstract:
  BACKGROUND: Respiratory viral infections lead to bronchial inflammation in patients with cystic fibrosis, especially during pulmonary exacerbations. The aim of this study was to determine the impact of viral‐associated pulmonary exacerbations in children with cystic fibrosis and failure to improve forced expiratory volume in 1 s (FEV (1)) after an appropriate treatment. METHODS: We lead a pilot study from January 2009 until March 2013. Children with a diagnosis of cystic fibrosis were longitudinally evaluated three times: at baseline (Visit 1), at the diagnosis of pulmonary exacerbation (Visit 2), and after exacerbation treatment (Visit 3). Nasal and bronchial samples were analyzed at each visit with multiplex viral respiratory PCR panel (qualitative detection of 16 viruses). Pulmonary function tests were recorded at each visit, in order to highlight a possible failure to improve them after treatment. Lack of improvement was defined by an increase in FEV (1) less than 5% between Visit 2 and Visit 3. RESULTS: Eighteen children were analyzed in the study. 10 patients failed to improve by more than 5% their FEV (1) between Visit 2 and Visit 3. Rhinovirus infection at Visit 2 or Visit 3 was the only risk factor significantly associated with such a failure (OR, 12; 95% CI, 1·3–111·3), P = 0·03. CONCLUSIONS: Rhinovirus infection seems to play a role in the FEV (1) recovery after pulmonary exacerbation treatment in children with cystic fibrosis. Such an association needs to be confirmed by a large‐scale study because this finding may have important implications for pulmonary exacerbation management.


id: cord-269665-byuv48wi
author: MacIntyre, Chandini Raina
date: 2011-01-27
txt: ./txt/cord-269665-byuv48wi.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21477136/
doi: 10.1111/j.1750-2659.2011.00198.x
summary:
  title: A cluster randomized clinical trial comparing fit‐tested and non‐fit‐tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers (2011) A cluster randomized clinical trial comparing fit‐tested and non‐fit‐tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750‐2659.2010.00198.x. Background We compared the efficacy of medical masks, N95 respirators (fit tested and non fit tested), in health care workers (HCWs). [16] [17] [18] The aim of this study was to determine the efficacy of medical masks compared to fit-tested and non-fit-tested N95 respirators in HCWs in the prevention of disease because of influenza and other respiratory viruses. For all outcomes, non-fit-tested N95 respirators had lower rates of infections compared to fit-tested N95s (for all N95 versus medical masks, the rates were 3AE9% versus 6AE7% for CRI, 0AE3% versus 0AE6% for ILI, 1AE4% versus 2AE6% for laboratory-confirmed virus and 0AE3% versus 1% for influenza) but these differences were not significant.

title:
  A cluster randomized clinical trial comparing fit‐tested and non‐fit‐tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers

abstract:
  Please cite this paper as: MacIntyre et al. (2011) A cluster randomized clinical trial comparing fit‐tested and non‐fit‐tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750‐2659.2010.00198.x. Background We compared the efficacy of medical masks, N95 respirators (fit tested and non fit tested), in health care workers (HCWs). Methods A cluster randomized clinical trial (RCT) of 1441 HCWs in 15 Beijing hospitals was performed during the 2008/2009 winter. Participants wore masks or respirators during the entire work shift for 4 weeks. Outcomes included clinical respiratory illness (CRI), influenza‐like illness (ILI), laboratory‐confirmed respiratory virus infection and influenza. A convenience no‐mask/respirator group of 481 health workers from nine hospitals was compared. Findings The rates of CRI (3·9% versus 6·7%), ILI (0·3% versus 0·6%), laboratory‐confirmed respiratory virus (1·4% versus 2·6%) and influenza (0·3% versus 1%) infection were consistently lower for the N95 group compared to medical masks. By intention‐to‐treat analysis, when P values were adjusted for clustering, non‐fit‐tested N95 respirators were significantly more protective than medical masks against CRI, but no other outcomes were significant. The rates of all outcomes were higher in the convenience no‐mask group compared to the intervention arms. There was no significant difference in outcomes between the N95 arms with and without fit testing. Rates of fit test failure were low. In a post hoc analysis adjusted for potential confounders, N95 masks and hospital level were significant, but medical masks, vaccination, handwashing and high‐risk procedures were not. Interpretation Rates of infection in the medical mask group were double that in the N95 group. A benefit of respirators is suggested but would need to be confirmed by a larger trial, as this study may have been underpowered. The finding on fit testing is specific to the type of respirator used in the study and cannot be generalized to other respirators. Trial registration Australian New Zealand Clinical Trials Registry (ANZCTR), ACTRN: ACTRN12609000257268 (http://www.anzctr.org.au).


id: cord-273620-gn8g6suq
author: Szczawinska‐Poplonyk, Aleksandra
date: 2012-11-30
url: https://www.ncbi.nlm.nih.gov/pubmed/23199056/
doi: 10.1111/irv.12059
title:
  Fatal respiratory distress syndrome due to coronavirus infection in a child with severe combined immunodeficiency

abstract:
  Please cite this paper as: Szczawinska‐Poplonyk et al. (2012) Fatal respiratory distress syndrome due to coronavirus infection in a child with severe combined immunodeficiency. Influenza and Other Respiratory Viruses DOI: 10.1111/irv.12059. Coronaviruses have been demonstrated to contribute substantially to respiratory tract infections among the child population. Though infected children commonly present mild upper airway symptoms, in high‐risk patients with underlying conditions, particularly in immunocompromised children these pathogens may lead to severe lung infection and extrapulmonary disorders. In this paper, we provide the first report of the case of a 15‐month‐old child with severe combined immunodeficiency and coronavirus HKU1‐related pneumonia with fatal respiratory distress syndrome.


id: cord-273861-sg7esn4p
author: Yi, Lina
date: 2017-06-26
txt: ./txt/cord-273861-sg7esn4p.txt
cache: ./cache/cord-273861-sg7esn4p.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12457
doi: 10.1111/irv.12457
summary:
  title: A cluster of adenovirus type B55 infection in a neurosurgical inpatient department of a general hospital in Guangdong, China All staff and patients in the involved neurosurgical department were surveyed for any symptoms of fever (≥38°C) and enlarged tonsils during the outbreak period. On June 30, 2016, one local Center for Disease Control and Prevention of Guangdong was informed that several staff members, including nurses and doctors working in a general hospital, fell ill with symptoms of a fever and sore throat. This study identified a cluster of adenovirus type B55 infection in the neurosurgical inpatient department of a general hospital. Outbreak of acute respiratory disease in China caused by B2 species of adenovirus type 11 An outbreak of acute respiratory disease in China caused by human adenovirus type B55 in a physical training facility A cluster of adenovirus type B55 infection in a neurosurgical inpatient department of a general hospital in Guangdong, China.

title:
  A cluster of adenovirus type B55 infection in a neurosurgical inpatient department of a general hospital in Guangdong, China

abstract:
  BACKGROUND: Human adenovirus type 55 is a re‐emerging human respiratory pathogen that is associated with several respiratory infections outbreaks in military and school populations. In this study, we describe the first HAdV55‐associated hospital outbreak documented in Guangdong, China. METHODS: Active surveillance was conducted in the involved neurosurgical inpatient department. All staff and patients in the involved neurosurgical department were surveyed for any symptoms of fever (≥38°C) and enlarged tonsils during the outbreak period. Throat swabs and demographic information were collected for all cases. For each specimen, assays for common respiratory viruses were performed using one‐step reverse transcription‐polymerase chain reaction. HAdV‐positive samples were inoculated onto Hep‐2 cells for isolation. Hexon genes, fiber genes, penton genes, and whole genomes were sequenced. A phylogenetic tree was constructed. RESULTS AND CONCLUSIONS: Forty‐three cases, including 24 laboratory‐confirmed cases and 19 possible cases, were identified. Nurses had the highest attack rate of infection, with a rate of 36.4%. The attack rate for doctors and inpatients was 20.0% and 16.7%, respectively. HAdV55 was the sole pathogen identified during this outbreak. The hexon, fiber, and penton genes from seven isolated HAdV55 stains were sequenced. All these genes showed 100% homology and fell into the HAdV55 [P14H11F14] cluster, indicating that HAdV55 was the single viral strain for the outbreak. While not conclusive, the epidemic investigation revealed that the outbreak was introduced by nurses from sources outside the hospital. It was likely that a transmission from staff to inpatients had occurred.


id: cord-276363-m8di6dpt
author: Holm, Majbrit V.
date: 2008-06-28
url: https://doi.org/10.1111/j.1750-2659.2008.00036.x
doi: 10.1111/j.1750-2659.2008.00036.x
title:
  Influenza vaccination coverage rates in Europe – covering five consecutive seasons (2001–2006) in five countries

abstract:
  Objective To understand potential drivers and barriers to influenza vaccination in the general population. Methods 47 982 household surveys were conducted in five European countries between 2001 and 2006. Results Overall influenza vaccination coverage increased over the years and reached 26·2% in 2005/06. Among the elderly ≥65 years, the rate increased significantly to 67·8% (2005/06). The most common reason for being vaccinated over the 5 years was the perception of influenza as a serious illness, which people want to avoid. The main reason for not getting vaccinated among those never previously vaccinated was feeling that they were unlikely to catch influenza. A recommendation by the family physician was the most encouraging factor for vaccination.


id: cord-278554-rg92gcc6
author: Aoyagi, Yumiko
date: 2015-04-23
txt: ./txt/cord-278554-rg92gcc6.txt
cache: ./cache/cord-278554-rg92gcc6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25807865/
doi: 10.1111/irv.12310
summary:
  To estimate the proportion of healthcare workers (HCWs) willing to work during an influenza pandemic and identify associated risk factors, we undertook a systematic review and meta-analysis compliant with PRISMA guidance. Meta-analyses of specific factors showed that male HCWs, physicians and nurses, full-time employment, perceived personal safety, awareness of pandemic risk and clinical knowledge of influenza pandemics, role-specific knowledge, pandemic response training, and confidence in personal skills were statistically significantly associated with increased willingness. Data extraction was performed by a single researcher (YA) using a piloted form collecting details of study characteristics {title, author, publication year, place, study period, study design, participants, subject [pandemic of avian influenza origin/influenza A(H1N1)pdm09/non-specified, hypothetical influenza pandemic]}; definition of outcome measures; questionnaire type; validation; statistical analysis and any stated limitations; percentage of willingness to work; and risk factors association with willingness.

title:
  Healthcare workers'' willingness to work during an influenza pandemic: a systematic review and meta-analysis

abstract:
  To estimate the proportion of healthcare workers (HCWs) willing to work during an influenza pandemic and identify associated risk factors, we undertook a systematic review and meta-analysis compliant with PRISMA guidance. Databases and grey literature were searched to April 2013, and records were screened against protocol eligibility criteria. Data extraction and risk of bias assessments were undertaken using a piloted form. Random-effects meta-analyses estimated (i) pooled proportion of HCWs willing to work and (ii) pooled odds ratios of risk factors associated with willingness to work. Heterogeneity was quantified using the I(2) statistic, and publication bias was assessed using funnel plots and Egger's test. Data were synthesized narratively where meta-analyses were not possible. Forty-three studies met our inclusion criteria. Meta-analysis of the proportion of HCWs willing to work was abandoned due to excessive heterogeneity (I(2) = 99·2%). Narrative synthesis showed study estimates ranged from 23·1% to 95·8% willingness to work, depending on context. Meta-analyses of specific factors showed that male HCWs, physicians and nurses, full-time employment, perceived personal safety, awareness of pandemic risk and clinical knowledge of influenza pandemics, role-specific knowledge, pandemic response training, and confidence in personal skills were statistically significantly associated with increased willingness. Childcare obligations were significantly associated with decreased willingness. HCWs' willingness to work during an influenza pandemic was moderately high, albeit highly variable. Numerous risk factors showed a statistically significant association with willingness to work despite significant heterogeneity between studies. None of the included studies were based on appropriate theoretical constructs of population behaviour.


id: cord-279615-yne753y6
title: Influenza C infections in Western Australia and Victoria from 2008 to 2014
author: Jelley, Lauren
date: 2016-07-23
txt: ./txt/cord-279615-yne753y6.txt
cache: ./cache/cord-279615-yne753y6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27373693/
doi: 10.1111/irv.12402
summary:
  OBJECTIVES: This study aimed at analyzing the available influenza C clinical samples from two widely separated states of Australia, collected over a 7‐year period and to compare them with influenza C viruses detected in other parts of the world in recent years. RESULTS AND CONCLUSIONS: Detections of influenza C in respiratory samples were sporadic in most years studied, but higher rates of infection occurred in 2012 and 2014. This study analyzed influenza C viruses detected in respiratory samples collected from two influenza illness surveillance programs operating in the state of Western Australia (WA) from 2001 to 2014: one covering patients of all ages presenting to general practitioners with an influenza-like illness (ILI), and the other covering young children presenting with a respiratory illness to a metropolitan pediatric hospital emergency department or a general practitioner.

abstract:
  BACKGROUND: Influenza C is usually considered a minor cause of respiratory illness in humans with many infections being asymptomatic or clinically mild. Large outbreaks can occur periodically resulting in significant morbidity. OBJECTIVES: This study aimed at analyzing the available influenza C clinical samples from two widely separated states of Australia, collected over a 7‐year period and to compare them with influenza C viruses detected in other parts of the world in recent years. PATIENTS/METHODS: Between 2008 and 2014, 86 respiratory samples that were influenza C positive were collected from subjects with influenza‐like illness living in the states of Victoria and Western Australia. A battery of other respiratory viruses were also tested for in these influenza C‐positive samples. Virus isolation was attempted on all of these clinical samples, and gene sequencing was performed on all influenza C‐positive cultures. RESULTS AND CONCLUSIONS: Detections of influenza C in respiratory samples were sporadic in most years studied, but higher rates of infection occurred in 2012 and 2014. Many of the patients with influenza C had coinfections with other respiratory pathogens. Phylogenetic analysis of the full‐length hemagglutinin–esterase–fusion (HE) gene found that most of the viruses grouped in the C/Sao Paulo/378/82 clade with the remainder grouping in the C/Kanagawa/1/76 clade.


id: cord-279716-kxfc4npg
title: Bioaerosol sampling for the detection of aerosolized influenza virus
author: Blachere, Francoise M.
date: 2007-10-22
txt: ./txt/cord-279716-kxfc4npg.txt
cache: ./cache/cord-279716-kxfc4npg.txt
extension: .txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/19453416/
doi: 10.1111/j.1750-2659.2007.00020.x
summary:
  Background Influenza virus was used to characterize the efficacy of a cyclone‐based, two‐stage personal bioaerosol sampler for the collection and size fractionation of aerosolized viral particles. Results Based on qPCR results, we demonstrate that aerosolized viral particles were efficiently collected and separated according to aerodynamic size using the two‐stage bioaerosol sampler. In order to quantify the relative amount of viral particles or fungal spores collected at each stage of the bioaerosol sampler, qPCR was performed in parallel using either serial 10-fold dilutions of cDNA generated from a single dose of non-aerosolized FluMist Ò containing approximately 10 7 TCID 50 per influenza strain or genomic DNA isolated from 10 7 spores. In this study, by aerosolizing FluMist Ò , we demonstrate the recovery of aerosolized viral particles using the bioaerosol sampler and detection of influenza by qPCR.

abstract:
  Background Influenza virus was used to characterize the efficacy of a cyclone‐based, two‐stage personal bioaerosol sampler for the collection and size fractionation of aerosolized viral particles. Methods A Collison single‐jet nebulizer was used to aerosolize the attenuated FluMist® vaccine into a calm‐air settling chamber. Viral particles were captured with bioaerosol samplers that utilize 2 microcentrifuge tubes to collect airborne particulates. The first tube (T1) collects particles greater than 1.8 μm in diameter, while the second tube (T2) collects particles between 1.0 and 1.8 μm, and the back‐up filter (F) collects submicron particles. Following aerosolization, quantitative PCR was used to detect and quantify H1N1 and H3N2 influenza strains. Results Based on qPCR results, we demonstrate that aerosolized viral particles were efficiently collected and separated according to aerodynamic size using the two‐stage bioaerosol sampler. Most viral particles were collected in T2 (1‐1.8 μm) and on the back‐up filter (< 1 μm) of the bioaerosol sampler. Furthermore, we found that the detection of viral particles with the two‐stage sampler was directly proportional to the collection time. Consequently, viral particle counts were significantly greater at 40 minutes in comparison to 5, 10 and 20 minute aerosol collection points. Conclusions Due to a lack of empirical data, aerosol transmission of influenza is often questioned. Using FluMist®, we demonstrated that a newly developed bioaerosol sampler is able to recover and size fractionate aerosolized viral particles. This sampler should be an important tool for studying viral transmission in clinical settings and may significantly contribute towards understanding the modes of influenza virus transmission.


id: cord-285425-3v1bid02
title: The efficacy of medical masks and respirators against respiratory infection in healthcare workers
author: MacIntyre, Chandini Raina
date: 2017-08-30
txt: ./txt/cord-285425-3v1bid02.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12474
doi: 10.1111/irv.12474
summary:
  OBJECTIVE: We aimed to examine the efficacy of medical masks and respirators in protecting against respiratory infections using pooled data from two homogenous randomised control clinical trials (RCTs). There is currently a lack of consensus around the efficacy of medical masks and respirators for healthcare workers (HCWs) against influenza, with only five published randomised control trials (RCTs) in HCWs conducted to date. 3, 4 Finally, a recent study examined the efficacy of cloth masks compared to medical mask and control groups, and found that cloth masks may increase the risk of infection in HCWs. 5 Guidelines for respiratory protection have been driven by presumed transmission mode alone, and under an assumption that influenza and other pathogens are spread by one mode alone. A cluster randomized clinical trial comparing fit-tested and non-fit-tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers.

abstract:
  OBJECTIVE: We aimed to examine the efficacy of medical masks and respirators in protecting against respiratory infections using pooled data from two homogenous randomised control clinical trials (RCTs). METHODS: The data collected on 3591 subjects in two similar RCTs conducted in Beijing, China, which examined the same infection outcomes, were pooled. Four interventions were compared: (i) continuous N95 respirator use, (ii) targeted N95 respirator use, (iii) medical mask use and (iv) control arm. The outcomes were laboratory‐confirmed viral respiratory infection, influenza A or B, laboratory‐confirmed bacterial colonisation and pathogens grouped by mode of transmission. RESULTS: Rates of all outcomes were consistently lower in the continuous N95 and/or targeted N95 arms. In adjusted analysis, rates of laboratory‐confirmed bacterial colonisation (RR 0.33, 95% CI 0.21‐0.51), laboratory‐confirmed viral infections (RR 0.46, 95% CI 0.23‐0.91) and droplet‐transmitted infections (RR 0.26, 95% CI 0.16‐0.42) were significantly lower in the continuous N95 arm. Laboratory‐confirmed influenza was also lowest in the continuous N95 arm (RR 0.34, 95% CI 0.10‐1.11), but the difference was not statistically significant. Rates of laboratory‐confirmed bacterial colonisation (RR 0.54, 95% CI 0.33‐0.87) and droplet‐transmitted infections (RR 0.43, 95% CI 0.25‐0.72) were also lower in the targeted N95 arm, but not in medical mask arm. CONCLUSION: The results suggest that the classification of infections into droplet versus airborne transmission is an oversimplification. Most guidelines recommend masks for infections spread by droplets. N95 respirators, as “airborne precautions,” provide superior protection for droplet‐transmitted infections. To ensure the occupational health and safety of healthcare worker, the superiority of respirators in preventing respiratory infections should be reflected in infection control guidelines.


id: cord-286096-h275nner
title: Viral and bacterial aetiology of community‐acquired pneumonia in adults
author: Huijskens, Elisabeth G. W.
date: 2012-08-22
txt: ./txt/cord-286096-h275nner.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1111/j.1750-2659.2012.00425.x
doi: 10.1111/j.1750-2659.2012.00425.x
summary:
  Methods Between April 2008 and April 2009, 408 adult patients (aged between 20 and 94 years) with community‐acquired pneumonia were tested for the presence of respiratory pathogens using bacterial cultures, real‐time PCR for viruses and bacteria, urinary antigen testing for Legionella and Pneumococci and serology for the presence of viral and bacterial pathogens. All samples were tested using real-time PCR for the presence of respiratory viruses and bacteria including adenovirus (AdV), human bocavirus (hBoV), KI-and WU polyomaviruses (KIPyV and WUPyV), human metapneumovirus (hMPV), human rhinovirus (HRV), human coronaviruses (HCoV) (OC43, NL63, HKU and 229E), parainfluenza viruses (PIV), 1-4 influenza viruses A and B (InfA, InfB), respiratory syncytial virus (RSV), Legionella pneumophila, Mycoplasma pneumoniae, Chlamydophila psittaci, Chlamydophila pneumoniae, Coxiella burnetii and Streptococcus pneumoniae. This study revealed the viral and bacterial aetiology in 263 (64AE5%) of 408 patients with community-acquired pneumonia.

abstract:
  Please cite this paper as: Huijskens et al. (2012) Viral and bacterial aetiology of community‐acquired pneumonia in adults. Influenza and Other Respiratory Viruses 7(4), 567–573. Background Modern molecular techniques reveal new information on the role of respiratory viruses in community‐acquired pneumonia. In this study, we tried to determine the prevalence of respiratory viruses and bacteria in patients with community‐acquired pneumonia who were admitted to the hospital. Methods Between April 2008 and April 2009, 408 adult patients (aged between 20 and 94 years) with community‐acquired pneumonia were tested for the presence of respiratory pathogens using bacterial cultures, real‐time PCR for viruses and bacteria, urinary antigen testing for Legionella and Pneumococci and serology for the presence of viral and bacterial pathogens. Results Pathogens were identified in 263 (64·5%) of the 408 patients. The most common single organisms in these 263 patients were Streptococcus pneumoniae (22·8%), Coxiella burnetii (6·8%) and influenza A virus (3·8%). Of the 263 patients detected with pathogens, 117 (44·5%) patients were positive for one or more viral pathogens. Of these 117 patients, 52 (44·4%) had no bacterial pathogen. Multiple virus infections (≥2) were found in 16 patients. Conclusion In conclusion, respiratory viruses are frequently found in patients with CAP and may therefore play an important role in the aetiology of this disease.


id: cord-289358-4abypk6o
title: Clinical severity of rhinovirus/enterovirus compared to other respiratory viruses in children
author: Asner, Sandra A.
date: 2014-05-07
txt: ./txt/cord-289358-4abypk6o.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12255
doi: 10.1111/irv.12255
summary:
  Children with single HRV/ENT infections presented with significantly higher rates of underlying immunosuppressive conditions compared to those with RSV (37·9% versus 13·6%; P < 0·001), FLU (37·9% versus 22%; P = 0·018) or any other single viral infection (37·9% versus 22·5%; P = 0·024). Human rhinovirus/enterovirus (HRV/ENT) has been recently identified as the leading pathogen in acute asthma exacerbations, bronchiolitis, and viral pneumonia, although the clinical severity of respiratory illnesses attributed to HRV/ENT remains uncertain. The objective of this study was to compare the clinical characteristics and the severity of illness of HRV-/ENT-positive children to those positive for RSV A/B, FLU-A/ FLU-B, and other respiratory viruses by (i) using a large dataset with a broad pediatric inpatient and outpatient population; (ii) considering several clinical endpoints to assess disease severity, and (iii) conducting multivariable analysis to adjust for potential confounding variables.

abstract:
  BACKGROUND: Human rhinovirus/enterovirus (HRV/ENT) infections are commonly identified in children with acute respiratory infections (ARIs), but data on their clinical severity remain limited. OBJECTIVES: We compared the clinical severity of HRV/ENT to respiratory syncytial virus (RSV), influenza A/B (FLU), and other common respiratory viruses in children. PATIENTS/METHODS: Retrospective study of children with ARIs and confirmed single positive viral infections on mid‐turbinate swabs by molecular assays. Outcome measures included hospital admission and, for inpatients, a composite endpoint consisting of intensive care admission, hospitalization >5 days, oxygen requirements or death. RESULTS: A total of 116 HRV/ENT, 102 RSV, 99 FLU, and 64 other common respiratory viruses were identified. Children with single HRV/ENT infections presented with significantly higher rates of underlying immunosuppressive conditions compared to those with RSV (37·9% versus 13·6%; P < 0·001), FLU (37·9% versus 22%; P = 0·018) or any other single viral infection (37·9% versus 22·5%; P = 0·024). In multivariable analysis adjusted for underlying conditions and age, children with HRV/ENT infections had increased odds of hospitalization compared to children with RSV infections (OR 2·6; 95% CI 1·4, 4·8; P < 0·003) or FLU infections (OR 3·0; 95% CI 1·6, 5·8; <0·001) and increased odds of severe clinical disease among inpatients (OR 3·0; 95% CI 1·6,5·6; P = 0·001) when compared to those with FLU infections. CONCLUSIONS: Children with HRV/ENT had a more severe clinical course than those with RSV and FLUA/B infections and often had significant comorbidities. These findings emphasize the importance of considering HRV/ENT infection in children presenting with severe acute respiratory tract infections.


id: cord-292946-iggv9f0k
title: Influenza C virus–associated community‐acquired pneumonia in children
author: Principi, Nicola
date: 2012-12-07
txt: ./txt/cord-292946-iggv9f0k.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23594251/
doi: 10.1111/irv.12062
summary:
  Despite its widespread circulation, influenza C virus (ICV) is traditionally considered a scarcely virulent infectious agent because, unlike influenza A (IAV) and B viruses (IBV), it is thought to be associated with infections that, when symptomatic, are mild and mainly involve the upper respiratory tract. [1] [2] [3] However, the frequency and clinical picture of ICVassociated pediatric community-acquired pneumonia (CAP) have not been defined, nor which virus lineages more frequently cause the disease. This prospective study was designed to evaluate the incidence and clinical relevance of ICV infection in children with radiographically confirmed CAP aged <15 years. Similarities in the clinical pictures of diseases due to IAV and ICV have been found by other authors in studies evaluating the global clinical features of influenza virus disease. Impact of viral infections in children with community-acquired pneumonia: results of a study of 17 respiratory viruses.

abstract:
  To evaluate the impact of influenza C (ICV) infection in children with community‐acquired pneumonia (CAP), all of the children consecutively seen during 4 influenza seasons with respiratory symptoms and radiographically confirmed CAP were prospectively evaluated. ICV was identified in the respiratory secretions of five of 391 patients (1·3%). In children with ICV‐associated CAP, clinical data were similar to those observed in children with IAV‐associated CAP and worse than those observed in children with IBV‐associated. The phylogenetic tree showed that the sequenced strains clustered in two of the six ICV lineages. These findings highlight that ICV can be a cause of CAP of children and that this can be severe enough to require hospitalization.


id: cord-293354-55nawxos
author: Kenmoe, Sebastien
date: 2016-05-09
url: https://www.ncbi.nlm.nih.gov/pubmed/27012372/
doi: 10.1111/irv.12391
title:
  Viral etiology of severe acute respiratory infections in hospitalized children in Cameroon, 2011–2013

abstract:
  BACKGROUND: Severe acute respiratory illness (SARI) is recognized as an important cause of morbidity, mortality, and hospitalization among children in developing countries. Little is known, however, in tropical countries like Cameroon about the cause and seasonality of respiratory infections, especially in hospitalized settings. Objectives: Our study investigates the viral etiology and seasonality of SARI in hospitalized children in Yaounde, Cameroon. METHODS: Prospective clinic surveillance was conducted to identify hospitalized children aged ≤15 years presenting with respiratory symptoms ≤5‐day duration. Demographic and clinical data, and respiratory specimens were collected. Nasopharyngeal samples were tested for 17 respiratory viruses using a multiplex polymerase chain reaction. The viral distribution and demographic data were statistically analyzed. RESULTS: From September 2011 through September 2013, 347 children aged ≤15 years were enrolled. At least one virus was identified in each of 65·4% children, of which 29·5% were coinfections; 27·3% were positive for human adenovirus (hAdV), 13·2% for human respiratory syncytial virus (hRSV), 11·5% for rhinovirus/enterovirus (RV/EV), 10·6% for human bocavirus (hBoV), 9·8% for influenza virus (Inf), 6·6% for human parainfluenza virus (hPIV), 5·7% for human coronavirus (hCoV), and 2·3% for human metapneumovirus (hMPV). While hRSV showed seasonal patterns, hAdV and RV/EV were detected throughout the year and no evident temporal patterns were observed for the remaining viruses. CONCLUSION: Respiratory viruses were associated with a high burden of hospitalizations among children in Cameroon. Nevertheless, additional studies evaluating asymptomatic Cameroonian children will be important in understanding the relationship between viral carriage and disease.


id: cord-297609-6g39lu1y
author: Wertheim, Heiman F L
date: 2015-10-13
txt: ./txt/cord-297609-6g39lu1y.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12326
doi: 10.1111/irv.12326
summary:
  title: Viral and atypical bacterial aetiologies of infection in hospitalised patients admitted with clinical suspicion of influenza in Thailand, Vietnam and Indonesia METHODS: Respiratory specimens archived from July 2008 to June 2009 from patients hospitalised with suspected influenza from Indonesia, Thailand and Vietnam were tested for respiratory viruses and atypical bacteria by polymerase chain reaction. Data on the epidemiology and disease burden of influenza-related disease in South-East Asia (SEA) are emerging, and this, in turn, is shedding more light on the epidemiology of other viral and bacterial aetiologies of influenza-like illnesses (ILIs) in hospitalised adults and children in this region. The detection of influenza viruses and respiratory pathogens other than influenza viruses in specimens that were sent for routine influenza testing can provide valuable insights into the epidemiology of ILI across all age groups in three SEA countries over the same time period. 21 In this 1-year study, we used molecular techniques to detect viruses and atypical bacteria from samples collected from patients hospitalised with ILI.

title:
  Viral and atypical bacterial aetiologies of infection in hospitalised patients admitted with clinical suspicion of influenza in Thailand, Vietnam and Indonesia

abstract:
  BACKGROUND: Influenza constitutes a leading cause of morbidity and mortality worldwide. There is limited information about the aetiology of infection presenting clinically as influenza in hospitalised adults and children in South-East Asia. Such data are important for future management of respiratory infections. OBJECTIVES: To describe the aetiology of infection presenting clinically as influenza in those hospitalised in South-East Asia. METHODS: Respiratory specimens archived from July 2008 to June 2009 from patients hospitalised with suspected influenza from Indonesia, Thailand and Vietnam were tested for respiratory viruses and atypical bacteria by polymerase chain reaction. RESULTS: A total of 1222 patients’ samples were tested. Of 1222, 776 patients (63·5%) were under the age of 5. Viruses detected included rhinoviruses in 229 of 1222 patients (18·7%), bocaviruses in 200 (16·4%), respiratory syncytial viruses in 144 (11·8%), parainfluenza viruses in 140 (11·5%; PIV1: 32; PIV2: 12; PIV3: 71; PIV4: 25), adenovirus in 102 (8·4%), influenza viruses in 93 (7·6%; influenza A: 77; influenza B: 16) and coronaviruses in 23 (1·8%; OC43: 14; E229: 9). Bacterial pathogens were Mycoplasma pneumoniae (n = 33, 2·7%), Chlamydophila psittaci (n = 2), C. pneumoniae (n = 1), Bordetella pertussis (n = 1) and Legionella pneumophila (n = 2). Overall, in-hospital case fatality rate was 29 of 1222 (2·4%). CONCLUSION: Respiratory viruses were the most commonly detected pathogens in patients hospitalised with a clinical suspicion of influenza. Rhinovirus was the most frequently detected virus, and M. pneumoniae, the most common atypical bacterium. The low number of detected influenza viruses demonstrates a low benefit for empirical oseltamivir therapy, unless during an influenza outbreak.


id: cord-299790-vciposnk
author: Ho, Zheng Jie Marc
date: 2015-06-09
txt: ./txt/cord-299790-vciposnk.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25827870/
doi: 10.1111/irv.12312
summary:
  Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. For instance, one study showed that 15.3% of ambulatory patients with influenza-like illness had two viruses detected, 6 and another found that in 28.2% of children with community-acquired pneumonia, the illness was due to mixed viral-bacterial infections. 7 Others also previously described respiratory viral 8, 9 and bacterial co-infections 10, 11 in various settings, although most focus on specific pathogen combinations, especially of the synergism between influenza and Streptococcus pneumoniae (S. Mean proportion for dual infections with nasal symptoms lay in between at 0.748, statistically different from both viral (P = 0.002) and bacterial (P < 0.001) mono-pathogen levels.

title:
  Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness

abstract:
  BACKGROUND: Although it is known that febrile respiratory illnesses (FRI) may be caused by multiple respiratory pathogens, there are no population-level studies describing its impact on clinical disease. METHODS: Between May 2009 and October 2012, 7733 FRI patients and controls in the Singapore military had clinical data and nasal wash samples collected prospectively and sent for PCR testing. Patients with one pathogen detected (mono-pathogen) were compared with those with two pathogens (dual pathogen) for differences in basic demographics and clinical presentation. RESULTS: In total, 45.8% had one pathogen detected, 20.2% had two pathogens detected, 30.9% had no pathogens detected, and 3.1% had more than two pathogens. Multiple pathogens were associated with recruits, those with asthma and non-smokers. Influenza A (80.0%), influenza B (73.0%) and mycoplasma (70.6%) were most commonly associated with mono-infections, while adenovirus was most commonly associated with dual infections (62.9%). Influenza A paired with S. pneumoniae had higher proportions of chills and rigors than their respective mono-pathogens (P = 0.03, P = 0.009). H. influenzae paired with either enterovirus or parainfluenzae had higher proportions of cough with phlegm than their respective mono-pathogens. Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. CONCLUSION: A substantial number of FRI patients have multiple pathogens detected. Observed clinical differences between patients of dual pathogen and mono-pathogen indicate the likely presence of complex microbial interactions between the various pathogens.


id: cord-304473-6aivjett
author: Tenforde, Mark W.
date: 2020-08-04
txt: ./txt/cord-304473-6aivjett.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32755020/
doi: 10.1111/irv.12792
abstract: nan
summary:
  authors: Tenforde, Mark W.; Feldstein, Leora R.; Lindsell, Christopher J.; Patel, Manish M.; Self, Wesley H. In this cross-sectional survey, we generated insights into individual-level exposures and behaviors among non-hospitalized adults with COVID-19 in Tennessee in the early days following national social distancing guidelines. Transmission of SARS-CoV-2 is likely facilitated through a pre-symptomatic or pauci-symptomatic shedding period in infected individuals, 2,3 which, along with limited early testing, could in part explain this common lack of a known case contact and highlights the need for robust testing infrastructure. However, a sizeable majority reported working regularly in the two weeks before illness with few able to telework, suggesting workplace-related exposures were an important early source of transmission in Tennessee. Conceptualization (equal); Formal analysis (lead) Leora R Feldstein: Conceptualization (equal); Formal analysis (supporting) Manish M Patel: Conceptualization (equal) Self WH; for the IVY Network Investigators, CDC COVID-19 Response Team. Exposures in adult outpatients with COVID-19 infection during early community transmission

title:
  Exposures in adult outpatients with COVID‐19 infection during early community transmission, Tennessee


id: cord-304569-o39kl5k4
title: From the Editor''s desk
author: Nguyen-Van-Tam, Jonathan S
date: 2015-04-23
txt: ./txt/cord-304569-o39kl5k4.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25824028/
doi: 10.1111/irv.12311
abstract: nan
summary:
  If one shifts the focus away from influenza, the ongoing MERS-CoV outbreak in the Middle East, is also of substantial concern, because despite its likely introduction into humans via close contact with dromedary camels, 9 nosocomial transmission appears to be a central concern, 10,11 case-fatality is high, household transmission is also described, 12 and there are currently no vaccines or specific therapies available. Papers considered for rapid peer-review will need to be of immediate relevance, interest, or importance to scientists, clinicians, public health practitioners or policy makers, usually in relation to a current or evolving event related to respiratory virus activity. Accepted Articles are published online a few days after final acceptance, appear in PDF format only, are given a Digital Object Identifier (DOI), which allows them to be cited and tracked, and are indexed by PubMed. Effectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with influenza A H1N1pdm09 virus infection: a meta-analysis of individual participant data


id: cord-306923-eujbxdqi
author: Ahmed, Anwar E.
date: 2018-04-25
txt: ./txt/cord-306923-eujbxdqi.txt
cache: ./cache/cord-306923-eujbxdqi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29624866/
doi: 10.1111/irv.12560
summary:
  Data on the time intervals between a patient''s presentation or admission to a healthcare facility and the first specimen sample have been limited in patients suspected and screened for MERS-CoV by a real-time reverse-transcription polymerase chain reaction (rRT-PCR) test, as it might correlate with recovery delay intervals. This chart review study was based on information from multicenters and a large sample size, and it provides valuable information on factors associated with prolonged or shorter recovery delay of patients suspected and screened for MERS-CoV by the rRT-PCR test. The study evidence supports that longer recovery delay was seen in patients with older age, MERS-CoV infection, ICU admission, and abnormal radiology findings in a sample of patients diagnosed by rRT-PCR. Factors associated with recovery delay in a sample of patients diagnosed by MERS-CoV rRT-PCR: A Saudi Arabian multicenter retrospective study

title:
  Factors associated with recovery delay in a sample of patients diagnosed by MERS‐CoV rRT‐PCR: A Saudi Arabian multicenter retrospective study

abstract:
  BACKGROUND: Research evidence exists that poor prognosis is common in Middle East respiratory syndrome coronavirus (MERS‐CoV) patients. OBJECTIVES: This study estimates recovery delay intervals and identifies associated factors in a sample of Saudi Arabian patients admitted for suspected MERS‐CoV and diagnosed by rRT‐PCR assay. METHODS: A multicenter retrospective study was conducted on 829 patients admitted between September 2012 and June 2016 and diagnosed by rRT‐PCR procedures to have MERS‐CoV and non‐MERS‐CoV infection in which 396 achieved recovery. Detailed medical charts were reviewed for each patient who achieved recovery. Time intervals in days were calculated from presentation to the initial rRT‐PCR diagnosis (diagnosis delay) and from the initial rRT‐PCR diagnosis to recovery (recovery delay). RESULTS: The median recovery delay in our sample was 5 days. According to the multivariate negative binomial model, elderly (age ≥ 65), MERS‐CoV infection, ICU admission, and abnormal radiology findings were associated with longer recovery delay (adjusted relative risk (aRR): 1.741, 2.138, 2.048, and 1.473, respectively). Camel contact and the presence of respiratory symptoms at presentation were associated with a shorter recovery delay (expedited recovery) (aRR: 0.267 and 0.537, respectively). Diagnosis delay is a positive predictor for recovery delay (r = .421; P = .001). CONCLUSIONS: The study evidence supports that longer recovery delay was seen in patients of older age, MERS‐CoV infection, ICU admission, and abnormal radiology findings. Shorter recovery delay was found in patients who had camel contact and respiratory symptoms at presentation. These findings may help us understand clinical decision making on directing hospital resources toward prompt screening, monitoring, and implementing clinical recovery and treatment strategies.


id: cord-307338-4nta9b6w
author: Slomka, Marek J.
date: 2010-08-17
txt: ./txt/cord-307338-4nta9b6w.txt
cache: ./cache/cord-307338-4nta9b6w.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20716157/
doi: 10.1111/j.1750-2659.2010.00149.x
summary:
  Fifteen of these specimens (six swabs and nine tissues) were shown to be Avian influenza viruses, with highly pathogenic (HP) H5 and H7 isolates indicated positive for H1N1v by non-RRT PCR approaches (Table 3) , i.e. amplification of RNA extracted from the clinical specimen by conventional RT PCR using primers that had been designed specifically for the HA gene of current H1N1v isolates, available at: http://www.who.int/csr/resources/publications/swineflu/GenomePrimers_20090512.pdf Amplicons were electrophoresed in 2% agarose and stained with RedSafeÔ (iNtRON Biotechnology, Kyungki-Do, Korea) for visualisation, excised and purified from agarose using the QIAquick Ò Gel Extraction Kit (Qiagen, Crawley, UK). These test results with archived tissue specimens obtained from the field reinforced the observation that the ''''perfect match'''' M gene RRT PCR is the most sensitive for detecting contemporary European and UK SIVs. All 31 archived UK tissue samples from SIV-positive pigs were negative by the ''''H1-118'''' RRT PCR assay (Table 2) .

title:
  Original Article: Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs

abstract:
  Please cite this paper as: Slomka et al. (2010) Real time reverse transcription (RRT)‐polymerase chain reaction (PCR) methods for detection of pandemic (H1N1) 2009 influenza virus and European swine influenza A virus infections in pigs. Influenza and Other Respiratory Viruses 4(5), 277–293. Background There is a requirement to detect and differentiate pandemic (H1N1) 2009 (H1N1v) and established swine influenza A viruses (SIVs) by real time reverse transcription (RRT) PCR methods. Objectives First, modify an existing matrix (M) gene RRT PCR for sensitive generic detection of H1N1v and other European SIVs. Second, design an H1 RRT PCR to specifically detect H1N1v infections. Methods RRT PCR assays were used to test laboratory isolates of SIV (n = 51; 37 European and 14 North American), H1N1v (n = 5) and avian influenza virus (AIV; n = 43). Diagnostic sensitivity and specificity were calculated for swabs (n = 133) and tissues (n = 116) collected from field cases and pigs infected experimentally with SIVs and H1N1v. Results The “perfect match” M gene RRT PCR was the most sensitive variant of this test for detection of established European SIVs and H1N1v. H1 RRT PCR specifically detected H1N1v but not European SIVs. Validation with clinical specimens included comparison with virus isolation (VI) as a “gold standard”, while field infection with H1N1v in swine was independently confirmed by sequencing H1N1v amplified by conventional RT PCR. “Perfect match” M gene RRT PCR had 100% sensitivity and 95·2% specificity for swabs, 93·6% and 98·6% for tissues. H1 RRT PCR demonstrated sensitivity and specificity of 100% and 99·1%, respectively, for the swabs, and 100% and 100% for the tissues. Conclusions Two RRT PCRs for the purposes of (i) generic detection of SIV and H1N1v infection in European pigs, and for (ii) specific detection of H1N1v (pandemic influenza) infection were validated.


id: cord-309497-3v0asfa7
author: Asner, Sandra
date: 2012-02-21
txt: ./txt/cord-309497-3v0asfa7.txt
cache: ./cache/cord-309497-3v0asfa7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/22353417/
doi: 10.1111/j.1750-2659.2012.00336.x
summary:
  ENT/HRV was frequently identified in LTCF outbreaks involving elderly residents, whereas in CSDs, A(H1N1)pdm09 was primarily detected. 1 Recent data reported by Public Health Ontario (PHO) indicated that pandemic influenza A (H1N1) 2009 [A(H1N1)pdm09] was a rare cause of LTCF respiratory outbreaks during the first period of wave I (April 20-June 12, 2009) of the 2009 pandemic. 3 We used surveillance data from the late stage of the first wave and the duration of the second wave periods (June 11-November 30, 2009) to ascertain the impact of A(H1N1)pdm09 and other respiratory viruses on different outbreak settings such as LTCFs and schools. We investigated all respiratory outbreaks in LTCFs and camps, schools, day cares (CSDs) tested at PHO laboratories from June 11 through November 30, 2009, in Ontario, Canada. 10, 11 From June 11 to November 30, 2009, we found that ENT ⁄ HRV was frequently identified in LTCF outbreaks involving elderly residents, whereas in outbreak settings involving children and younger adults, A(H1N1)pdm09 was primarily detected.

title:
  Respiratory viral infections in institutions from late stage of the first and second waves of pandemic influenza A (H1N1) 2009, Ontario, Canada

abstract:
  Please cite this paper as: Asner et al. (2012) Respiratory viral infections in institutions from late stage of the first and second waves of pandemic A (H1N1) 2009, Ontario, Canada. Influenza and Other Respiratory Viruses 6(3), e11–e15. We report the impact of respiratory viruses on various outbreak settings by using surveillance data from the late first and second wave periods of the 2009 pandemic. A total of 278/345(78·5%) outbreaks tested positive for at least one respiratory virus by multiplex PCR. We detected A(H1N1)pdm09 in 20·6% of all reported outbreaks of which 54·9% were reported by camps, schools, and day cares (CSDs) and 29·6% by long‐term care facilities (LCFTs), whereas enterovirus/human rhinovirus (ENT/HRV) accounted for 62% outbreaks of which 83·7% were reported by long‐term care facilities (LCTFs). ENT/HRV was frequently identified in LTCF outbreaks involving elderly residents, whereas in CSDs, A(H1N1)pdm09 was primarily detected.


id: cord-309518-seonrtn3
title: Noninvasive ventilation in critically ill patients with the Middle East respiratory syndrome
author: Alraddadi, Basem M.
date: 2019-03-18
txt: ./txt/cord-309518-seonrtn3.txt
cache: ./cache/cord-309518-seonrtn3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30884185/
doi: 10.1111/irv.12635
summary:
  BACKGROUND: Noninvasive ventilation (NIV) has been used in patients with the Middle East respiratory syndrome (MERS) with acute hypoxemic respiratory failure, but the effectiveness of this approach has not been studied. [9] [10] [11] [12] While NIV may initially avoid the need for intubation and invasive mechanical ventilation (MV) , several studies have reported high failure rates and the need for invasive ventilation among patients with severe acute respiratory distress syndrome (ARDS) and an association with increased mortality. 12 In a recent analysis from the LUNG SAFE study on unselected patients with ARDS, NIV was associated with higher intensive care unit (ICU) mortality in patients with the ratio of partial pressure of oxygen to the fraction of inspired oxygen (PaO 2 /FiO 2 ) lower than 150 mm Hg. 12 The role of NIV in AHRF secondary to viral respiratory infections is unclear.

abstract:
  BACKGROUND: Noninvasive ventilation (NIV) has been used in patients with the Middle East respiratory syndrome (MERS) with acute hypoxemic respiratory failure, but the effectiveness of this approach has not been studied. METHODS: Patients with MERS from 14 Saudi Arabian centers were included in this analysis. Patients who were initially managed with NIV were compared to patients who were managed only with invasive mechanical ventilation (invasive MV). RESULTS: Of 302 MERS critically ill patients, NIV was used initially in 105 (35%) patients, whereas 197 (65%) patients were only managed with invasive MV. Patients who were managed with NIV initially had lower baseline SOFA score and less extensive infiltrates on chest radiograph compared with patients managed with invasive MV. The vast majority (92.4%) of patients who were managed initially with NIV required intubation and invasive mechanical ventilation, and were more likely to require inhaled nitric oxide compared to those who were managed initially with invasive MV. ICU and hospital length of stay were similar between NIV patients and invasive MV patients. The use of NIV was not independently associated with 90‐day mortality (propensity score‐adjusted odds ratio 0.61, 95% CI [0.23, 1.60] P = 0.27). CONCLUSIONS: In patients with MERS and acute hypoxemic respiratory failure, NIV failure was very high. The use of NIV was not associated with improved outcomes.


id: cord-310956-qwe4ndvb
author: Qian, Yan‐Hua
date: 2011-04-18
txt: ./txt/cord-310956-qwe4ndvb.txt
cache: ./cache/cord-310956-qwe4ndvb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21668678/
doi: 10.1111/j.1750-2659.2011.00248.x
summary:
  Background To collect disease information and provide data for early detection of epidemics, two surveillance systems were established for influenza‐like illness (ILI) and unexplained pneumonia (UP) in Wuxi, People''s Republic of China. When the surveillance data of 2009 were fitted in the two detection models, alarms were produced on the occurrence of the first local case of influenza A (H1N1), outbreaks in schools and in general populations. Conclusions The results indicated the potential for using ILI and UP surveillance data as syndromic indicators to detect and provide an early warning for influenza epidemics. Two surveillance systems were established in Wuxi for influenza-like illness (ILI) and unexplained pneumonia (UP) after the severe acute respiratory syndrome (SARS) outbreak. To further evaluate the effectiveness of these surveillance systems in early warning of influenza epidemics, we monitored ILI data between 2004 and 2008 by both a control chart method and the Serfling method and tested goodness of fit using influenza A (H1N1) data of 2009.

title:
  Attempted early detection of influenza A (H1N1) pandemic with surveillance data of influenza‐like illness and unexplained pneumonia

abstract:
  Please cite this paper as: Qian et al. (2011) Attempted early detection of influenza A (H1N1) pandemic with surveillance data of influenza‐like illness and unexplained pneumonia. Influenza and Other Respiratory Viruses 5(6), e479–e486. Background To collect disease information and provide data for early detection of epidemics, two surveillance systems were established for influenza‐like illness (ILI) and unexplained pneumonia (UP) in Wuxi, People’s Republic of China. Objectives The current study aims to describe the performance of these surveillance systems during 2004–2009 and to evaluate the value of surveillance data in detection of influenza epidemics. Methods Two national ILI sentinel hospitals and three UP sentinel hospitals provided data to the surveillance systems. The surveillance data from hospital‐based outpatient clinics and emergency rooms were compared by year. The ILI data of 2009 were further modeled based on previous data using both a control chart method and a moving average regression method. Alarms of potential epidemics would be raised when the input surveillance data surpassed a threshold. Results In 2009, the proportions of ILI and respiratory illness with fever (one surveillance syndrome of the UP system) to total patient visits (3·40% and 11·76%, respectively) were higher than the previous years. The surveillance data of both systems also showed developing trends similar to the influenza A (H1N1) pandemic in 2009. When the surveillance data of 2009 were fitted in the two detection models, alarms were produced on the occurrence of the first local case of influenza A (H1N1), outbreaks in schools and in general populations. Conclusions The results indicated the potential for using ILI and UP surveillance data as syndromic indicators to detect and provide an early warning for influenza epidemics.


id: cord-311884-3lkkpg9g
title: Recent influenza activity in tropical Puerto Rico has become synchronized with mainland US
author: Paz–Bailey, Gabriela
date: 2020-07-02
txt: ./txt/cord-311884-3lkkpg9g.txt
cache: ./cache/cord-311884-3lkkpg9g.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32614504/
doi: 10.1111/irv.12744
summary:
  We compared influenza A and B infections identified from SEDSS and WHO/NREVSS laboratories reported by US Department of Health and Human Services (HHS) region using time series decomposition methods, and analysed coherence of climate and influenza trends by region. We compared the number of confirmed influenza A and B cases in SEDSS to virologic surveillance data collected by US WHO and To explore if differences in seasonality between Puerto Rico and HHS regions were due to differences in climate, we obtained regional climate data (absolute humidity, temperature and precipitation) from 2012 to 2018 from the North American Regional Reanalysis data set from the National Oceanic and Atmospheric Administration (NOAA). In terms of the overall time series climatic trends, Puerto Rico was consistently warmer and more humid over the time series compared with weekly average absolute humidity and temperature in HHS regions (Figure 2A 19, 20 and epidemiological studies showed lower humidity is associated with the onset of influenza epidemics in the United

abstract:
  BACKGROUND: We used data from the Sentinel Enhanced Dengue Surveillance System (SEDSS) to describe influenza trends in southern Puerto Rico during 2012‐2018 and compare them to trends in the United States. METHODS: Patients with fever onset ≤ 7 days presenting were enrolled. Nasal/oropharyngeal swabs were tested for influenza A and B viruses by PCR. Virologic data were obtained from the US World Health Organization (WHO) Collaborating Laboratories System and the National Respiratory and Enteric Virus Surveillance System (NREVSS). We compared influenza A and B infections identified from SEDSS and WHO/NREVSS laboratories reported by US Department of Health and Human Services (HHS) region using time series decomposition methods, and analysed coherence of climate and influenza trends by region. RESULTS: Among 23,124 participants, 9% were positive for influenza A and 5% for influenza B. Influenza A and B viruses were identified year‐round, with no clear seasonal patterns from 2012 to 2015 and peaks in December‐January in 2016‐2017 and 2017‐2018 seasons. Influenza seasons in HHS regions were relatively synchronized in recent years with the seasons in Puerto Rico. We observed high coherence between absolute humidity and influenza A and B virus in HHS regions. In Puerto Rico, coherence was much lower in the early years but increased to similar levels to HHS regions by 2017‐2018. CONCLUSIONS: Influenza seasons in Puerto Rico have recently become synchronized with seasons in US HHS regions. Current US recommendations are for everyone 6 months and older to receive influenza vaccination by the end of October seem appropriate for Puerto Rico.


id: cord-315949-7id5mitl
title: Respiratory virus infections in hospitalized children and adults in Lao PDR
author: Sentilhes, Anne‐Charlotte
date: 2013-06-25
txt: ./txt/cord-315949-7id5mitl.txt
cache: ./cache/cord-315949-7id5mitl.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12135
doi: 10.1111/irv.12135
summary:
  8, 9 The purpose of this study was to describe during a limited period of time the viral etiology of acute lower respiratory infections (ALRI) in patients hospitalized in two Lao hospitals by using a set of five multiplex RT-PCR/PCR targeting 18 common respiratory viruses. In this study, we report for the first time in Lao PDR the viral etiologies in patients hospitalized for ALRIs. We identified 186 respiratory viruses in 162 (55%) patients of all ages using 5 multiplex PCR/RT-PCR. Human respiratory syncytial virus is frequently defined as the predominant virus associated with hospitalizations for ALRI in children aged ≤5 years. Respiratory virus coinfections being frequent, 5, 19, 44 it demonstrates the usefulness of the multiplex RT-PCR approach, which allows the detection of the most important viruses in only few reactions while multiple infections are often undetected in viral culture or by direct immunofluorescence.

abstract:
  BACKGROUND: Acute respiratory infections are an important cause of morbidity and mortality worldwide, with a major burden of disease in developing countries. The relative contribution of viruses in acute lower respiratory infections (ALRI) is, however, poorly documented in Lao PDR. OBJECTIVE: The objective of this study is to investigate the etiology of ALRI in patients of all ages in two hospitals of Laos. METHODS: Multiplex PCR/RT‐PCR methods were used to target 18 major common respiratory viruses. Between August 2009 and October 2010, samples from 292 patients presenting with ALRI were collected. RESULTS AND CONCLUSION: Viruses were detected in 162 (55%) samples. In 48% (140/292) of the total ALRI cases, a single virus was detected while coinfections were observed in 8% (22/292) of the samples. The most frequent viruses were rhinovirus/enterovirus (35%), human respiratory syncytial virus (26%), and influenza viruses (13%). Parainfluenza viruses were detected in 9%, adenovirus in 6%, human metapneumovirus in 4%, coronaviruses (229E, NL63, OC43, HKU1) in 4%, and bocavirus in 3% of ALRI specimens. Most viral infections occurred in patients below 5 years of age. The distribution of viruses varied according to age‐groups. No significant correlation was observed between the severity of the disease and the age of patients or the virus species. This study provides the description of viral etiology among patients presenting with ALRI in Lao PDR. Additional investigations are required to better understand the clinical role of the different viruses and their seasonality in Laos.


id: cord-316217-ynh8d853
title: Influenza B associated paediatric acute respiratory infection hospitalization in central vietnam
author: Yoshihara, Keisuke
date: 2019-02-28
url: https://doi.org/10.1111/irv.12626
doi: 10.1111/irv.12626
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-316956-nnqi0dj1
author: Gamiño‐Arroyo, Ana E.
date: 2016-08-18
txt: ./txt/cord-316956-nnqi0dj1.txt
cache: ./cache/cord-316956-nnqi0dj1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12414
doi: 10.1111/irv.12414
summary:
  title: Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico Respiratory syncytial virus (RSV) is the major infectious cause of lower respiratory tract illness in infants and young children around the world. 11 In the present study, 570 cases of RSV infection identified during four epidemic years in Mexico were evaluated to clarify the epidemiology of this infection and to assess the possible variations in demographic and clinical characteristics according to viral groups. 6 In this report, we analyzed the characteristics of 570 patients (399 children and 171 adults) with confirmed RSV infection included in the study during a 4-year period. Epidemiological and clinical data of hospitalizations associated with respiratory syncytial virus infection in children under 5 years of age in Spain: FIVE multicenter study Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico

title:
  Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico

abstract:
  BACKGROUND: Respiratory syncytial virus (RSV) is a leading etiological agent of acute respiratory tract infections and hospitalizations in children. However, little information is available regarding RSV infections in Latin American countries, particularly among adult patients. OBJECTIVE: To describe the epidemiology of RSV infection and to analyze the factors associated with severe infections in children and adults in Mexico. METHODS: Patients ≥1 month old, who presented with an influenza‐like illness (ILI) to six hospitals in Mexico, were eligible for participation in the study. Multiplex reverse‐transcriptase polymerase chain reaction identified viral pathogens in nasal swabs from 5629 episodes of ILI. Patients in whom RSV was detected were included in this report. RESULTS: Respiratory syncytial virus was detected in 399 children and 171 adults. RSV A was detected in 413 cases and RSV B in 163, including six patients who had coinfection with both subtypes; 414 (72.6%) patients required hospital admission, including 96 (16.8%) patients that required admission to the intensive care unit. Coinfection with one or more respiratory pathogens other than RSV was detected in 159 cases. Young age (in children) and older age (in adults) as well as the presence of some underlying conditions were associated with more severe disease. CONCLUSIONS: This study confirms that RSV is an important respiratory pathogen in children in Mexico. In addition, a substantial number of cases in adults were also detected highlighting the relevance of this virus in all ages. It is important to identify subjects at high risk of complications who may benefit from current or future preventive interventions.


id: cord-317533-xpfqdeqv
author: Smuts, Heidi
date: 2008-07-24
txt: ./txt/cord-317533-xpfqdeqv.txt
cache: ./cache/cord-317533-xpfqdeqv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/j.1750-2659.2008.00049.x
doi: 10.1111/j.1750-2659.2008.00049.x
summary:
  Objective To determine the role of HCoV‐NL63 in infants and young children hospitalised with acute respiratory tract infections (ARI) in Cape Town, South Africa. A number of respiratory viruses including influenza viruses, respiratory syncytial virus (RSV), parainfluenza viruses, adenovirus and the recently described human metapneumovirus (hMPV) play an important role in acute respiratory tract infections (ARI) in children. In the South African setting, where the prevalence of HIV is high, all infant respiratory samples are routinely screened for CMV as in our setting this virus is a major cause of pneumonia in HIV-infected children. In conclusion these findings suggest that although HCoV-NL63 is circulating in the community it plays a minor role in severe respiratory tract infections in young children who require hospitalisation. A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalised with respiratory tract infections in Belgium Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children

title:
  Human coronavirus NL63 infections in infants hospitalised with acute respiratory tract infections in South Africa

abstract:
  Background Human coronavirus NL63 (HCoV‐NL63) is a novel respiratory virus which is associated with respiratory tract infections in children. Objective To determine the role of HCoV‐NL63 in infants and young children hospitalised with acute respiratory tract infections (ARI) in Cape Town, South Africa. Methods Respiratory specimens were collected from 1055 infants and young children hospitalised with ARI in 2003–2004. Samples were screened by RT‐PCR to detect HCoV‐NL63 and human metapneumovirus (hMPV). Standard shell vial culture and immunofluoresence was used to detect the common respiratory viruses including RSV, influenza A and B viruses, parainfluenza viruses 1, 2, 3, adenovirus and CMV. Results A respiratory virus was found in 401/1055 (38·0%) samples. HCoV‐NL63 was detected in 9/1055 (0·85%) with peak activity during autumn (67%). Most patients had a diagnosis of pneumonia or lower respiratory tract infection (6/9; 67%). Conclusions This is the first report of HCoV‐NL63 infections in hospitalised children in Africa. During the 2‐year period HCoV‐NL63 played a minor role in ARI in children.


id: cord-319129-o1kzb6dm
author: Peng, Jianhui
date: 2020-06-08
txt: ./txt/cord-319129-o1kzb6dm.txt
cache: ./cache/cord-319129-o1kzb6dm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32510865/
doi: 10.1111/irv.12768
abstract: nan
summary:
  Third, since early detection of asymptomatic carriers is critical to contain their transmission, current screening methods also need to be strengthened. 8 At present, persons who are significant epidemiological associations with COVID-19 patients (eg, close contacts) will be put under 14-day centralized medical observation in China. 3 As the epidemic enters a new stage, in order to consolidate the previous anti-epidemic achievements and prevent the epidemic from rebounding, we should further strengthen the monitoring of asymptomatic carriers and some special populations who may play a greater role in the spread of COVID-19, including front-line medical staff, disease control personnel, street epidemic prevention and control point staff, and delivery personnel. In future, further definition of high-risk populations and development of effective screening strategies and programs will support rapid identification and management of asymptomatic carrier transmission of COVID-19. Screening and management of asymptomatic infection of corona virus disease 2019 (COVID-19)

title:
  Identification and management of asymptomatic carriers of coronavirus disease 2019 (COVID‐19) in China


id: cord-320592-wnrzv4hg
author: Giuffrida, María J
date: 2013-08-21
url: https://www.ncbi.nlm.nih.gov/pubmed/23962134/
doi: 10.1111/irv.12155
title:
  Increased cytokine/chemokines in serum from asthmatic and non-asthmatic patients with viral respiratory infection

abstract:
  BACKGROUND: Respiratory viral infections can induce different cytokine/chemokine profiles in lung tissues and have a significant influence on patients with asthma. There is little information about the systemic cytokine status in viral respiratory-infected asthmatic patients compared with non-asthmatic patients. OBJECTIVES: The aim of this study was to determine changes in circulating cytokines (IL-1β, TNF-α, IL-4, IL-5) and chemokines (MCP1: monocyte chemoattractant protein-1 and RANTES: regulated on activation normal T cell expressed and secreted) in patients with an asthmatic versus a non-asthmatic background with respiratory syncytial virus, parainfluenza virus or adenovirus respiratory infection. In addition, human monocyte cultures were incubated with respiratory viruses to determine the cytokine/chemokine profiles. PATIENTS/METHODS: Patients with asthmatic (n = 34) and non-asthmatic (n = 18) history and respiratory infections with respiratory syncytial virus, parainfluenza, and adenovirus were studied. Healthy individuals with similar age and sex (n = 10) were used as controls. Cytokine/chemokine content in blood and culture supernatants was determined by ELISA. Monocytes were isolated by Hystopaque gradient and cocultured with each of the above-mentioned viruses. RESULTS: Similar increased cytokine concentrations were observed in asthmatic and non-asthmatic patients. However, higher concentrations of chemokines were observed in asthmatic patients. Virus-infected monocyte cultures showed similar cytokine/chemokine profiles to those observed in the patients. CONCLUSIONS: Circulating cytokine profiles induced by acute viral lung infection were not related to asthmatic status, except for chemokines that were already increased in the asthmatic status. Monocytes could play an important role in the increased circulating concentration of cytokines found during respiratory viral infections.


id: cord-323066-tvguutak
author: Praznik, Ajda
date: 2018-08-09
url: https://www.ncbi.nlm.nih.gov/pubmed/29944781/
doi: 10.1111/irv.12587
title:
  Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia

abstract:
  AIM: Study's objective was to identify risk factors associated with bronchiolitis severity. METHODS: A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). Detection of respiratory viruses in nasopharyngeal swab was accomplished by RT‐PCR. Severity was assessed by Wang Respiratory Score and hospitalization longer than 24 hours. RESULTS: The study included 761 children. The three most frequently detected viruses were respiratory syncytial virus (RSV), human rhinovirus (hRV) and human bocavirus (hBoV) (57.5%, 272/473; 25.6%, 121/473; 18.4%, 87/473). Patient groups differed in Wang Respiratory Score for the severity of bronchiolitis (P < 0.001). No differences regarding the causative viruses were found. There was a lower proportion of children with the presence of more than one virus in PICU group compared to other two groups (P = 0.017). The three groups significantly differed in age, birthweight, comorbidities, bronchodilator treatment and antibiotic usage. However, multiple regression analysis revealed that younger age and the use of antibiotics were associated with bronchiolitis severity defined as hospitalization for >24 hours. CONCLUSIONS: Respiratory syncytial virus, hRV and hBoV were the most frequently detected viruses. The majority of patients admitted to the PICU had only one virus detected. Younger age and the use of antibiotics were associated with bronchiolitis severity.


id: cord-324012-q2ilk6gs
author: Inui, Ken
date: 2019-09-05
txt: ./txt/cord-324012-q2ilk6gs.txt
cache: ./cache/cord-324012-q2ilk6gs.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31487118/
doi: 10.1111/irv.12646
summary:
  METHODS: A panel of 59 virus isolates, including H7N9, avian influenza viruses of subtype H1 to H13, swine and human influenza viruses, Newcastle disease virus, and infectious bursal disease virus, were tested by H7 and N9 iiRT‐PCR reagents, using probes and primers specific to H7 or N9, in comparison with laboratory‐based real‐time RT‐PCR assays to determine analytical sensitivity and specificity. Fifty oropharyngeal samples from experimentally infected chicken and ducks with H7N9 and 50 non‐infected control swabs were tested by the H7 iiRT‐PCR to determine diagnostic sensitivity and specificity. The H7 and N9 iiRT-PCR reagents yielded comparable levels of analytical sensitivity and specificity with real-time RT-PCR for the detection of H7N9 virus. Reverse transcription-insulated isothermal PCR (RT-iiRT-PCR) assay for rapid and sensitive detection of foot-and-mouth disease virus A rapid field-deployable reverse transcription-insulated isothermal polymerase chain reaction assay for sensitive and specific detection of bluetongue virus Rapid detection of equine influenza virus H3N8 subtype by insulated isothermal RT-PCR (iiRT-PCR) assay using the POCKIT nucleic acid analyzer

title:
  A field‐deployable insulated isothermal RT‐PCR assay for identification of influenza A (H7N9) shows good performance in the laboratory

abstract:
  BACKGROUND: Avian influenza A (H7N9) remains circulating in China. For countries at risk of introduction of H7N9, such as Vietnam, early detection of H7N9 virus is essential for the early containment of the virus. Insulated isothermal reverse transcriptase PCR (iiRT‐PCR) is a portable PCR system that can be deployed under field conditions to identify pathogens at the sampling site. Applying PCR at the sampling site will greatly reduce the time to obtain a diagnostic result which allows the veterinary authority to take immediate action to contain disease spreading. OBJECTIVE: To determine analytical and diagnostic sensitivity and specificity of the portable iiRT‐PCR for H7N9 virus detection. METHODS: A panel of 59 virus isolates, including H7N9, avian influenza viruses of subtype H1 to H13, swine and human influenza viruses, Newcastle disease virus, and infectious bursal disease virus, were tested by H7 and N9 iiRT‐PCR reagents, using probes and primers specific to H7 or N9, in comparison with laboratory‐based real‐time RT‐PCR assays to determine analytical sensitivity and specificity. Fifty oropharyngeal samples from experimentally infected chicken and ducks with H7N9 and 50 non‐infected control swabs were tested by the H7 iiRT‐PCR to determine diagnostic sensitivity and specificity. RESULTS: The H7 and N9 iiRT‐PCR reagents yielded comparable levels of analytical sensitivity and specificity with real‐time RT‐PCR for the detection of H7N9 virus. Diagnostic sensitivity and specificity of H7 iiRT‐PCR were 98% and 100%, respectively. CONCLUSION: The observed high sensitivity and specificity of iiRT‐PCR for H7N9 detection show its potential for early detection of H7N9 in risk‐based surveillance.


id: cord-324432-k0g3r1lw
title: Seasonality and clinical impact of human parainfluenza viruses
author: Maykowski, Philip
date: 2018-08-29
txt: ./txt/cord-324432-k0g3r1lw.txt
cache: ./cache/cord-324432-k0g3r1lw.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/irv.12597
doi: 10.1111/irv.12597
summary:
  PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. The community cohort was derived from the Mobile Surveillance for Acute Respiratory Infections (ARIs) and Influenza-like Illness (ILI) in the Community (MoSAIC) study, a 5-year community-based surveillance ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. epidemiology, parainfluenza, respiratory, seasonality, viruses F I G U R E 1 Flowcharts depicting the overall number of respiratory viral panel (RVP) tests ordered which yielded the final number of human parainfluenza virus (HPIV) types in the community cohort (1A) and in hospitalized patients (1B) study in New York City (NYC) that includes 250 households annually.

abstract:
  BACKGROUND: Widespread availability of rapid diagnostic testing for respiratory viruses allows more in‐depth studies of human parainfluenza viruses (HPIV). OBJECTIVES: This study aimed to assess seasonality of HPIV types 1‐4, clinical outcomes by HPIV type, and risk factors for illness severity. PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. Seasonality trends by HPIV type were compared between the community and hospital groups. The associations between HPIV type, demographics, clinical characteristics, and illness severity were assessed. RESULTS: HPIV was detected in 69 (4%) of 1753 community surveillance participants (median age 9.2 years) and 680 hospitalized patients (median age 6.8 years). Seasonality for HPIV types 1‐3 agreed with previously described patterns; HPIV‐4 occurred annually in late summer and fall. In the community cohort, 22 (32%) participants sought medical care, 9 (13%) reported antibiotic use, and 20 (29%) reported ≥1 day of missed work or school. Among hospitalized patients, 24% had ≥4 chronic conditions. Multivariable ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV‐4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. CONCLUSIONS: HPIV‐4 presented late summer and early fall annually and was associated with increased severity of illness in hospitalized children.


id: cord-326039-pnf2xjox
title: A review of medical masks and respirators for use during an influenza pandemic
author: Seale, Holly
date: 2009-08-18
txt: ./txt/cord-326039-pnf2xjox.txt
cache: ./cache/cord-326039-pnf2xjox.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/j.1750-2659.2009.00101.x
doi: 10.1111/j.1750-2659.2009.00101.x
abstract: nan
summary:
  Given the lack of a specific vaccine against the pandemic (H1N1) 2009 virus, mitigation measures in Australia have so far focused on identifying, treating, and isolating people who have the disease, and educating the public about the steps that individuals can take to reduce transmission. Non-pharmacological public health interventions including use of face masks are therefore likely to play a vital role in mitigating disease spread, particularly in developing countries. Jefferson and colleagues concluded that more experimental studies were needed to identify the effectiveness of wearing face masks or respirators in reducing exhaled infectious viral particles. Despite the lack of high level evidence, recommendations on the use of face masks and respirators for HCWs are made by many health authorities. Non-pharmaceutical public health interventions for pandemic influenza: an evaluation of the evidence base Face mask use and control of respiratory virus transmission in households


id: cord-328086-ji2emajn
author: Zhou, Jie‐ying
date: 2018-01-11
txt: ./txt/cord-328086-ji2emajn.txt
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url: https://doi.org/10.1111/irv.12535
doi: 10.1111/irv.12535
summary:
  BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). Clinical disease and viral load in children infected with respiratory syncytial virus or human metapneumovirus Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection High viral load of human bocavirus correlates with duration of wheezing in children with severe lower respiratory tract infection High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical significance of different virus load of human bocavirus in patients with lower respiratory tract infection

title:
  Human bocavirus and human metapneumovirus in hospitalized children with lower respiratory tract illness in Changsha, China

abstract:
  BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). We aimed to assay the correlation between viral load and clinical characteristics of HBoV and HMPV with LRTI in Changsha, China. METHODS: Nasopharyngeal aspirates (NPAs) from children with LRTI were collected. Real‐time PCR was used to screen HBoV and HMPV. Analyses were performed using SPSS 16.0 software. RESULTS: Pneumonia was the most frequent diagnosis. There was no significant difference between HBoV‐ and HMPV‐positive patients in age (P = .506) or hospitalization duration (P = .280); 24.1% and 18.2% were positive for HBoV and HMPV. HBoV infections peaked in summer (32.2%), and HMPV infections peaked in winter (28.9%). The HBoV‐positive patients had a shorter hospitalization duration than the HBoV‐negative patients (P = .021), and the HMPV‐positive patients had a higher prevalence of fever than the HMPV‐negative patients (P = .002). The HBoV viral load was significantly higher among patients aged <1 year (P = .006). The mean HBoV and HMPV viral loads were not significantly different between patients with single infections and coinfections. Patients infected with HBoV only were older than those coinfected with HBoV and other respiratory viruses (P = .005). No significant difference was found in the clinical characteristics of patients infected with HMPV only and those coinfected with HMPV and other respiratory viruses. CONCLUSION: Pneumonia was the most frequent diagnosis caused by HBoV and HMPV. Neither HBoV nor HMPV viral load was correlated with disease severity.


id: cord-332057-1vvlzuue
title: Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America
author: Pourbohloul, Babak
date: 2009-08-18
txt: ./txt/cord-332057-1vvlzuue.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/19702583/
doi: 10.1111/j.1750-2659.2009.00100.x
summary:
  authors: Pourbohloul, Babak; Ahued, Armando; Davoudi, Bahman; Meza, Rafael; Meyers, Lauren A.; Skowronski, Danuta M.; Villaseñor, Ignacio; Galván, Fernando; Cravioto, Patricia; Earn, David J. John; Hupert, Nathaniel; Scarpino, Samuel V.; Trujillo, Jesús; Lutzow, Miguel; Morales, Jorge; Contreras, Ada; Chávez, Carolina; Patrick, David M.; Brunham, Robert C. We estimated the initial reproduction number from 497 suspect cases identified prior to 20 April, using a novel contact network methodology incorporating dates of symptom onset and hospitalization, variation in contact rates, extrinsic sociological factors, and uncertainties in underreporting and disease progression. Using the time series of the first 497 suspect cases, we have estimated the initial rate of spread -the reproduction number R -of pandemic (H1N1) 2009, using methods of contact network epidemiology that incorporates extrinsic sociological drivers and uncertainties in disease progression and underreporting.

abstract:
  Background Between 5 and 25 April 2009, pandemic (H1N1) 2009 caused a substantial, severe outbreak in Mexico, and subsequently developed into the first global pandemic in 41 years. We determined the reproduction number of pandemic (H1N1) 2009 by analyzing the dynamics of the complete case series in Mexico City during this early period. Methods We analyzed three mutually exclusive datasets from Mexico City Distrito Federal which constituted all suspect cases from 15 March to 25 April: confirmed pandemic (H1N1) 2009 infections, non‐pandemic influenza A infections and patients who tested negative for influenza. We estimated the initial reproduction number from 497 suspect cases identified prior to 20 April, using a novel contact network methodology incorporating dates of symptom onset and hospitalization, variation in contact rates, extrinsic sociological factors, and uncertainties in underreporting and disease progression. We tested the robustness of this estimate using both the subset of laboratory‐confirmed pandemic (H1N1) 2009 infections and an extended case series through 25 April, adjusted for suspected ascertainment bias. Results The initial reproduction number (95% confidence interval range) for this novel virus is 1·51 (1·32–1·71) based on suspected cases and 1·43 (1·29–1·57) based on confirmed cases before 20 April. The longer time series (through 25 April) yielded a higher estimate of 2·04 (1·84–2·25), which reduced to 1·44 (1·38–1·51) after correction for ascertainment bias. Conclusions The estimated transmission characteristics of pandemic (H1N1) 2009 suggest that pharmaceutical and non‐pharmaceutical mitigation measures may appreciably limit its spread prior the development of an effective vaccine.


id: cord-335948-qkfxfmxb
author: Ampofo, William K.
date: 2011-08-08
txt: ./txt/cord-335948-qkfxfmxb.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1111/j.1750-2659.2011.00277.x
doi: 10.1111/j.1750-2659.2011.00277.x
summary:
  • The selection process is highly coordinated and involves continual year‐round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). • The selection process is highly coordinated and involves continual year-round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). The continuing threat posed by avian H5N1, the aftermath of the 2009 H1N1 pandemic, the increased knowledge of influenza, and the development and availability of new technologies provide a timely opportunity to review the complex processes and issues involved in influenza vaccine virus selection and to identify potential areas for improvement.

title:
  Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14–16 June 2010

abstract:
  • For almost 60 years, the WHO Global Influenza Surveillance and Response System (GISRS) has been the key player in monitoring the evolution and spread of influenza viruses and recommending the strains to be used in human influenza vaccines. The GISRS has also worked to continually monitor and assess the risk posed by potential pandemic viruses and to guide appropriate public health responses. • The expanded and enhanced role of the GISRS following the adoption of the International Health Regulations (2005), recognition of the continuing threat posed by avian H5N1 and the aftermath of the 2009 H1N1 pandemic provide an opportune time to critically review the process by which influenza vaccine viruses are selected. In addition to identifying potential areas for improvement, such a review will also help to promote greater appreciation by the wider influenza and policy‐making community of the complexity of influenza vaccine virus selection. • The selection process is highly coordinated and involves continual year‐round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs). • Ensuring the optimal effectiveness of vaccines has been assisted in recent years by advances in molecular diagnosis and the availability of more extensive genetic sequence data. However, there remain a number of challenging constraints including variations in the assays used, the possibility of complications resulting from non‐antigenic changes, the limited availability of suitable vaccine viruses and the requirement for recommendations to be made up to a year in advance of the peak of influenza season because of production constraints. • Effective collaboration and coordination between human and animal influenza networks is increasingly recognized as an essential requirement for the improved integration of data on animal and human viruses, the identification of unusual influenza A viruses infecting human, the evaluation of pandemic risk and the selection of candidate viruses for pandemic vaccines. • Training workshops, assessments and donations have led to significant increases in trained laboratory personnel and equipment with resulting expansion in both geographical surveillance coverage and in the capacities of NICs and other laboratories. This has resulted in a significant increase in the volume of information reported to WHO on the spread, intensity and impact of influenza. In addition, initiatives such as the WHO Shipment Fund Project have facilitated the timely sharing of clinical specimens and virus isolates and contributed to a more comprehensive understanding of the global distribution and temporal circulation of different viruses. It will be important to sustain and build upon the gains made in these and other areas. • Although the haemagglutination inhibition (HAI) assay is likely to remain the assay of choice for the antigenic characterization of viruses in the foreseeable future, alternative assays – for example based upon advanced recombinant DNA and protein technologies – may be more adaptable to automation. Other technologies such as microtitre neuraminidase inhibition assays may also have significant implications for both vaccine virus selection and vaccine development. • Microneutralization assays provide an important adjunct to the HAI assay in virus antigenic characterization. Improvements in the use and potential automation of such assays should facilitate large‐scale serological studies, while other advanced techniques such as epitope mapping should allow for a more accurate assessment of the quality of a protective immune response and aid the development of additional criteria for measuring immunity. • Standardized seroepidemiological surveys to assess the impact of influenza in a population could help to establish well‐characterized banks of age‐stratified representative sera as a national, regional and global resource, while providing direct evidence of the specific benefits of vaccination. • Advances in high‐throughput genetic sequencing coupled with advanced bioinformatics tools, together with more X‐ray crystallographic data, should accelerate understanding of the genetic and phenotypic changes that underlie virus evolution and more specifically help to predict the influence of amino acid changes on virus antigenicity. • Complex mathematical modelling techniques are increasingly being used to gain insights into the evolution and epidemiology of influenza viruses. However, their value in predicting the timing and nature of future antigenic and genetic changes is likely to be limited at present. The application of simpler non‐mechanistic statistical algorithms, such as those already used as the basis of antigenic cartography, and phylogenetic modelling are more likely to be useful in facilitating vaccine virus selection and in aiding assessment of the pandemic potential of avian and other animal influenza viruses. • The adoption of alternative vaccine technologies – such as live‐attenuated, quadrivalent or non‐HA‐based vaccines – has significant implications for vaccine virus selection, as well as for vaccine regulatory and manufacturing processes. Recent collaboration between the GISRS and vaccine manufacturers has resulted in the increased availability of egg isolates and high‐growth reassortants for vaccine production, the development of qualified cell cultures and the investigation of alternative methods of vaccine potency testing. WHO will continue to support these and other efforts to increase the reliability and timeliness of the global influenza vaccine supply. • The WHO GISRS and its partners are continually working to identify improvements, harness new technologies and strengthen and sustain collaboration. WHO will continue in its central role of coordinating worldwide expertise to meet the increasing public health need for influenza vaccines and will support efforts to improve the vaccine virus selection process, including through the convening of periodic international consultations.


id: cord-336335-spap39b7
author: Silva, Denise R
date: 2013-08-26
url: https://www.ncbi.nlm.nih.gov/pubmed/24034701/
doi: 10.1111/irv.12158
title:
  Respiratory viral infections and effects of meteorological parameters and air pollution in adults with respiratory symptoms admitted to the emergency room

abstract:
  BACKGROUND: Respiratory viral infections (RVIs) are the most common causes of respiratory infections. The prevalence of respiratory viruses in adults is underestimated. Meteorological variations and air pollution are likely to play a role in these infections. OBJECTIVES: The objectives of this study were to determine the number of emergency visits for influenza-like illness (ILI) and severe acute respiratory infection (SARI) and to evaluate the association between ILI/SARI, RVI prevalence, and meteorological factors/air pollution, in the city of Porto Alegre, Brazil, from November 2008 to October 2010. METHODS: Eleven thousand nine hundred and fifty-three hospitalizations (adults and children) for respiratory symptoms were correlated with meteorological parameters and air pollutants. In a subset of adults, nasopharyngeal aspirates were collected and analyzed through IFI test. The data were analyzed using time-series analysis. RESULTS: Influenza-like illness and SARI were diagnosed in 3698 (30·9%) and 2063 (17·7%) patients, respectively. Thirty-seven (9·0%) samples were positive by IFI and 93 of 410 (22·7%) were IFI and/or PCR positive. In a multivariate logistic regression model, IFI positivity was statistically associated with absolute humidity, use of air conditioning, and presence of mold in home. Sunshine duration was significantly associated with the frequency of ILI cases. For SARI cases, the variables mean temperature, sunshine duration, relative humidity, and mean concentration of pollutants were singnificant. CONCLUSIONS: At least 22% of infections in adult patients admitted to ER with respiratory complaints were caused by RVI. The correlations among meteorological variables, air pollution, ILI/SARI cases, and respiratory viruses demonstrated the relevance of climate factors as significant underlying contributors to the prevalence of RVI.


id: cord-337372-y43prnko
author: bin‐Reza, Faisal
date: 2011-12-21
txt: ./txt/cord-337372-y43prnko.txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/22188875/
doi: 10.1111/j.1750-2659.2011.00307.x
summary:
  A limited effort was made to identify additional studies: reference lists of review articles were examined; the European Centre for Disease Prevention and Control''s (ECDC) Antimicrobial Resistance and Health Care Associated Infection Programme was consulted; and MEC''s and AN''s hardcopy literature files were hand-searched. [7] [8] [9] [10] [11] Two of these studies compared N95 respirators (designed to seal tightly to the wearer''s face and filter out very small particles or aerosols that may contain viruses) and surgical masks (used to block large droplets from coming into contact with the wearer''s mouth or nose) amongst healthcare workers; one trial found a lower rate of clinical respiratory illness associated with the use of non-fit-tested N95 respirators compared with medical masks, 6 whilst a non-inferiority trial found that masks and respirators offered similar protection to nurses against laboratory-confirmed influenza infection.

title:
  The use of masks and respirators to prevent transmission of influenza: a systematic review of the scientific evidence

abstract:
  Please cite this paper as: bin‐Reza et al. (2012) The use of masks and respirators to prevent transmission of influenza: a systematic review of the scientific evidence. Influenza and Other Respiratory Viruses 6(4), 257–267. There are limited data on the use of masks and respirators to reduce transmission of influenza. A systematic review was undertaken to help inform pandemic influenza guidance in the United Kingdom. The initial review was performed in November 2009 and updated in June 2010 and January 2011. Inclusion criteria included randomised controlled trials and quasi‐experimental and observational studies of humans published in English with an outcome of laboratory‐confirmed or clinically‐diagnosed influenza and other viral respiratory infections. There were 17 eligible studies. Six of eight randomised controlled trials found no significant differences between control and intervention groups (masks with or without hand hygiene; N95/P2 respirators). One household trial found that mask wearing coupled with hand sanitiser use reduced secondary transmission of upper respiratory infection/influenza‐like illness/laboratory‐confirmed influenza compared with education; hand sanitiser alone resulted in no reduction. One hospital‐based trial found a lower rate of clinical respiratory illness associated with non‐fit‐tested N95 respirator use compared with medical masks. Eight of nine retrospective observational studies found that mask and/or respirator use was independently associated with a reduced risk of severe acute respiratory syndrome (SARS). Findings, however, may not be applicable to influenza and many studies were suboptimal. None of the studies established a conclusive relationship between mask/respirator use and protection against influenza infection. Some evidence suggests that mask use is best undertaken as part of a package of personal protection especially hand hygiene. The effectiveness of masks and respirators is likely linked to early, consistent and correct usage.


id: cord-338390-v4ncshav
title: Managing public health crises: the role of models in pandemic preparedness
author: Moghadas, Seyed M.
date: 2009-03-02
url: https://www.ncbi.nlm.nih.gov/pubmed/19496845/
doi: 10.1111/j.1750-2659.2009.00081.x
abstract:
  Background Given the enormity of challenges involved in pandemic preparedness, design and implementation of effective and cost‐effective public health policies is a major task that requires an integrated approach through engagement of scientific, administrative, and political communities across disciplines. There is ample evidence to suggest that modeling may be a viable approach to accomplish this task. Methods To demonstrate the importance of synergism between modelers, public health experts, and policymakers, the University of Winnipeg organized an interdisciplinary workshop on the role of models in pandemic preparedness in September 2008. The workshop provided an excellent opportunity to present outcomes of recent scientific investigations that thoroughly evaluate the merits of preventive, therapeutic, and social distancing mechanisms, where community structures, priority groups, healthcare providers, and responders to emergency situations are given specific consideration. Results This interactive workshop was clearly successful in strengthening ties between various disciplines and creating venues for modelers to effectively communicate with policymakers. The importance of modeling in pandemic planning was highlighted, and key parameters that affect policy decision‐making were identified. Core assumptions and important activities in Canadian pandemic plans at the provincial and national levels were also discussed. Conclusions There will be little time for thoughtful and rapid reflection once an influenza pandemic strikes, and therefore preparedness is an unavoidable priority. Modeling and simulations are key resources in pandemic planning to map out interdependencies and support complex decision‐making. Models are most effective in formulating strategies for managing public health crises when there are synergies between modelers, planners, and policymakers.


id: cord-343050-1pfqgvie
title: Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance
author: Huang, Qiu Sue
date: 2015-06-09
txt: ./txt/cord-343050-1pfqgvie.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25912617/
doi: 10.1111/irv.12315
summary:
  The results during the first 2 years (2012-2013) provided scientific evidence to (a) support a change to NZ''s vaccination policy for young children due to high influenza hospitalizations in these children; (b) contribute to the revision of the World Health Organization''s case definition for severe acute respiratory illness for global influenza surveillance; and (c) contribute in part to vaccine strain selection using vaccine effectiveness assessment in the prevention of influenza-related consultations and hospitalizations. Over 5 years, we hope this project will shed more light on the burden of influenza and other respiratory pathogens in our study population and subgroups and estimate key epidemiologic parameters such as relative rates of infection, clinical disease, general practice visits and hospitalizations as well as risk factors for illness, effectiveness of vaccination, mechanisms of immunity and monitoring for new influenza viruses with pandemic potential such as A(H7N9) and other emerging viruses (e.g. MERS-CoV) and provide a framework for timely assessment of severity which is essential in an event of emergence of these pathogens.

abstract:
  The 2009 influenza A(H1N1)pdm09 pandemic highlighted the need for improved scientific knowledge to support better pandemic preparedness and seasonal influenza control. The Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance (SHIVERS) project, a 5-year (2012–2016) multiagency and multidisciplinary collaboration, aimed to measure disease burden, epidemiology, aetiology, risk factors, immunology, effectiveness of vaccination and other prevention strategies for influenza and other respiratory infectious diseases of public health importance. Two active, prospective, population-based surveillance systems were established for monitoring influenza and other respiratory pathogens among those hospitalized patients with acute respiratory illness and those enrolled patients seeking consultations at sentinel general practices. In 2015, a sero-epidemiological study will use a sample of patients from the same practices. These data will provide a full picture of the disease burden and risk factors from asymptomatic infections to severe hospitalized disease and deaths and related economic burden. The results during the first 2 years (2012–2013) provided scientific evidence to (a) support a change to NZ's vaccination policy for young children due to high influenza hospitalizations in these children; (b) contribute to the revision of the World Health Organization's case definition for severe acute respiratory illness for global influenza surveillance; and (c) contribute in part to vaccine strain selection using vaccine effectiveness assessment in the prevention of influenza-related consultations and hospitalizations. In summary, SHIVERS provides valuable international platforms for supporting seasonal influenza control and pandemic preparedness, and responding to other emerging/endemic respiratory-related infections.


id: cord-349330-akwxwfg3
author: Wabe, Nasir
date: 2020-08-20
txt: ./txt/cord-349330-akwxwfg3.txt
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url: https://doi.org/10.1111/irv.12799
doi: 10.1111/irv.12799
summary:
  title: Cepheid Xpert(®) Flu/RSV and Seegene Allplex(™) RP1 show high diagnostic agreement for the detection of influenza A/B and respiratory syncytial viruses in clinical practice This study determined the agreement between the RT‐PCR assays (Xpert(®) Flu/RSV vs Allplex(™) RP1) in detecting influenza A, influenza B, and respiratory syncytial viruses (RSVs) in clinical practice. The objective of the study was to determine the diagnostic agreement between Xpert ® Flu/RSV vs Allplex ™ RP1 for the detection of influenza A, influenza B, and RSV in the hospital emergency department (ED) or inpatient settings. While both assays were available to clinicians during the study period, the use of Xpert ® Flu/RSV was recommended to be used by the laboratory service for patients at high risk of influenza, where a result was required more urgently. Prospective and retrospective evaluation of the Cepheid Xpert ® Flu/RSV XC assay for rapid detection of influenza A, influenza B, and respiratory syncytial virus

title:
  Cepheid Xpert(®) Flu/RSV and Seegene Allplex(™) RP1 show high diagnostic agreement for the detection of influenza A/B and respiratory syncytial viruses in clinical practice

abstract:
  BACKGROUND: Molecular assays based on reverse transcription‐polymerase chain reaction (RT‐PCR) provide reliable results for the detection of respiratory pathogens, although diagnostic agreement varies. This study determined the agreement between the RT‐PCR assays (Xpert(®) Flu/RSV vs Allplex(™) RP1) in detecting influenza A, influenza B, and respiratory syncytial viruses (RSVs) in clinical practice. METHODS: We retrospectively identified 914 patient encounters where testing with both Xpert(®) Flu/RSV and Allplex(™) RP1 was undertaken between October 2015 and September 2019 in seven hospitals across New South Wales, Australia. The diagnostic agreement of the two assays was evaluated using positive percent agreement, negative percent agreement, and prevalence and bias‐adjusted kappa. RESULTS: The positive percent agreement was 95.1% for influenza A, 87.5% for influenza B, and 77.8% for RSV. The negative percent agreement was 99.4% for influenza A, 99.9% for influenza B, and 100% for RSV. The prevalence and bias‐adjusted kappa was 0.98 for influenza A, 0.99 for influenza B, and 0.97 for RSV. In a sensitivity analysis, the positive percent agreement values were significantly higher during the non‐influenza season than the influenza season for influenza B and RSV. CONCLUSIONS: The Xpert(®) Flu/RSV and Allplex(™) RP1 demonstrated a high diagnostic agreement for all three viruses assessed. The seasonal variation in the positive percent agreement of the two assays for influenza B and RSV may have been due to lower numbers assessed, variability in the virology of infections outside the peak season, or changes in the physiology of the infected host in different seasons.


id: cord-350928-vj5qlzpj
author: Arnott, Alicia
date: 2012-04-25
txt: ./txt/cord-350928-vj5qlzpj.txt
cache: ./cache/cord-350928-vj5qlzpj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/22531100/
doi: 10.1111/j.1750-2659.2012.00369.x
summary:
  Objectives To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. In patients where HBoV is the only virus detected, the clinical symptoms reported are similar to those occurring as a result of infection with respiratory syncytial virus (RSV) and human metapneumovirus (HMPV), including bronchiolitis, bronchitis, pneumonia and exacerbation of asthma. 20 Here, we report the findings of the first study investigating the prevalence, seasonality, clinical characteristics and the molecular epidemiology of HBoV in amongst an all-ages population of patients hospitalized for acute lower respiratory illness (ALRI) in Cambodia over 3 consecutive years. 5 In this study, ALRI patient samples were screened for HBoV infection using a highly sensitive multiplex PCR assay previously shown to have a lower limit of detection of 4 copies of HBoV DNA ⁄ ll of viral transport medium.

title:
  Human bocavirus amongst an all‐ages population hospitalised with acute lower respiratory infections in Cambodia

abstract:
  Please cite this paper as: Arnott et al. (2013) Human bocavirus amongst an all‐ages population hospitalised with acute lower respiratory infections in Cambodia. Influenza and Other Respiratory Viruses 7(2) 201–210. Background Human bocavirus (HBoV) is a novel parvovirus that is associated with respiratory and gastrointestinal tract disease. Objectives To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. Study Design Samples were collected from 2773 patients of all ages hospitalised with symptoms of ALRI between 2007 and 2009. All samples were screened by multiplex RT‐PCR/PCR for 18 respiratory viruses. All samples positive for HBoV were sequenced and included in this study. Results Of the samples tested, 43 (1·5%) were positive for HBoV. The incidence of HBoV did not vary between the consecutive seasons investigated, and HBoV infections were detected year‐round. The incidence of HBoV infection was highest in patients aged <2 years, with pneumonia or bronchopneumonia the most common clinical diagnosis, regardless of age. A total of 19 patients (44%) were co‐infected with HBoV and an additional respiratory pathogen. All isolates were classified as HBoV type 1 (HBoV‐1). High conservation between Cambodian NP1 and V1V2 gene sequences was observed. Conclusions Human bocavirus infection can result in serious illness, however is frequently detected in the context of viral co‐infection. Specific studies are required to further understand the true pathogenesis of HBoV in the context of severe respiratory illness.


id: cord-351008-p0n1fdxw
author: Monge, Susana
date: 2020-05-14
url: https://www.ncbi.nlm.nih.gov/pubmed/32410358/
doi: 10.1111/irv.12731
title:
  Ambulance dispatch calls attributable to influenza A and other common respiratory viruses in the Netherlands (2014‐2016)

abstract:
  BACKGROUND: Ambulance dispatches could be useful for syndromic surveillance of severe respiratory infections. We evaluated whether ambulance dispatch calls of highest urgency reflect the circulation of influenza A virus, influenza B virus, respiratory syncytial virus (RSV), rhinovirus, adenovirus, coronavirus, parainfluenzavirus and human metapneumovirus (hMPV). METHODS: We analysed calls from four ambulance call centres serving 25% of the population in the Netherlands (2014‐2016). The chief symptom and urgency level is recorded during triage; we restricted our analysis to calls with the highest urgency and identified those compatible with a respiratory syndrome. We modelled the relation between respiratory syndrome calls (RSC) and respiratory virus trends using binomial regression with identity link function. RESULTS: We included 211 739 calls, of which 15 385 (7.3%) were RSC. Proportion of RSC showed periodicity with winter peaks and smaller interseasonal increases. Overall, 15% of RSC were attributable to respiratory viruses (20% in out‐of‐office hour calls). There was large variation by age group: in <15 years, only RSV was associated and explained 11% of RSC; in 15‐64 years, only influenza A (explained 3% of RSC); and in ≥65 years adenovirus explained 9% of RSC, distributed throughout the year, and hMPV (4%) and influenza A (1%) mainly during the winter peaks. Additionally, rhinovirus was associated with total RSC. CONCLUSION: High urgency ambulance dispatches reflect the burden of different respiratory viruses and might be useful to monitor the respiratory season overall. Influenza plays a smaller role than other viruses: RSV is important in children while adenovirus and hMPV are the biggest contributors to emergency calls in the elderly.


id: cord-354151-psog34u3
author: van Asten, Liselotte
date: 2015-12-11
url: https://doi.org/10.1111/irv.12348
doi: 10.1111/irv.12348
title:
  Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections

abstract:
  BACKGROUND: Viral interaction in which outbreaks of influenza and other common respiratory viruses might affect each other has been postulated by several short studies. Regarding longer time periods, influenza epidemics occasionally occur very early in the season, as during the 2009 pandemic. Whether early occurrence of influenza epidemics impacts outbreaks of other common seasonal viruses is not clear. OBJECTIVES: We investigated whether early occurrence of influenza outbreaks coincides with shifts in the occurrence of other common viruses, including both respiratory and non‐respiratory viruses. METHODS: We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10‐year time period (2003–2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. We compared trends in viruses between early and late influenza seasons. RESULTS: Between 2003 and 2012, influenza B, RSV, and coronavirus showed shifts in their occurrence when influenza A epidemics occurred earlier than usual (before week 1). Although shifts were not always consistently of the same type, when influenza type A hit early, RSV outbreaks tended to be delayed, coronavirus outbreaks tended to be intensified, and influenza virus type B tended not to occur at all. Occurrence of rhinovirus, norovirus, rotavirus, and enterovirus did not change. CONCLUSION: When influenza A epidemics occured early, timing of the epidemics of several respiratory winter viruses usually occurring close in time to influenza A was affected, while trends in rhinoviruses (occurring in autumn) and trends in enteral viruses were not.


