cord-000114-f0vud3gu	2009	
cord-001521-l36f1gp7	2011	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.
cord-002136-mkl89qkt	2009	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
cord-002137-j5sfiyz8	2010	
cord-002138-uywz5nqw	2011	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.
cord-002257-30s14h9j	2016	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
cord-002852-m4l2l2r1	2012	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.
cord-003298-vojbn0p4	2010	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).
cord-255946-bcuivyku	2020	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
cord-259368-k8t8brjy	2020	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.
cord-263927-hnsyas9q	2012	Objectives To describe respiratory viruses, including co‐infection and associated attributes such as age, sex or comorbidity, in patients presenting with influenza‐like illness to a community sentinel network, during the pandemic A(H1N1)pdm09 in Ontario, Canada. In multinomial logistic regression analyses adjusted for age, sex, comorbidity, and timeliness of sample collection, single infection was less often detected in the elderly and co‐infection more often in patients <30 years of age. Co‐infection, but not single infection, was more likely detected in patients who had a sample collected within 2 days of symptom onset as compared to 3–7 days. [8] [9] [10] [11] [12] [13] Higher proportions of influenza A, respiratory syncytial virus (RSV), parainfluenza viruses, and rhinovirus, compared with other circulating viruses have been detected in patients with co-infections. 9, 15, 16, 20, 21 This study enrolled community patients presenting with (ILI) to a community sentinel network, during the influenza pandemic A(H1N1)pdm09 in Ontario, Canada and documented the profile of respiratory viruses causing ILI symptoms.
cord-267531-tqqj4cy0	2014	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.
cord-268105-617qcgpe	2016	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
cord-269644-94yrkzns	2016	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
cord-269665-byuv48wi	2011	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.
cord-273620-gn8g6suq	2012	
cord-273861-sg7esn4p	2017	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.
cord-276363-m8di6dpt	2008	
cord-278554-rg92gcc6	2015	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.
cord-279615-yne753y6	2016	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.
cord-279716-kxfc4npg	2007	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.
cord-285425-3v1bid02	2017	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.
cord-286096-h275nner	2012	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.
cord-289358-4abypk6o	2014	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.
cord-292946-iggv9f0k	2012	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.
cord-293354-55nawxos	2016	
cord-297609-6g39lu1y	2015	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.
cord-299790-vciposnk	2015	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.
cord-304473-6aivjett	2020	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
cord-304569-o39kl5k4	2015	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
cord-306923-eujbxdqi	2018	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
cord-307338-4nta9b6w	2010	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) .
cord-309497-3v0asfa7	2012	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.
cord-309518-seonrtn3	2019	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.
cord-310956-qwe4ndvb	2011	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.
cord-311884-3lkkpg9g	2020	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
cord-315949-7id5mitl	2013	8, 9 The purpose of this study was to describe during a limited period of time the viral etiology of acute lower respiratory infections (ALRI) in patients hospitalized in two Lao hospitals by using a set of five multiplex RT-PCR/PCR targeting 18 common respiratory viruses. In this study, we report for the first time in Lao PDR the viral etiologies in patients hospitalized for ALRIs. We identified 186 respiratory viruses in 162 (55%) patients of all ages using 5 multiplex PCR/RT-PCR. Human respiratory syncytial virus is frequently defined as the predominant virus associated with hospitalizations for ALRI in children aged ≤5 years. Respiratory virus coinfections being frequent, 5, 19, 44 it demonstrates the usefulness of the multiplex RT-PCR approach, which allows the detection of the most important viruses in only few reactions while multiple infections are often undetected in viral culture or by direct immunofluorescence.
cord-316217-ynh8d853	2019	
cord-316956-nnqi0dj1	2016	title: Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico Respiratory syncytial virus (RSV) is the major infectious cause of lower respiratory tract illness in infants and young children around the world. 11 In the present study, 570 cases of RSV infection identified during four epidemic years in Mexico were evaluated to clarify the epidemiology of this infection and to assess the possible variations in demographic and clinical characteristics according to viral groups. 6 In this report, we analyzed the characteristics of 570 patients (399 children and 171 adults) with confirmed RSV infection included in the study during a 4-year period. Epidemiological and clinical data of hospitalizations associated with respiratory syncytial virus infection in children under 5 years of age in Spain: FIVE multicenter study Epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in Mexico
cord-317533-xpfqdeqv	2008	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
cord-319129-o1kzb6dm	2020	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)
cord-320592-wnrzv4hg	2013	
cord-323066-tvguutak	2018	
cord-324012-q2ilk6gs	2019	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
cord-324432-k0g3r1lw	2018	PATIENTS/METHODS: This retrospective study was performed from January 2013 to December 2015 in children and adults with HPIV, detected by multiplex reverse transcription polymerase chain reaction, participating in a community surveillance study of acute respiratory infections (ARIs) in New York City and patients admitted to a tertiary care center in the same neighborhood. The community cohort was derived from the Mobile Surveillance for Acute Respiratory Infections (ARIs) and Influenza-like Illness (ILI) in the Community (MoSAIC) study, a 5-year community-based surveillance ordinal logistic regression demonstrated that increased severity of illness was significantly associated with HPIV-4 and chronic cardiovascular and respiratory conditions in children and with age ≥65 years and chronic respiratory conditions in adults. epidemiology, parainfluenza, respiratory, seasonality, viruses F I G U R E 1 Flowcharts depicting the overall number of respiratory viral panel (RVP) tests ordered which yielded the final number of human parainfluenza virus (HPIV) types in the community cohort (1A) and in hospitalized patients (1B) study in New York City (NYC) that includes 250 households annually.
cord-326039-pnf2xjox	2009	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
cord-328086-ji2emajn	2018	BACKGROUND: Lower respiratory tract illness is a major cause of morbidity and mortality in children worldwide, however, information about the epidemiological and clinical characteristics of LRTIs caused by HMPV and HBoV in China is limited. OBJECTIVES: Human bocavirus (HBoV) and human metapneumovirus (HMPV) are two important viruses for children with lower respiratory tract infections (LRTI). Clinical disease and viral load in children infected with respiratory syncytial virus or human metapneumovirus Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection High viral load of human bocavirus correlates with duration of wheezing in children with severe lower respiratory tract infection High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical significance of different virus load of human bocavirus in patients with lower respiratory tract infection
cord-332057-1vvlzuue	2009	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.
cord-335948-qkfxfmxb	2011	• 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.
cord-336335-spap39b7	2013	
cord-337372-y43prnko	2011	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.
cord-338390-v4ncshav	2009	
cord-343050-1pfqgvie	2015	The results during the first 2 years (2012-2013) provided scientific evidence to (a) support a change to NZ''s vaccination policy for young children due to high influenza hospitalizations in these children; (b) contribute to the revision of the World Health Organization''s case definition for severe acute respiratory illness for global influenza surveillance; and (c) contribute in part to vaccine strain selection using vaccine effectiveness assessment in the prevention of influenza-related consultations and hospitalizations. Over 5 years, we hope this project will shed more light on the burden of influenza and other respiratory pathogens in our study population and subgroups and estimate key epidemiologic parameters such as relative rates of infection, clinical disease, general practice visits and hospitalizations as well as risk factors for illness, effectiveness of vaccination, mechanisms of immunity and monitoring for new influenza viruses with pandemic potential such as A(H7N9) and other emerging viruses (e.g. MERS-CoV) and provide a framework for timely assessment of severity which is essential in an event of emergence of these pathogens.
cord-349330-akwxwfg3	2020	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
cord-350928-vj5qlzpj	2012	Objectives To investigate the prevalence and genetic diversity of HBoV amongst hospitalized patients with acute lower respiratory infection (ALRI) in Cambodia. In patients where HBoV is the only virus detected, the clinical symptoms reported are similar to those occurring as a result of infection with respiratory syncytial virus (RSV) and human metapneumovirus (HMPV), including bronchiolitis, bronchitis, pneumonia and exacerbation of asthma. 20 Here, we report the findings of the first study investigating the prevalence, seasonality, clinical characteristics and the molecular epidemiology of HBoV in amongst an all-ages population of patients hospitalized for acute lower respiratory illness (ALRI) in Cambodia over 3 consecutive years. 5 In this study, ALRI patient samples were screened for HBoV infection using a highly sensitive multiplex PCR assay previously shown to have a lower limit of detection of 4 copies of HBoV DNA ⁄ ll of viral transport medium.
cord-351008-p0n1fdxw	2020	
cord-354151-psog34u3	2015