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-002438-b8t4a57r	2017	Our study use the surveillance data collected from 16 sentinel hospitals across Zhejiang Province during March 2011 through June 2015, including the demographic information and respiratory specimens from influenza-like illness (ILI) patients and severe acute respiratory illness (SARI) patients. In this study, we used four-year continuous surveillance data to compare the epidemic and virological characteristics of influenza virus between ILI cases and SARI cases in Zhejiang Province. Correlation analysis of weekly influenza virus type/subtype constitution among total positive numbers between influenza-like illness (ILI) and severe acute respiratory illness (SARI). Our findings further demonstrated that young children are vulnerable for both mild and severe respiratory infection, and the low influenza detection rate among 0-4 years age-group in both SARI and ILI patients foreshadow the need of expand the respiratory illness surveillance to more types of pathogens [12, 24] .
cord-002451-r7a0orh7	2017	
cord-002753-lvlbwcl0	2017	
cord-028048-0oqv2jom	2020	The objective of this study was to evaluate the performance of two methods using means and medians to establish thresholds using data from the Moroccan national influenza-like illness (ILI) syndromic surveillance system. Using three seasons of virologic ILI surveillance data (2014/2015 to 2016/2017), we used the MEM method to make calculations using the composite parameter recommended by WHO [20] ; this method estimates the proportion of laboratory-confirmed influenza ILI consultations among all outpatient consultations, or the product of weekly ILI consultations of total outpatient visits and weekly percentage of influenzapositive specimens among respiratory tests. Whichever method is used, analysis of surveillance data will provide information about seasonal thresholds and epidemic curves that may help health care personnel in the clinical management of respiratory illness after the start of influenza season.
cord-252884-miptf6od	2013	3 This outbreak resulted in a mass vaccination program across the United States and initiated a collaborative approach between CHAMPUS (now TRICARE, the system of health care plans for the U.S. Armed Forces and beneficiaries), the Centers for Disease Control and Prevention, and local/ regional health departments. This study exam-ines the burden of disease caused by the 2009 H1N1 pandemic strain on the MHS with respect to health care utilization and associated costs and provides insight into DoD resource management of pandemics compared to previous nonpandemic influenza seasons. Cost data included costs associated with outpatient and emergency department visits, inpatient stays, influenza vaccine administration, and antiviral prescriptions rendered in the military and civilian settings from October 2004 to January 2010 (the last month when full cost data were available at the time of analysis).
cord-254556-1zthrgy1	2016	METHODS: The epidemiology of respiratory viruses among healthy children (6 months to <10 years) with influenza-like illness (ILI) was determined in a population sample derived from an influenza vaccine trial (NCT01051661) in 17 centers in eight countries (Australia, South East Asia and Latin America). As part of a trial of pandemic influenza vaccines, which included 1 year of prospective, active, community-based surveillance for influenza-like illness (ILI) in 17 centers in eight countries, 8 we evaluated the prevalence and incidence of respiratory viruses in children 6 months to less than 10 years of age at first vaccination. Rhinovirus/enterovirus had the highest prevalence and incidence in ILI of all respiratory viruses tested in all countries, followed by influenza, adenovirus, parainfluenza and RSV, coronavirus, hMPV and HBov. The burden of ILI associated with respiratory viruses was considerable, with a high proportion of children being seen by a medical professional and many missing school or daycare.
cord-256943-71tnv4lp	2014	Search query information from a clinician''s database, UpToDate, is shown to predict influenza epidemics in the United States in a timely manner. Google Flu Trends (GFT) demonstrated a link between influenzarelated search query data and the Centers for Disease Control and Prevention''s (CDC) influenza-like Illness (ILI) index [5] . Internet search queries are available much earlier than data from validated traditional surveillance systems and have the potential to provide timely epidemiologic intelligence to inform prevention messaging and healthcare facility staffing decisions. Specifically, we use UpTo-Date''s search query activity related to ILI to design a timely sentinel of influenza incidence in the United States. In this study, we demonstrate that search queries from the Up-ToDate database in conjunction with a dynamic multivariate methodology can be successfully utilized to obtain real-time estimates of influenza incidence in the United States before the release of official reports.
cord-261241-eqf6ame6	2017	The aim of this prospective observational study was to determine the relative contribution of influenza virus and other respiratory pathogens to ILI in older adults (aged ≥60 years) in 2 consecutive seasons in the Netherlands. In 60.8% (2011-2012) and 44.7% (2012-2013) of ILI samples, potential pathogens other than influenza virus were detected (Figure 3 ; Supplementary Table 1 ). Coronaviruses of all 4 common human subtypes (18.2% in 2011-2012 and 11.3% in 2012-2013), human metapneumovirus (hMPV) (20.3% and 3.6%), rhinoviruses (8.4% and 21.1%), respiratory syncytial virus (RSV) (4.9% and 6.5%), and parainfluenza viruses (2.8% and 5.1%) were detected in >5% of the ILI samples in at least 1 season. In this study in a cohort of community-dwelling older adults in the Netherlands, we show that influenza virus was present in 18.9% and 34.2% of ILI cases in 2 consecutive seasons and that influenza vaccination significantly reduced laboratory-confirmed influenza virus infection. Effectiveness of seasonal influenza vaccine in community-dwelling elderly people: a meta-analysis of test-negative design case-control studies
cord-261282-r1nprlne	2016	[13] examined clinical trial data of 3744 adult ILI cases (defined as body temperature 537·8°C or patients subjective feeling of feverishness) and of those 2470 (66%) had laboratory-confirmed influenza. The aim of this study was to compare the rates of fever in adult subjects with confirmed influenza and other respiratory virus infections and examine predictors of fever. Rates of fever in influenza and other viral respiratory infections in this study were lower compared to other studies which report fever in around 50-70% adult cases [1, 5, 13, 15] . Clinical signs and symptoms are less studied for other viral respiratory infections, but available evidence suggests that other respiratory viruses are associated with a lower rate of fever compared to influenza [5, [30] [31] [32] [33] . Compared to children, this study shows that adults are less likely to have fever with a respiratory viral infection, even influenza.
cord-263353-4mnsjbib	2014	The departments involved in this surveillance are the Division of Epidemiology, the National Influenza Reference Laboratory (NIL) hosted by the Institut National d''Hygiène (INH), and the sentinel sites located at the Hôpital de Bè and Military Health Services in the capital city Lomé (Figure 1) . The ILI sentinel surveillance sites were selected based on their accessibility and affordability to patients with low socioeconomic status, the qualifications of medical staff, adequate specimen storage capacity, and an established transportation system to the National Influenza Reference Laboratory (NIL). The study population included every outpatient, between April 2010 to December 2012, presenting at any of the sentinel sites and meeting the ILI case definitions regardless of age or sex and who consented to participate in the surveillance.
cord-263464-fdosch11	2019	We evaluated the ILI surveillance system in the Greater Accra region, Ghana, to assess the system''s attributes and its performance on set objectives. In collaboration with the Ghana Health Service (GHS) and the Ministry of Defense (MOD), it currently operates sentinel surveillance for influenza in 27 sites across all regions in Ghana with support from the U.S. Naval Medical Research Unit No. 3 (NAMRU-3), Centers for Disease Control and Prevention (CDC) and WHO [8] . We found that data on patients meeting the ILI case definition (S2 Table) from the sentinel sites are collected together with nasopharyngeal or oropharyngeal specimen. Our study provides evidence, that the ILI sentinel surveillance system in the Greater Accra Region (GAR), Ghana, is only partially meeting its objectives because it did not have thresholds for alerting the health system and does not perform antiviral resistance testing.
cord-264140-5cxzc3z8	2018	Our results emphasize the need for improved infection prevention and control in military environments, given the high burden of illness and potential for intense transmission of respiratory pathogens. 2 Studies among military recruits have found high rates of illness and infection with respiratory viruses. 9, 10 Studies in military populations can provide valuable information regarding the epidemiology and transmission of respiratory infections in adults because of the availability of well-defined populations that can be followed up over time. 12, 13 We also tested acute samples (from both camps) and the routine enrolment and follow-up specimens (from one camp) using a multiplex real-time PCR assay comprising 33 bacterial, viral, and fungal targets (FTD33 kit; Fast Track Diagnostics, Esch-sur-Alzette, Luxembourg). A quarter of URI cases in our study were prescribed broad-spectrum antibiotics, of whom 50% were more likely to have infections caused by viral pathogens based on multiplex PCR results.
cord-272878-6f0q661e	2011	In the two academic hospitals, Saint-Louis hospital (SLS) in Paris and Tours hospital (TRS), influenza-like illness (ILI) was defined as a patient suffering from at least one general symptom (fever above 38uC, asthenia, myalgia, shivers or headache) and one respiratory symptom (cough, dyspnoea, rhinitis or pharyngitis), in agreement with the guidelines from the French Institut de Veille Sanitaire (InVS), a governmental institution responsible for surveillance and alert in all domains of public health [12] . Two hundred and twelve were positive for non influenza pathogens (189 single infections and 23 mixed infections with two, three or four viruses) and three additional single infections by influenza A were identified in SLS, including two by pandemic H1N1v and one by seasonal H3N2, as determined after molecular typing (data not shown). As RHV was the most frequent aetiology in ILI, we also compared clinical symptoms observed in patients with a single infection by RHV or by H1N1v (data not shown).
cord-275605-mbiojk39	2018	
cord-282668-bs634hti	2017	In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenzalike Illness cases. From January 2012 to December 2015 we collected specimens (nasal-pharyngeal and oral-pharyngeal swabs) and surveillance data for influenza and other viral respiratory pathogens from outpatients presenting with influenza-like-illness (ILI) at different sentinel sites in Senegal. So the circulation of such HAdV genome types in Senegal emphasizes the need to reinforce HAdV surveillance, especially in hospitalized patients, by including HAdV genome detection and genotyping in the documentation of severe respiratory infections. Molecular epidemiology of human adenovirus isolated from children hospitalized with acute respiratory infection in São Paulo, Brazil
cord-286837-j2sqs20q	2013	METHODS: We calculated the time lag and correlation between ILI incidence (from ILI sentinel surveillance, based on general practitioners (GP) consultations) and percentages of ICU admissions with a respiratory infection (from the Dutch National Intensive Care Registry) over the years 2003–2011. In the season 2009/2010 as well as in the season 2010/2011, ILI incidence as measured by GP sentinel practices, reached the epidemic threshold of 5.1 consultations per 10.000 enlisted patients at a time when already more than 100 patients had been hospitalized, with several ICU admissions and deaths from laboratory confirmed Influenza (National Institute for Public Health and the Environment, unpublished surveillance data). In our study we built three additive Poisson GEE regression models with ICU data to predict the incidence of ILI patients, thereby detecting influenza epidemics and aimed at detecting opportunities for enhancing the current national surveillance method.
cord-288372-48wao8a0	2014	The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. Viral aetiology, prevalence and diversity data in people with influenza like illness (ILI) and/or acute respiratory illness (ARI) in Africa, (especially in West Africa), are scarce and often limited to the influenza viruses'' infection. For example in the United States alone, up to 40% of non-pneumonic lower respiratory illnesses in the elderly have been associated with respiratory viral infection [10] , and an estimated 54,000 deaths annually have been attributed to the influenza and respiratory syncytial viruses (RSV) [11] . The present study is the first description of the etiology of respiratory viruses associated with patients with ILI in a cohort of elderly people in the West African context.
cord-289017-vwye3pk9	2012	CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Recent prospective studies, which utilized more sensitive methods for detecting respiratory viruses such as multiplex polymerase chain reaction (PCR), have similarly demonstrated that the highest rates of viral respiratory infection occur among children and the frequency of infection tends to decrease with age due to increasing acquired immunity [8] . On the other hand, the percentage of influenza viruses (not including pH1N1) detected in our study during a similar period of time, but in different years accounted for the significant differences found in both studies: a) the collection, preservation and further processing of respiratory samples, and b) the type of cells and IFA reagents used for virus isolation and identification. In contrast, a prospective study of ILI among Brazilian adults, which utilized viral isolation and RT-PCR testing on respiratory samples, detected rhinoviruses in 19.6% of patients [14] .
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-305460-wln758og	2020	This study assessed Australian Hajj pilgrims'' knowledge, attitude and practices throughout their Hajj journey to understand their health behaviors, use of preventative measures and development of illness symptoms. Similarly, hand hygiene and other preventative practices also vary among pilgrims, making it more difficult for researchers to ascertain whether vaccine uptake and health behaviors overall have improved in comparison to previous years or studies [5] [6] [7] . To address these research gaps, we conducted a cohort study to explore Australian Hajj pilgrims'' knowledge about the risk of diseases during Hajj, assess their preparedness and use of preventive measures at three times points (before, during and after Hajj) , investigate the factors affecting their preventive health behavior, and determine the number of reported infections during and after Hajj. This cohort study captured and compared the health behavior, knowledge, attitudes and practices of Australian Hajj pilgrims regarding preventative measures against communicable diseases throughout the course of Hajj travel (before, during and after the journey).
cord-305473-w30hsr4m	2017	To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Our study concurrently assessed the role of routine laboratory diagnostics, and usefulness of the novel PathChip platform as well as ILI case definitions in identifying respiratory virus infection in a community cohort and hospital inpatients from a broad range of age groups (6 to 81, and 20 to 89 years respectively), to reflect what may be encountered in either community or primary care (mild-ARI) as well as tertiary care settings (severe-ARI) in a tropical environment with less distinct seasonal patterns.
cord-307674-4fb5xnil	2017	It is, therefore, important to identify and address modifiable factors associated with secondary ILI, defined as ILI in another household compound member after the first patient has been identified, at the household level in Bangladesh and other highburden, low-income settings in order to design interventions to reduce transmission. We examined the following household-level characteristics as potential risk factors for secondary ILI: crowding, building materials of homes, exposure to indoor air pollution, presence of handwashing materials, water source, latrine quality and sharing, education of the household respondent and household wealth status. We assessed indicators of exposure to indoor air pollution, such as frequency of index-case patients with influenza-like illness (ILI) identified at hospitals, health complexes, pharmacies, tested for influenza (N = 377) Household compound members of index-case patients recruited, baseline questionnaire given (N = 3159) Smoking in the home and use of shared latrines are associated with an increased risk of secondary influenza-like illness in households in this study.
cord-309860-otx45b8x	2012	
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-312493-wbhji81g	2013	For all datasets, including the composite datasets, we aligned data on the median week of peak influenza or ILI activity and assigned three threshold levels: seasonal threshold, determined by inspection; and two intensity thresholds termed average and alert thresholds, determined by calculations of means, medians, confidence intervals (CI) and percentiles. Comparison of thresholds revealed variations in defining the start of a season but good agreement in describing the end and intensity of influenza seasons, except in hospital admissions data after the pandemic year of 2009. Four independent surveillance data sources were used: (i) the Victorian GPSS, (ii) sentinel data from the Melbourne Medical Deputising Service (MMDS), (iii) routine laboratoryconfirmed influenza (LAB data) from the Victorian Infectious Diseases Reference Laboratory (VIDRL) and the (iv) Victoria Admitted Episode Dataset (VAED) for hospital admissions. Comparison of thresholds derived from different datasets revealed variations in defining the start of a season but relatively good agreement in describing the end and intensity of influenza seasons, except in the hospital data after the pandemic year.
cord-318856-f0m3wuyj	2020	
cord-321704-jozrgcq3	2014	
cord-325794-lir8ht2i	2020	the use of an existing EMR-based model for predicting complications due to influenza combined with available epidemiological data to create a model that identifies individuals at high risk to develop complications due to COVID-19 and b. The available dataset for COVID-based model included a total 2137 SARS-CoV-2 positive individuals who were either not hospitalized (n=1658), or hospitalized and marked as mild (n=332), or as having moderate (n=83) or severe (n=64) complications. Here, we describe two approaches and tools to assess the individual risk of developing COVID-19 complications based on medical records: a model developed by combining a machinelearning approach for influenza-like illness (ILI) to be used as a proxy model for COVID-19 and a second model using data on COVID-19 patients. As an initial prior we used the information based on COVID-19 mortality available from China [https://www.worldometers.info/coronavirus/coronavirus-age-sex-demographics/] as proxy for complications probabilities (appendix table 1).
cord-334424-z7ygy25e	2012	
cord-336335-spap39b7	2013	
cord-338674-tnnd1s57	2011	This study explored methods of follow up and sample collection for a proposed randomised controlled trial of influenza vaccination in children attending childcare. Efficacious influenza vaccines have been available for over 50 years, and yet, routine use in childhood remains the What is already known on this topic 1 Children in childcare are more likely to contract influenza and transmit infection to their siblings, parents, extended families and child-care workers. 3 Evidence for the effectiveness of influenza vaccine in children aged less than 24 months is limited and high quality, appropriately powered, randomised controlled trials are needed. A population-based surveillance study showed that less than 10% of hospitalised children aged Յ59 months with ILI had confirmed influenza infection. Studies of the 1996-1997 inactivated influenza vaccine among children attending day care: immunologic response, protection against infection, and clinical effectiveness
cord-341260-vxsbv8t9	2017	title: Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France Abstract Objectives The aim of this study was to analyse characteristics and outcome of respiratory syncytial virus (RSV) infection in adults hospitalized with influenza-like illness (ILI). We analysed cases of laboratory-confirmed RSV infection during three consecutive influenza seasons (2012/13, 2013/14 and 2014/ 15), in a post hoc analysis of patients hospitalized with ILI in the FLUVAC study. Covariates with a p value <0.2 in univariate analysis were tested in the multivariate model, namely age (considered as a continuous variable), chronic heart disease, chronic respiratory disease, cancer (solid and haematological malignancies), diabetes, chronic renal failure, immunosuppressive treatment, RSV infection, influenza virus infection, and influenza vaccination. Respiratory syncytial virus was associated with significant morbidity: the median length of hospital stay was 9 days; 15% (8/ 53) of RSV-infected patients were admitted to the intensive care unit, and 8% (4/53) died.
cord-344070-17oac3bg	2020	
cord-345315-y3bdjnhg	2020	
cord-347079-1zbsbcdd	2020	
cord-348061-ssjl2w7l	2020	Leveraging data from a geospatial network of thermometers encompassing more than one million users across the US, we identify anomalies by generating accurate, county-specific forecasts of seasonal ILI from a point prior to a potential outbreak and comparing real-time data to these expectations. is the (which was not peer-reviewed) The copyright holder for this preprint Here, we outline a method to identify illness incidence anomalies using a geospatial network of smart thermometers, where county-scale anomalies are flagged in real-time. Our anomaly detection method follows three core steps: 1) Generate county-specific forecasts of influenza-like illness (ILI) from a time point prior to a potential outbreak, 2) compare real-time thermometer-derived ILI to forecast expectations when new data is aggregated daily, and 3) flag anomalous ILI values by evaluating the probability that the current signal is driven by regular seasonal influenza.
cord-354143-p2ofapbd	2017	Enteroviruses can cause outbreaks of severe acute respiratory illness (SARI) and EV‐A, ‐B, ‐C, and ‐D species have different pathogenic profiles and circulation patterns. We observed a high number of enterovirus genotypes in patients with respiratory illness and in controls from South Africa with no disease association of EV species with disease severity. We identified high diversity among EVs circulating in hospitalized South African patients, 25 however it is unknown whether different EV genotypes are associated with mild or severe respiratory illness in South Africa. Unconditional exact logistic regression was used to assess the association of EV species with disease severity among patients with mild (ILI) or severe illness (SARI) using asymptomatic individuals as control group. 9, 31 The E30 strains identified in this study clustered together (designated genotype k) although no differences were observed between viruses from SARI compared to ILI cases.