Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 38 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 10784 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 49 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 37 ILI 10 influenza 4 virus 4 respiratory 3 child 3 PCR 3 H1N1 2 pilgrim 2 infection 2 household 2 Senegal 2 SARS 2 SARI 2 RSV 2 Hajj 2 China 2 COVID-19 2 CDC 1 ΔILI 1 week 1 table 1 surveillance 1 search 1 pandemic 1 ns1 1 like 1 flu 1 figure 1 fever 1 epidemic 1 cell 1 break 1 Vietnam 1 Venezuela 1 USA 1 URI 1 TCID 1 Singapore 1 SLS 1 RNA 1 PB1-F2 1 Nguyen 1 March 1 MMDS 1 MEM 1 MDCK 1 LAIV 1 Kong 1 Influenza 1 IFI Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 4548 influenza 3946 virus 2390 % 1516 infection 1486 study 1164 case 1095 pandemic 1027 datum 1016 patient 816 vaccine 806 surveillance 796 year 782 cell 680 rate 649 time 592 sample 571 analysis 549 disease 547 model 547 age 544 child 506 strain 505 group 493 week 493 epidemic 485 illness 482 result 474 day 461 number 454 assay 446 symptom 446 population 441 method 417 detection 414 vaccination 402 a 399 system 394 transmission 390 health 379 season 379 gene 356 household 354 figure 344 antibody 338 response 333 risk 326 control 323 adult 321 level 320 period Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 2310 ⁄ 1536 ILI 874 H1N1 419 H5N1 406 Influenza 364 PCR 325 HA 297 NA 265 Hajj 237 Health 222 A 187 C 166 China 162 H3N2 159 RSV 158 RT 158 ARI 149 US 148 CDC 141 Kong 136 Hong 131 pH1N1 130 SARS 127 SARI 123 Table 123 MDCK 122 ICU 117 USA 112 RNA 110 • 109 B 108 HI 106 al 106 United 106 H1N1v 105 WHO 104 LAIV 104 COVID-19 102 States 97 National 97 California 95 H9N2 93 et 93 H1N1pdm 92 CoV-2 92 CI 92 April 91 M 88 March 84 Disease Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 1346 we 568 it 180 they 86 i 64 them 29 us 12 itself 8 themselves 8 one 7 he 4 she 3 you 2 ourselves 1 t202 1 ours 1 mrnas 1 me 1 himself 1 him 1 a-172 1 's Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 10475 be 1678 have 1299 use 682 show 492 include 490 detect 444 compare 427 report 413 base 360 do 357 identify 354 associate 328 find 322 test 316 collect 314 provide 308 follow 296 observe 291 infect 281 increase 281 confirm 253 determine 243 estimate 242 perform 239 suggest 231 obtain 225 develop 224 isolate 210 describe 202 reduce 183 present 182 cause 175 require 174 consider 171 define 169 conduct 161 occur 157 give 156 circulate 154 evaluate 151 make 147 induce 146 accord 142 remain 142 contain 141 age 140 demonstrate 137 see 137 indicate 137 assess Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1213 respiratory 988 not 777 - 738 high 718 viral 668 other 582 human 576 also 568 seasonal 545 clinical 516 more 458 low 420 positive 365 only 351 like 334 first 318 such 317 old 308 however 306 different 296 well 292 severe 289 most 278 early 275 acute 273 non 271 specific 256 similar 216 antiviral 215 real 206 new 202 avian 200 significant 197 respectively 185 as 179 available 178 further 177 public 174 antigenic 173 infectious 169 common 165 less 161 same 158 significantly 153 therefore 153 likely 152 immune 151 average 150 large 150 influenza Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 82 most 79 high 47 least 30 Most 24 good 15 ⁄ 15 low 14 large 6 strong 6 old 6 early 5 great 5 big 4 late 4 common 3 young 3 slow 3 simple 2 small 2 short 2 poor 2 fast 2 close 1 weak 1 steep 1 slight 1 eld 1 bad 1 -which 1 -G4 Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 207 most 90 least 3 well 1 slowest 1 near Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 21 doi.org 3 www.who.int 3 www.r-project.org 2 www.ncbi.nlm.nih.gov 2 www.cdc.gov 2 www 2 sysbio.cvm.msstate.edu 2 github.com 2 dx.doi.org 1 www.worldometers.info 1 www.trialregister.nl 1 www.stat.gov.tw 1 www.seaicrn.org 1 www.prismastatement.org 1 www.plosone.org 1 www.normativasanitaria.it 1 www.netflixprize.com 1 www.nature.com 1 www.jstatsoft.org 1 www.gisaid.org 1 www.geneious.com 1 www.flu.mn 1 www.flu.iss.it 1 www.euroflu.org 1 worldpopulationreview.com 1 sysbio.cvm 1 seb 1 index.baidu.com 1 hcc.unl.edu 1 apps.who.int 1 admin.taiwan.net.tw Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 10 http://doi.org/10.1101/2020.04.06.20039909 9 http://doi.org/10.1101/2020.06.03.20121574 2 http://www.who.int 2 http://www.r-project.org/ 2 http://www 2 http://sysbio.cvm.msstate.edu/IPMiner 2 http://doi.org/10.1101/2020.04.01.20050542 1 http://www.worldometers.info/coronavirus/coronavirus-age-sex-demographics/] 1 http://www.who.int/csr/disease/avian_influenza/ 1 http://www.trialregister.nl 1 http://www.stat.gov.tw/ 1 http://www.seaicrn.org/ 1 http://www.r-project.org 1 http://www.prismastatement.org 1 http://www.plosone.org/ 1 http://www.normativasanitaria.it 1 http://www.netflixprize.com/ 1 http://www.ncbi.nlm.nih.gov/Taxonomy/ 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.nature.com/srep 1 http://www.jstatsoft.org/v08/i21/paper 1 http://www.gisaid.org 1 http://www.geneious.com 1 http://www.flu.mn/eng/index.php?option=com_ 1 http://www.flu.iss.it 1 http://www.euroflu.org 1 http://www.cdc.gov/mmwr/volumes/69/wr/mm6913e2.htm#F1_down] 1 http://www.cdc.gov/flu/weekly/pastreports.htm 1 http://worldpopulationreview.com/states/ 1 http://sysbio.cvm 1 http://seb 1 http://index.baidu.com/v2/#/ 1 http://hcc.unl.edu/main/index.php 1 http://github.com/nytimes/covid-19-data 1 http://github.com/kinsahealth/therm_anomaly_detection 1 http://dx.doi.org/10.1016/j.jinf.2016.09.003 1 http://dx.doi.org/10.1016/j.cmi.2016.11.014 1 http://apps.who.int/flumart/Default?ReportNo=1 1 http://admin.taiwan.net.tw/english/statistics/year.asp? Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 5 virus infected cells 5 virus infected mice 5 virus was not 5 viruses were able 4 case report form 4 cells were then 4 results were consistent 4 study has several 4 viruses did not 3 % tested positive 3 % were influenza 3 cases are not 3 cases was significantly 3 cases were significantly 3 children using parent 3 group had high 3 infection were cancer 3 infections did not 3 influenza include use 3 rate is less 3 rate was higher 3 rate was highest 3 results are mean 3 samples were positive 3 samples were then 3 studies provide complementary 3 study suggest strong 3 study using data 3 study was not 3 vaccine does not 3 virus infected lung 3 viruses isolated characteristics 3 viruses were also 3 viruses were detectable 3 viruses were first 2 % were female 2 % were pilgrims 2 analysis did not 2 case report forms 2 case reporting rate 2 cases were due 2 cases were more 2 cases were not 2 cases were positive 2 cells was much 2 cells were also 2 child has influenza 2 children are less 2 data are available 2 data are important Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 cases are not due 2 patients shows no statistically 1 % having no acute 1 cases are not routinely 1 cases had no risk 1 data are not available 1 data are not normally 1 data do not accurately 1 group are not surprising 1 group do not necessarily 1 groups showed no signs 1 h1n1 have not yet 1 ili did not substantially 1 infection have not well 1 infections did not significantly 1 infections is not clear 1 influenza is not clearly 1 influenza is not notifiable 1 influenza was not significantly 1 models were not sensitive 1 pandemics is not yet 1 patient had no fever 1 patients were not significantly 1 rate was not high 1 results show not only 1 samples showed no amplification 1 samples showed no consistent 1 strains has not yet 1 studies are not always 1 study provides not only 1 study showed no evidence 1 study showed no significant 1 study were not serious 1 time is not only 1 vaccine was not available 1 vaccine was not effective 1 virus are not fully 1 virus did not completely 1 virus has not yet 1 virus is not sufficient 1 viruses are not readily 1 viruses were not available 1 year has not substantially 1 year suggested no seasonal 1 years is not sufficient A rudimentary bibliography -------------------------- id = cord-305460-wln758og author = Alqahtani, Amani Salem title = Tracking Australian Hajj Pilgrims’ Health Behavior before, during and after Hajj, and the Effective Use of Preventive Measures in Reducing Hajj-Related Illness: A Cohort Study date = 2020-05-04 keywords = Hajj; ILI; pilgrim summary = 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). doi = 10.3390/pharmacy8020078 id = cord-275605-mbiojk39 author = Benkouiten, Samir title = Clinical respiratory infections and pneumonia during the Hajj pilgrimage: A systematic review date = 2018-12-04 keywords = Hajj; ILI; pilgrim; respiratory summary = doi = 10.1016/j.tmaid.2018.12.002 id = cord-261282-r1nprlne author = CHUGHTAI, A. A. title = The presence of fever in adults with influenza and other viral respiratory infections date = 2016-10-03 keywords = ILI; fever; influenza summary = [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. doi = 10.1017/s0950268816002181 id = cord-348061-ssjl2w7l author = Chamberlain, Samuel D title = Real-time detection of COVID-19 epicenters within the United States using a network of smart thermometers date = 2020-04-10 keywords = Fig; ILI summary = 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. doi = 10.1101/2020.04.06.20039909 id = cord-002438-b8t4a57r author = Cheng, Wei title = Comparison of Influenza Epidemiological and Virological Characteristics between Outpatients and Inpatients in Zhejiang Province, China, March 2011–June 2015 date = 2017-02-22 keywords = ILI; SARI; influenza summary = 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] . doi = 10.3390/ijerph14020217 id = cord-002451-r7a0orh7 author = Chu, Yanhui title = Effects of school breaks on influenza-like illness incidence in a temperate Chinese region: an ecological study from 2008 to 2015 date = 2017-03-06 keywords = ILI; break summary = doi = 10.1136/bmjopen-2016-013159 id = cord-289017-vwye3pk9 author = Comach, Guillermo title = Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date = 2012-09-11 keywords = ILI; PCR; Venezuela; virus summary = 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] . doi = 10.1371/journal.pone.0044511 id = cord-309860-otx45b8x author = Conway, Nicholas T. title = Clinical Predictors of Influenza in Young Children: The Limitations of “Influenza-Like Illness” date = 2012-09-03 keywords = ILI; child; influenza summary = doi = 10.1093/jpids/pis081 id = cord-345315-y3bdjnhg author = Dai, Yaoyao title = Identifying the outbreak signal of COVID-19 before the response of the traditional disease monitoring system date = 2020-10-01 keywords = COVID-19; China; ILI summary = doi = 10.1371/journal.pntd.0008758 id = cord-288372-48wao8a0 author = Dia, Ndongo title = Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011 date = 2014-04-08 keywords = ILI; Senegal; virus summary = 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. doi = 10.1186/1471-2334-14-189 id = cord-354143-p2ofapbd author = Hellferscee, Orienka title = Enterovirus genotypes among patients with severe acute respiratory illness, influenza‐like illness, and asymptomatic individuals in South Africa, 2012‐2014 date = 2017-07-06 keywords = D68; ILI summary = 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. doi = 10.1002/jmv.24869 id = cord-318856-f0m3wuyj author = Hoogeveen, Martijn J. title = Can pollen explain the seasonality of flu-like illnesses in the Netherlands? date = 2020-10-22 keywords = flu; like; ΔILI summary = doi = 10.1016/j.scitotenv.2020.143182 id = cord-252884-miptf6od author = Jeffery, Diana D. title = Impact of the 2009 Influenza (H1N1) Pandemic on the United States Military Health Care System date = 2013-06-17 keywords = H1N1; ILI summary = 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). doi = 10.7205/milmed-d-12-00345 id = cord-305473-w30hsr4m author = Jiang, Lili title = Detection of viral respiratory pathogens in mild and severe acute respiratory infections in Singapore date = 2017-02-20 keywords = ARI; ILI; PCR summary = To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Our study concurrently assessed the role of routine laboratory diagnostics, and usefulness of the novel PathChip platform as well as ILI case definitions in identifying respiratory virus infection in a community cohort and hospital inpatients from a broad range of age groups (6 to 81, and 20 to 89 years respectively), to reflect what may be encountered in either community or primary care (mild-ARI) as well as tertiary care settings (severe-ARI) in a tropical environment with less distinct seasonal patterns. doi = 10.1038/srep42963 id = cord-325794-lir8ht2i author = Kinar, Y. title = Predicting individual risk for COVID19 complications using EMR data date = 2020-06-05 keywords = COVID-19; ILI summary = 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). doi = 10.1101/2020.06.03.20121574 id = cord-286837-j2sqs20q author = Koetsier, Antonie title = Do Intensive Care Data on Respiratory Infections Reflect Influenza Epidemics? date = 2013-12-31 keywords = ICU; ILI; week summary = 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. doi = 10.1371/journal.pone.0083854 id = cord-341260-vxsbv8t9 author = Loubet, P. title = Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France date = 2017-04-30 keywords = ILI; RSV summary = 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. doi = 10.1016/j.cmi.2016.11.014 id = cord-263353-4mnsjbib author = Maman, Issaka title = Implementation of Influenza-like illness Sentinel Surveillance in Togo date = 2014-09-20 keywords = H1N1; ILI; influenza summary = 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. doi = 10.1186/1471-2458-14-981 id = cord-334424-z7ygy25e author = McCaw, James M title = Household transmission of respiratory viruses – assessment of viral, individual and household characteristics in a population study of healthy Australian adults date = 2012-12-11 keywords = ILI; household; influenza summary = doi = 10.1186/1471-2334-12-345 id = cord-282668-bs634hti author = Niang, Mbayame Ndiaye title = Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses date = 2017-03-22 keywords = ILI; Senegal; infection; respiratory summary = 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 doi = 10.1371/journal.pone.0174287 id = cord-263464-fdosch11 author = Nuvey, Francis Sena title = Evaluation of the sentinel surveillance system for influenza-like illnesses in the Greater Accra region, Ghana, 2018 date = 2019-03-14 keywords = Ghana; ILI; influenza summary = 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. doi = 10.1371/journal.pone.0213627 id = cord-310956-qwe4ndvb author = Qian, Yan‐Hua title = Attempted early detection of influenza A (H1N1) pandemic with surveillance data of influenza‐like illness and unexplained pneumonia date = 2011-04-18 keywords = ILI; influenza; surveillance 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. doi = 10.1111/j.1750-2659.2011.00248.x id = cord-028048-0oqv2jom author = Rguig, Ahmed title = Establishing seasonal and alert influenza thresholds in Morocco date = 2020-06-29 keywords = ILI; MEM; epidemic summary = 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. doi = 10.1186/s12889-020-09145-y id = cord-002753-lvlbwcl0 author = Rogers, Kimberly B. title = Laboratory-based respiratory virus surveillance pilot project on select cruise ships in Alaska, 2013–15() date = 2017-10-06 keywords = Alaska; CDC; ILI summary = doi = 10.1093/jtm/tax069 id = cord-256943-71tnv4lp author = Santillana, Mauricio title = Using Clinicians’ Search Query Data to Monitor Influenza Epidemics date = 2014-08-12 keywords = ILI; search summary = 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. doi = 10.1093/cid/ciu647 id = cord-272878-6f0q661e author = Schnepf, Nathalie title = High Burden of Non-Influenza Viruses in Influenza-Like Illness in the Early Weeks of H1N1v Epidemic in France date = 2011-08-17 keywords = ILI; SLS; respiratory summary = 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). doi = 10.1371/journal.pone.0023514 id = cord-336335-spap39b7 author = Silva, Denise R title = Respiratory viral infections and effects of meteorological parameters and air pollution in adults with respiratory symptoms admitted to the emergency room date = 2013-08-26 keywords = IFI; ILI; SARI; respiratory summary = doi = 10.1111/irv.12158 id = cord-344070-17oac3bg author = Silverman, Justin D title = Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States date = 2020-04-03 keywords = COVID; ILI; SARS summary = doi = 10.1101/2020.04.01.20050542 id = cord-347079-1zbsbcdd author = Silverman, Justin D. title = Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States date = 2020-06-22 keywords = ILI; March; SARS summary = doi = 10.1126/scitranslmed.abc1126 id = cord-264140-5cxzc3z8 author = Tam, Clarence C. title = Epidemiology and Transmission of Respiratory Infections in Thai Army Recruits: A Prospective Cohort Study date = 2018-09-04 keywords = ILI; URI summary = 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. doi = 10.4269/ajtmh.18-0219 id = cord-321704-jozrgcq3 author = Tan, Xin Quan title = Respiratory viral pathogens among Singapore military servicemen 2009 – 2012: epidemiology and clinical characteristics date = 2014-04-15 keywords = FRI; ILI; Singapore summary = doi = 10.1186/1471-2334-14-204 id = cord-312493-wbhji81g author = Tay, Ee Laine title = Exploring a Proposed WHO Method to Determine Thresholds for Seasonal Influenza Surveillance date = 2013-10-11 keywords = ILI; MMDS; influenza summary = 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. doi = 10.1371/journal.pone.0077244 id = cord-254556-1zthrgy1 author = Taylor, Sylvia title = Respiratory viruses and influenza-like illness: Epidemiology and outcomes in children aged 6 months to 10 years in a multi-country population sample date = 2016-09-22 keywords = ILI; RSV; child summary = 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. doi = 10.1016/j.jinf.2016.09.003 id = cord-307674-4fb5xnil author = Weaver, Anne M. title = Household‐level risk factors for secondary influenza‐like illness in a rural area of Bangladesh date = 2017-01-05 keywords = Bangladesh; ILI; household summary = 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. doi = 10.1111/tmi.12820 id = cord-297609-6g39lu1y author = Wertheim, Heiman F L title = Viral and atypical bacterial aetiologies of infection in hospitalised patients admitted with clinical suspicion of influenza in Thailand, Vietnam and Indonesia date = 2015-10-13 keywords = ILI; Nguyen; Vietnam 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. doi = 10.1111/irv.12326 id = cord-338674-tnnd1s57 author = Yin, J Kevin title = Pilot study of influenza vaccine effectiveness in urban Australian children attending childcare date = 2011-06-10 keywords = ILI; child; influenza summary = 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 doi = 10.1111/j.1440-1754.2011.02098.x id = cord-001521-l36f1gp7 author = nan title = Oral and Poster Manuscripts date = 2011-04-08 keywords = A(H1N1; CDC; China; ELISA; H1N1; H3N2; H5N1; H9N2; HAI; Health; Hong; ILI; Influenza; Kong; LAIV; MDCK; PB1-F2; PCR; RNA; TCID; USA; cell; figure; infection; ns1; pandemic; table; virus 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. doi = 10.1111/j.1750-2659.2011.00209.x id = cord-261241-eqf6ame6 author = van Beek, Josine title = Influenza-like Illness Incidence Is Not Reduced by Influenza Vaccination in a Cohort of Older Adults, Despite Effectively Reducing Laboratory-Confirmed Influenza Virus Infections date = 2017-08-15 keywords = ILI; influenza; virus summary = 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 doi = 10.1093/infdis/jix268