# ent

id: cord-286837-j2sqs20q
type: WORK_OF_ART
entity:
  the Acute Physiology and Chronic Health Evaluation II APACHE II 7 reason for ICU admission diagnosis


id: cord-264140-5cxzc3z8
type: PROTEIN
entity:
  H influenzae type B 82 3 H influenzae non type B 31 5 Klebsiella pneumoniae 14 6 Staphylococcus aureus 8 5 and Streptococcus pneumoniae 8 5


id: cord-288372-48wao8a0
type: PROTEIN
entity:
  PIV3 6 PIV4 8 7 7 human respiratory syncytial viruses 6 RSV A and 1 RSV B 4 7 6 coronaviruses 4 coronaviruses NL63


id: cord-288372-48wao8a0
type: TAXON
entity:
  human respiratory syncytial virus B human adenovirus human metapneumovirus human coronavirus 229E human coronavirus NL63 human coronavirus OC43 human


id: cord-288372-48wao8a0
type: DISEASE
entity:
  influenza A virus influenza B virus human respiratory syncytial virus A human respiratory syncytial virus B human adenovirus human metapneumovirus human coronavirus 229E human coronavirus NL63 human coronavirus OC43 human parainfluenza virus 1 2 3 4 human rhinovirus A B C human enterovirus and human bocavirus Reactions


id: cord-288372-48wao8a0
type: DISEASE
entity:
  influenza B viruses influenza viruses represented 45 67 150 of viruses detected This influenza detection rate was expected as the enrollment of patients was directed towards patients with ILI


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


id: cord-282668-bs634hti
type: ORG
entity:
  Acute Respiratory Infections in Hospitalized Children in Southern China Molecular Typing and Epidemiology Profiles of Human Adenovirus Infection


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


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


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


id: cord-261241-eqf6ame6
type: DISEASE
entity:
  influenza virus coronaviruses rhinoviruses human metapneumovirus respiratory syncytial virus parainfluenza viruses


id: cord-307674-4fb5xnil
type: ORG
entity:
  Government of the People s Republic of Bangladesh Global Affairs Canada Swedish International Development Cooperation Agency


id: cord-305460-wln758og
type: ORG
entity:
  the Hajj Exploring Australian Hajj Tour Operators Knowledge and Practices Regarding Pilgrims Health Risks A Qualitative Study Hajj Research Team Influenza Vaccination


id: cord-305460-wln758og
type: ORG
entity:
  Abubakar Baaba A Assessment of Knowledge Attitude and Practice towards Prevention of Respiratory Tract Infections


id: cord-263353-4mnsjbib
type: DISEASE
entity:
  influenza type B Influenza viruses circulated throughout the year with the positivity rate peaking around the months of January May and again in October corresponding respectively to the dry dusty harmattan season and the long and then the short raining season The pandemic A H1N1 pdm09 was the predominantly circulating strain in 2010 while influenza B


id: cord-263353-4mnsjbib
type: DISEASE
entity:
  influenza A virus and 100 10 5 for influenza B virus Table 2 Table 2 The proportion of influenza positive


id: cord-272878-6f0q661e
type: ORG
entity:
  South Eastern France Rapid Detection of Respiratory Tract Viral Infections and Coinfections in Patients


id: cord-321704-jozrgcq3
type: DISEASE
entity:
  Coronavirus HKU1 CoV HKU1 Parainfluenza 1 hPIV 1 hPIV 2 hPIV 4 Influenza A H1N1 the prepandemic strain respiratory syncytial virus A RSV A RSV B CoV


id: cord-338674-tnnd1s57
type: DNA
entity:
  human rhinoviruses HRV 28 influenza A influenza B RSV adenoviruses HMPV parainfluenza viruses I II and III 29 bocavirus 30 hPyV WU hPyV KI 31


id: cord-341260-vxsbv8t9
type: PROTEIN
entity:
  Mal H Brugiere O Papo T Goulenok T Boisseau M Jouenne R Alexandra J F Raynaud Simon A Lilamand M Cloppet Fontaine A Becheur K Pelletier A L Fidouh N Ralaimazava P Beaumale F Costa Y Munier E Betend F Amour S Loeffert S Francourt K Merle C Letois F Géraud P Driss V Noslier S Ray M Sebbane M Konaté A Bourdin A Klouche K Léglise M S Couve Deacon E Fruit D Fenerol C Vallejo C Jouneau S Lainé F Thébault E Fillatre P Le Pape C Beuzit L Chau F Goderel I title Clinical


id: cord-341260-vxsbv8t9
type: ORG
entity:
  Cochin Hospital Paris Bichat Hospital Paris Pontchaillou Hospital Rennes Limoges Hospital University


id: cord-341260-vxsbv8t9
type: CHEMICAL
entity:
  Houhou N Lagathu G Rogez S Alain S Duval X Galtier F Postil D Tattevin P Vanhems P Carrat F Lina B Launay O Seddik K


id: cord-341260-vxsbv8t9
type: DISEASE
entity:
  chronic heart disease chronic respiratory disease cancer solid and haematological malignancies diabetes chronic renal failure


id: cord-252884-miptf6od
type: ORG
entity:
  The National Strategy for Pandemic Influenza Implementation Plan NSPIIP Armed Forces Health Surveillance Center AFHSC Pertussis


id: cord-289017-vwye3pk9
type: FAC
entity:
  Enfermedades Virales Instituto de Investigaciones Biomedicas de la Universidad de Carabobo LARDIDEV BIOMED


id: cord-318856-f0m3wuyj
type: WORK_OF_ART
entity:
  Humidity and Latitude Analysis to Predict Potential Spread and Seasonality for COVID Absolute Humidity and Pandemic


id: cord-312493-wbhji81g
type: RNA
entity:
  GPSS 33 to 164 per week for the MMDS 24 to 135 per week for test positive influenza and 28 to 204 per week for influenza admissions Testing for normality of


id: cord-312493-wbhji81g
type: ORG
entity:
  Virological Surveillance Influenza Weekly Updates Centers CDCfor Disease Control and Prevention 2013


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


id: cord-334424-z7ygy25e
type: DISEASE
entity:
  influenza viruses rhinoviruses HRVs adenoviruses respiratory syncytial virus RSV and parainfluenza viruses PIVs


id: cord-334424-z7ygy25e
type: DISEASE
entity:
  human rhinoviruses paramyxoviruses coronaviruses and bocavirus during acute respiratory tract infections


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


# bib

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


id: cord-002438-b8t4a57r
author: Cheng, Wei
date: 2017-02-22
txt: ./txt/cord-002438-b8t4a57r.txt
cache: ./cache/cord-002438-b8t4a57r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5334771/
doi: 10.3390/ijerph14020217
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] .

title:
  Comparison of Influenza Epidemiological and Virological Characteristics between Outpatients and Inpatients in Zhejiang Province, China, March 2011–June 2015

abstract:
  Given the rapid rate of global spread and consequently healthcare costs related to influenza, surveillance plays an important role in monitoring the emerging pandemics in China. However, the characteristics of influenza in Southeast of China haven’t been fully studied. 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. As analysis results, most SARI and ILI patients were in the age group of 0–4 years old (62.38% of ILI and 71.54% of SARI). The respiratory specimens have statistically significantly higher positive rate for influenza among ILI patients than that among SARI patients (p < 0.001). The comparison between ILI patients and SARI patients shows no statistically significantly difference in detecting influenza virus type and influenza A virus subtype. The SARI and ILI patients were found to be positively correlated for overall positive rate (r = 0.63, p < 0.001), the weekly percentage of A(H1N1)pdm09 (r = 0.51, p < 0.001), influenza B virus (r = 0.17, p = 0.013), and A/H3N2 (r = 0.43, p < 0.001) among all the positive numbers. Our study demonstrated that the activities of influenza virus, including its subtypes, had a similar temporal pattern between ILI and SARI cases.


id: cord-002451-r7a0orh7
author: Chu, Yanhui
date: 2017-03-06
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353286/
doi: 10.1136/bmjopen-2016-013159
title:
  Effects of school breaks on influenza-like illness incidence in a temperate Chinese region: an ecological study from 2008 to 2015

abstract:
  OBJECTIVE: To assess the effects of winter/summer school breaks on occurrences of influenza-like illness (ILI). METHODS: We jointly analysed ILI surveillance data with the timing of school breaks in a temperate district in Beijing, China from 2008 to 2015. ILI incidence rate ratios (IRRs) of schoolchildren (5–14 and 15–24 years of age) to adults (25–59 and >60 years of age) were used to measure the age shift of ILI incidence before, during and after the 4-week winter/7-week summer breaks. Serfling-based Poisson regression model with adjustment for unmeasured confounders was built to further assess the effect of winter school breaks. RESULTS: ILI incidences were consistently lower during winter breaks than before winter breaks for all age groups. IRRs of younger schoolchildren aged 5–14 to adults were higher during winter school breaks than before breaks, while the opposite was true for the IRRs of older schoolchildren aged 15–24 to adults. Schoolchildren-to-adults IRRs during summer breaks were significantly lower than before or after school breaks (p<0.001). CONCLUSIONS: Both winter and summer breaks were associated with reductions of ILI incidences among schoolchildren and adults. Our study contributes additional evidence on the effects of school breaks on ILI incidence, suggesting school closure could be effective in controlling influenza transmission in developing countries.


id: cord-002753-lvlbwcl0
author: Rogers, Kimberly B.
date: 2017-10-06
url: https://academic.oup.com/jtm/article-pdf/24/6/tax069/21576761/tax069.pdf
doi: 10.1093/jtm/tax069
title:
  Laboratory-based respiratory virus surveillance pilot project on select cruise ships in Alaska, 2013–15()

abstract:
  BACKGROUND: Influenza outbreaks can occur among passengers and crews during the Alaska summertime cruise season. Ill travellers represent a potential source for introduction of novel or antigenically drifted influenza virus strains to the United States. From May to September 2013–2015, the Alaska Division of Public Health, the Centers for Disease Control and Prevention (CDC), and two cruise lines implemented a laboratory-based public health surveillance project to detect influenza and other respiratory viruses among ill crew members and passengers on select cruise ships in Alaska. METHODS: Cruise ship medical staff collected 2–3 nasopharyngeal swab specimens per week from passengers and crew members presenting to the ship infirmary with acute respiratory illness (ARI). Specimens were tested for respiratory viruses at the Alaska State Virology Laboratory (ASVL); a subset of specimens positive for influenza virus were sent to CDC for further antigenic characterization. RESULTS: Of 410 nasopharyngeal specimens, 83% tested positive for at least one respiratory virus; 71% tested positive for influenza A or B virus. Antigenic characterization of pilot project specimens identified strains matching predominant circulating seasonal influenza virus strains, which were included in the northern or southern hemisphere influenza vaccines during those years. Results were relatively consistent across age groups, recent travel history, and influenza vaccination status. Onset dates of illness relative to date of boarding differed between northbound (occurring later in the voyage) and southbound (occurring within the first days of the voyage) cruises. CONCLUSIONS: The high yield of positive results indicated that influenza was common among passengers and crews sampled with ARI. This finding reinforces the need to bolster influenza prevention and control activities on cruise ships. Laboratory-based influenza surveillance on cruise ships may augment inland influenza surveillance and inform control activities. However, these benefits should be weighed against the costs and operational limitations of instituting laboratory-based surveillance programs on ships.


id: cord-028048-0oqv2jom
title: Establishing seasonal and alert influenza thresholds in Morocco
author: Rguig, Ahmed
date: 2020-06-29
txt: ./txt/cord-028048-0oqv2jom.txt
cache: ./cache/cord-028048-0oqv2jom.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7323370/
doi: 10.1186/s12889-020-09145-y
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.

abstract:
  BACKGROUND: Several statistical methods of variable complexity have been developed to establish thresholds for influenza activity that may be used to inform public health guidance. We compared the results of two methods and explored how they worked to characterize the 2018 influenza season performance–2018 season. METHODS: Historical data from the 2005/2006 to 2016/2018 influenza season performance seasons were provided by a network of 412 primary health centers in charge of influenza like illness (ILI) sentinel surveillance. We used the WHO averages and the moving epidemic method (MEM) to evaluate the proportion of ILI visits among all outpatient consultations (ILI%) as a proxy for influenza activity. We also used the MEM method to evaluate three seasons of composite data (ILI% multiplied by percent of ILI with laboratory-confirmed influenza) as recommended by WHO. RESULTS: The WHO method estimated the seasonal ILI% threshold at 0.9%. The annual epidemic period began on average at week 46 and lasted an average of 18 weeks. The MEM model estimated the epidemic threshold (corresponding to the WHO seasonal threshold) at 1.5% of ILI visits among all outpatient consultations. The annual epidemic period began on week 49 and lasted on average 14 weeks. Intensity thresholds were similar using both methods. When using the composite measure, the MEM method showed a clearer estimate of the beginning of the influenza epidemic, which was coincident with a sharp increase in confirmed ILI cases. CONCLUSIONS: We found that the threshold methodology presented in the WHO manual is simple to implement and easy to adopt for use by the Moroccan influenza surveillance system. The MEM method is more statistically sophisticated and may allow a better detection of the start of seasonal epidemics. Incorporation of virologic data into the composite parameter as recommended by WHO has the potential to increase the accuracy of seasonal threshold estimation.


id: cord-252884-miptf6od
title: Impact of the 2009 Influenza (H1N1) Pandemic on the United States Military Health Care System
author: Jeffery, Diana D.
date: 2013-06-17
txt: ./txt/cord-252884-miptf6od.txt
cache: ./cache/cord-252884-miptf6od.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.7205/milmed-d-12-00345
doi: 10.7205/milmed-d-12-00345
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).

abstract:
  Background: During public health emergencies, the Military Health System experiences challenges similar to those across the U.S. public and private health systems. This study explored how 1 such event, the 2009/2010 influenza (H1N1) pandemic, impacted health care utilization and associated costs in the Military Health System. Methods: Data from the Military Data Repository were used to examine diagnoses, claims data, and dates of services with respect to military or civilian care during 2004–2009/2010 influenza seasons. Comparison analysis was conducted through two-tailed t-tests and regression models. Results: There was a significant increase in inpatient and outpatient health care utilization during the 2009/2010 H1N1 pandemic year, most markedly for emergency department visits. The 2009/2010 H1N1 pandemic cost the Department of Defense $100 million compared to influenza-related health care costs incurred in previous influenza seasons. Highest health care utilization costs were found in children less than age 5. The greatest cost burden was attributed to immunizations for active duty personnel delivered at military facilities. Conclusion: Annual trend analysis of costs and health care utilization would be helpful to plan and resource emerging influenza pandemics and to identify subgroups at greatest risk for contracting influenza.


id: cord-254556-1zthrgy1
author: Taylor, Sylvia
date: 2016-09-22
txt: ./txt/cord-254556-1zthrgy1.txt
cache: ./cache/cord-254556-1zthrgy1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27667752/
doi: 10.1016/j.jinf.2016.09.003
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.

title:
  Respiratory viruses and influenza-like illness: Epidemiology and outcomes in children aged 6 months to 10 years in a multi-country population sample

abstract:
  BACKGROUND: Better population data on respiratory viruses in children in tropical and southern hemisphere countries is needed. 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). Active surveillance for ILI was conducted for approximately 1 year (between February 2010 and August 2011), with PCR analysis of nasal and throat swabs. RESULTS: 6266 children were included, of whom 2421 experienced 3717 ILI episodes. Rhinovirus/enterovirus had the highest prevalence (41.5%), followed by influenza (15.8%), adenovirus (9.8%), parainfluenza and respiratory syncytial virus (RSV) (both 9.7%), coronavirus (5.6%), human metapneumovirus (5.5%) and human bocavirus (HBov) (2.0%). Corresponding incidence per 100 person-years was 29.78, 11.34, 7.03, 6.96, 6.94, 4.00, 3.98 and 1.41. Except for influenza, respiratory virus prevalence declined with age. The incidence of medically-attended ILI associated with viral infection ranged from 1.03 (HBov) to 23.69 (rhinovirus/enterovirus). The percentage of children missing school or daycare ranged from 21.4% (HBov) to 52.1% (influenza). CONCLUSIONS: Active surveillance of healthy children provided evidence of respiratory illness burden associated with several viruses, with a substantial burden in older children.


id: cord-256943-71tnv4lp
title: Using Clinicians’ Search Query Data to Monitor Influenza Epidemics
author: Santillana, Mauricio
date: 2014-08-12
txt: ./txt/cord-256943-71tnv4lp.txt
cache: ./cache/cord-256943-71tnv4lp.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/cid/ciu647
doi: 10.1093/cid/ciu647
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.

abstract:
  Search query information from a clinician's database, UpToDate, is shown to predict influenza epidemics in the United States in a timely manner. Our results show that digital disease surveillance tools based on experts' databases may be able to provide an alternative, reliable, and stable signal for accurate predictions of influenza outbreaks.


id: cord-261241-eqf6ame6
author: van Beek, Josine
date: 2017-08-15
txt: ./txt/cord-261241-eqf6ame6.txt
cache: ./cache/cord-261241-eqf6ame6.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/infdis/jix268
doi: 10.1093/infdis/jix268
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

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

abstract:
  BACKGROUND: Data on the relative contribution of influenza virus and other respiratory pathogens to respiratory infections in community-dwelling older adults (≥60 years) are needed. METHODS: A prospective observational cohort study was performed in the Netherlands during 2 winters. Nasopharyngeal and oropharyngeal swabs were collected during influenza-like illness (ILI) episodes and from controls. Viruses and bacteria were identified by multiplex ligation–dependent probe amplification assay and conventional bacterial culture. RESULTS: The ILI incidence in the consecutive seasons was 7.2% and 11.6%, and influenza virus caused 18.9% and 34.2% of ILI episodes. Potential pathogen were detected in 80% of the ILI events with influenza virus, coronaviruses, rhinoviruses, human metapneumovirus, respiratory syncytial virus, parainfluenza viruses, and Haemophilus influenzae being the most common. Influenza vaccination reduced influenza virus infection by 73% (95% confidence interval [CI], 26%–90%) and 51% (95% CI, 7%–74%) in ILI patients. However, ILI incidence was similar between vaccinated (7.6% and 10.8%) and nonvaccinated (4.2% and 11.4%) participants in 2011–2012 and 2012–2013, respectively (P > .05). CONCLUSIONS: Influenza virus is a frequent pathogen in older adults with ILI. Vaccination reduces the number of influenza virus infections but not the overall number of ILI episodes: other pathogens fill the gap. We suggest the existence of a pool of individuals with high susceptibility to respiratory infections. CLINICAL TRIALS REGISTRATION: NTR3386.


id: cord-261282-r1nprlne
title: The presence of fever in adults with influenza and other viral respiratory infections
author: CHUGHTAI, A. A.
date: 2016-10-03
txt: ./txt/cord-261282-r1nprlne.txt
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extension: .txt
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url: https://www.ncbi.nlm.nih.gov/pubmed/27691995/
doi: 10.1017/s0950268816002181
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.

abstract:
  We compared the rates of fever in adult subjects with laboratory-confirmed influenza and other respiratory viruses and examined the factors that predict fever in adults. Symptom data on 158 healthcare workers (HCWs) with a laboratory-confirmed respiratory virus infection were collected using standardized data collection forms from three separate studies. Overall, the rate of fever in confirmed viral respiratory infections in adult HCWs was 23·4% (37/158). Rates varied by virus: human rhinovirus (25·3%, 19/75), influenza A virus (30%, 3/10), coronavirus (28·6%, 2/7), human metapneumovirus (28·6%, 2/7), respiratory syncytial virus (14·3%, 4/28) and parainfluenza virus (8·3%, 1/12). Smoking [relative risk (RR) 4·65, 95% confidence interval (CI) 1·33–16·25] and co-infection with two or more viruses (RR 4·19, 95% CI 1·21–14·52) were significant predictors of fever. Fever is less common in adults with confirmed viral respiratory infections, including influenza, than described in children. More than 75% of adults with a viral respiratory infection do not have fever, which is an important finding for clinical triage of adult patients with respiratory infections. The accepted definition of ‘influenza-like illness’ includes fever and may be insensitive for surveillance when high case-finding is required. A more sensitive case definition could be used to identify adult cases, particularly in event of an emerging viral infection.


id: cord-263353-4mnsjbib
title: Implementation of Influenza-like illness Sentinel Surveillance in Togo
author: Maman, Issaka
date: 2014-09-20
txt: ./txt/cord-263353-4mnsjbib.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2458-14-981
doi: 10.1186/1471-2458-14-981
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.

abstract:
  BACKGROUND: The emergence of avian influenza A/H5N1 in 2003 as well as the pandemic influenza A (H1N1) pdm09 highlighted the need to establish influenza sentinel surveillance in Togo. The Ministry of Health decided to introduce Influenza to the list of diseases with epidemic potential. By April 2010, Togo was actively involved in influenza surveillance. This study aims to describe the implementation of ILI surveillance and results obtained from April 2010 to December 2012. METHODS: Two sites were selected based on their accessibility and affordability to patients, their adequate specimen storage capacity and transportation system. Patients with ILI presenting at sentinel sites were enrolled by trained medical staff based on the World Health Organization (WHO) case definitions. Oropharyngeal and nasopharyngeal samples were collected and they were tested at the National Influenza Reference Laboratory using a U.S. Centers for Disease Control and Prevention (CDC) validated real time RT-PCR protocol. Laboratory results and epidemiological data were reported weekly and shared with all sentinel sites, Ministry of Health, Division of Epidemiology, WHO and CDC/NAMRU-3. RESULTS: From April 2010 to December 2012, a total of 955 samples were collected with 52% of the study population aged between 0 and 4 years. Of the 955 samples, 236 (24.7%) tested positive for influenza viruses; with 136 (14.2%) positive for influenza A and 100 (10.5%) positive for influenza B. The highest influenza positive percentage (30%) was observed in 5–14 years old and patients aged 0–4 and >60 years had the lowest percentage (20%). Clinical symptoms such as cough and rhinorrhea were associated more with ILI patients who were positive for influenza type A than influenza type B. Influenza viruses circulated throughout the year with the positivity rate peaking around the months of January, May and again in October; corresponding respectively to the dry-dusty harmattan season and the long and then the short raining season. The pandemic A (H1N1) pdm09 was the predominantly circulating strain in 2010 while influenza B was the predominantly circulating strain in 2011. The seasonal A/H3N2 was observed throughout 2012 year. CONCLUSIONS: This study provides information on influenza epidemiology in the capital city of Togo.


id: cord-263464-fdosch11
author: Nuvey, Francis Sena
date: 2019-03-14
txt: ./txt/cord-263464-fdosch11.txt
cache: ./cache/cord-263464-fdosch11.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0213627
doi: 10.1371/journal.pone.0213627
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.

title:
  Evaluation of the sentinel surveillance system for influenza-like illnesses in the Greater Accra region, Ghana, 2018

abstract:
  BACKGROUND: Influenza-like Illness (ILI) is a medical diagnosis of possible influenza or another respiratory illness with a common set of symptoms. The deaths of four schoolchildren, during a pandemic influenza outbreak in December 2017 in Ghana, raised doubts about the ILI surveillance system’s performance. We evaluated the ILI surveillance system in the Greater Accra region, Ghana, to assess the system’s attributes and its performance on set objectives. METHODS: CDC guidelines were used to evaluate the data of the ILI surveillance system between 2013 and 2017. We interviewed the surveillance personnel on the system’s description and operation. Additionally, routinely entered ILI data from the National Influenza Center provided by the six sentinel sites in Accra was extracted. We sampled and reviewed 120 ILI case-investigation forms from these sites. Surveillance activities were examined on system’s performance indicators, each being scored on a scale of 1 to 3 (poorest to best performance). RESULTS: All population and age groups were under ILI surveillance over the period evaluated. Overall, 2948 suspected case-patients, including 392 (13.3%) children under-five were reported, with 219 being positive for influenza virus (Predictive value positive = 7.4%). The predominant influenza subtype was H3N2, recorded in 90 (41.1%) of positive case-patients. The system only met two out of its four objectives. None of the six sentinel sites consistently met their annual 260 suspected case-detection quota. Samples reached the laboratory on average 48 hours after collection and results were disseminated within 7 days. Of 120 case-investigation forms sampled, 91 (76.3%) were completely filled in. CONCLUSIONS: The ILI surveillance system in the Greater Accra region is only partially meeting its objectives. While it is found to be sensitive, representative and timely, the data quality was sub-optimal. We recommend the determination of thresholds for alert and outbreak detection and ensuring that sentinel sites meet their weekly case-detection targets.


id: cord-264140-5cxzc3z8
author: Tam, Clarence C.
date: 2018-09-04
txt: ./txt/cord-264140-5cxzc3z8.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30182916/
doi: 10.4269/ajtmh.18-0219
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.

title:
  Epidemiology and Transmission of Respiratory Infections in Thai Army Recruits: A Prospective Cohort Study

abstract:
  Military recruits are at high risk of respiratory infections. However, limited data exist on military populations in tropical settings, where the epidemiology of respiratory infections differs substantially from temperate settings. We enrolled recruits undertaking a 10-week military training at two Royal Thai Army barracks between May 2014 and July 2015. We used a multiplex respiratory panel to analyze nose and throat swabs collected at the start and end of the training period, and from participants experiencing respiratory symptoms during follow-up. Paired sera were tested for influenza seroconversion using a hemagglutinin inhibition assay. Overall rates of upper respiratory illness and influenza-like illness were 3.1 and 2.0 episodes per 100 person-weeks, respectively. A pathogen was detected in 96% of samples. The most commonly detected microbes were Haemophilus influenzae type B (62.7%) or non–type B (58.2%) and rhinovirus (22.4%). At baseline, bacterial colonization was high and included H. influenzae type B (82.3%), H. influenzae non–type B (31.5%), Klebsiella pneumoniae (14.6%), Staphylococcus aureus (8.5%), and Streptococcus pneumoniae (8.5%). At the end of follow-up, colonization with H. influenzae non–type B had increased to 74.1%, and S. pneumoniae to 33.6%. In the serology subset, the rate of influenza infection was 3.4 per 100 person-months; 58% of influenza infections resulted in clinical disease. Our study provides key data on the epidemiology and transmission of respiratory pathogens in tropical settings. 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.


id: cord-272878-6f0q661e
author: Schnepf, Nathalie
date: 2011-08-17
txt: ./txt/cord-272878-6f0q661e.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21858150/
doi: 10.1371/journal.pone.0023514
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).

title:
  High Burden of Non-Influenza Viruses in Influenza-Like Illness in the Early Weeks of H1N1v Epidemic in France

abstract:
  BACKGROUND: Influenza-like illness (ILI) may be caused by a variety of pathogens. Clinical observations are of little help to recognise myxovirus infection and implement appropriate prevention measures. The limited use of molecular tools underestimates the role of other common pathogens. OBJECTIVES: During the early weeks of the 2009–2010 flu pandemic, a clinical and virological survey was conducted in adult and paediatric patients with ILI referred to two French University hospitals in Paris and Tours. Aims were to investigate the different pathogens involved in ILI and describe the associated symptoms. METHODS: H1N1v pandemic influenza diagnosis was performed with real time RT-PCR assay. Other viral aetiologies were investigated by the molecular multiplex assay RespiFinder19®. Clinical data were collected prospectively by physicians using a standard questionnaire. RESULTS: From week 35 to 44, endonasal swabs were collected in 413 patients. Overall, 68 samples (16.5%) were positive for H1N1v. In 13 of them, other respiratory pathogens were also detected. Among H1N1v negative samples, 213 (61.9%) were positive for various respiratory agents, 190 in single infections and 23 in mixed infections. The most prevalent viruses in H1N1v negative single infections were rhinovirus (62.6%), followed by parainfluenza viruses (24.2%) and adenovirus (5.3%). 70.6% of H1N1v cases were identified in patients under 40 years and none after 65 years. There was no difference between clinical symptoms observed in patients infected with H1N1v or with other pathogens. CONCLUSION: Our results highlight the high frequency of non-influenza viruses involved in ILI during the pre-epidemic period of a flu alert and the lack of specific clinical signs associated with influenza infections. Rapid diagnostic screening of a large panel of respiratory pathogens may be critical to define and survey the epidemic situation and to provide critical information for patient management.


id: cord-275605-mbiojk39
title: Clinical respiratory infections and pneumonia during the Hajj pilgrimage: A systematic review
author: Benkouiten, Samir
date: 2018-12-04
url: https://doi.org/10.1016/j.tmaid.2018.12.002
doi: 10.1016/j.tmaid.2018.12.002
abstract:
  BACKGROUND: The Islamic Hajj pilgrimage to Mecca is one of the world's largest annual mass gatherings. Inevitable overcrowding during the pilgrims' stay greatly increases the risk of acquiring and spreading infectious diseases, especially respiratory diseases. METHOD: The MEDLINE/PubMed and Scopus databases were searched for all relevant papers published prior to February 2018 that evaluated the prevalence of clinical symptoms of respiratory infections, including pneumonia, among Hajj pilgrims, as well as their influenza and pneumococcal vaccination status. RESULTS: A total of 61 papers were included in the review. Both cohort- and hospital-based studies provide complementary data, and both are therefore necessary to provide a complete picture of the total burden of respiratory diseases during the Hajj. Respiratory symptoms have been common among Hajj pilgrims over the last 15 years. In cohorts of pilgrims, cough ranged from 1.9% to 91.5%. However, the prevalence rates of the most common symptoms (cough, sore throat, and subjective fever) of influenza-like illness (ILI) varied widely across the included studies. These studies have shown variable results, with overall rates of ILI ranging from 8% to 78.2%. These differences might result from differences in study design, study period, and rates of vaccination against seasonal influenza that ranged from 1.1% to 100% among study participants. Moreover, the definition of ILI was inconsistent across studies. In hospitalized Hajj pilgrims, the prevalence of pneumonia, that remains a major concern in critically ill patients, ranged from 0.2% to 54.8%. CONCLUSIONS: Large multinational follow-up studies are recommended for clinic-based syndromic surveillance, in conjunction with microbiological surveillance. Matched cohorts ensure better comparability across studies. However, study design and data collection procedures should be standardized to facilitate reporting and to achieve comparability between studies. Furthermore, the definition of ILI, and of most common symptoms used to define respiratory infections (e.g., upper respiratory tract infection), need to be precisely defined and consistently used. Future studies need to address potential effect of influenza and pneumococcal vaccine in the context of the Hajj pilgrimage.


id: cord-282668-bs634hti
author: Niang, Mbayame Ndiaye
date: 2017-03-22
txt: ./txt/cord-282668-bs634hti.txt
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mime: text/plain
url: https://doi.org/10.1371/journal.pone.0174287
doi: 10.1371/journal.pone.0174287
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

title:
  Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses

abstract:
  BACKGROUND: Human adenoviruses (HAdVs) are highly contagious pathogens that are associated with a wide spectrum of human illnesses involving the respiratory tract. 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. METHODOLOGY AND RESULTS: From January 2012 to December 2015 swabs were collected from consenting ILI outpatients. Adenoviral detection is performed by rRT-PCR with the Anyplex(™) II RV16 Detection kit (Seegene) and molecular characterization was performed using a partial hexon gene sequence. 6381 samples were collected. More than half of patients (51.7%; 3297/6381) were children of ≤ 5 years. 1967 (30.8%) were positive for HAdV with 1561 (79.4%) found in co-infection with at least one another respiratory virus. The most common co-detections were with influenza viruses (53.1%; 1045/1967), rhinoviruses (30%; 591/1967), enteroviruses (18.5%; 364/1967) and RSV (13.5%; 266/1967). Children under 5 were the most infected group (62.2%; 1224/1967; p <0.05). We noted that HAdV was detected throughout the year at a high level with detection peaks of different amplitudes without any clear seasonality. Phylogenetic analysis revealed species HAdV-C in majority, species HAdV-B and one HAdV- 4 genome type. The 9 HAdV-B species like strains from Senegal grouped with genome types HAdV-7, HAdV-55 and HAdV-11 as shown by a phylogenetic branch with a high bootstrap value of (88%). CONCLUSION: In conclusion, the results of the present study suggest strong year-round HAdV activity in Senegal, especially in children up to 5 years of age. Molecular studies revealed that the dominant species in circulation in patients with ILI appears to be HAdV-C and HAdV-B species. The circulation of though HAdV-7 and HAdV-55 genome types is of note as these serotypes are recognized causes of more severe and even fatal acute respiratory infections.


id: cord-286837-j2sqs20q
title: Do Intensive Care Data on Respiratory Infections Reflect Influenza Epidemics?
author: Koetsier, Antonie
date: 2013-12-31
txt: ./txt/cord-286837-j2sqs20q.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24391837/
doi: 10.1371/journal.pone.0083854
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.

abstract:
  OBJECTIVES: Severe influenza can lead to Intensive Care Unit (ICU) admission. We explored whether ICU data reflect influenza like illness (ILI) activity in the general population, and whether ICU respiratory infections can predict influenza epidemics. 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 addition, ICU data of the first three years was used to build three regression models to predict the start and end of influenza epidemics in the years thereafter, one to three weeks ahead. The predicted start and end of influenza epidemics were compared with observed start and end of such epidemics according to the incidence of ILI. RESULTS: Peaks in respiratory ICU admissions lasted longer than peaks in ILI incidence rates. Increases in ICU admissions occurred on average two days earlier compared to ILI. Predicting influenza epidemics one, two, or three weeks ahead yielded positive predictive values ranging from 0.52 to 0.78, and sensitivities from 0.34 to 0.51. CONCLUSIONS: ICU data was associated with ILI activity, with increases in ICU data often occurring earlier and for a longer time period. However, in the Netherlands, predicting influenza epidemics in the general population using ICU data was imprecise, with low positive predictive values and sensitivities.


id: cord-288372-48wao8a0
author: Dia, Ndongo
date: 2014-04-08
txt: ./txt/cord-288372-48wao8a0.txt
cache: ./cache/cord-288372-48wao8a0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2334-14-189
doi: 10.1186/1471-2334-14-189
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.

title:
  Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011

abstract:
  BACKGROUND: In Africa, especially in West Africa, studies about the prevalence and diversity of respiratory viruses (influenza and others) in elderly people are largely lacking. In studies done elsewhere, it is well established that older people, when compared with younger adults, are at greater risk of significant morbidity and mortality from complications arising from influenza. 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. METHODS: The recruitment period of this study was from January 2009 to December 2011. 232 patients aged 50 years and above presenting ILI cases were enrolled. Nasal-pharyngeal and/or oral pharyngeal swabs were collected from patients. RNA was extracted from 200 μl of each sample followed by a two-step real-time RT-PCR. The Anyplex™ II RV16 Detection kit was used for viral detection. The kit enabled the simultaneous detection of the presence of 16 respiratory viruses. RESULTS: 150 viruses were detected: influenza viruses (44.7%) and rhinoviruses (26.7%) were the most prevalent. We detected 13 human parainfluenza viruses (8.7%), 7 human respiratory syncytial viruses (4.7%), 6 coronaviruses (4%), 5 human metapneumoviruses (3.3%), 5 human adenoviruses (3.3%) and 1 human bocavirus (0.7%). 14 cases (6%) of dual virus infections and one triple viral detection case were encountered. 56 (56.6%) viruses detected were found in the 50-64 year old age group, 59 (76.6%; P < 0.001) from 65–74 year old age group and 35 (62.5%) were detected in the ≥75 year old age group. The viral co-infections were more frequent in the 65-74 age group (9/15). CONCLUSIONS: This pilot study demonstrates a variety of respiratory viruses in the elderly. It also highlights a high prevalence of these viruses in this age group. We speculate from these results that the impact of respiratory viruses other than influenza on the elderly has been considerably underestimated. A more exhaustive study seems necessary in order to provide a more complete picture of the burden of respiratory viruses on morbidity among adults over 50 years old in the sub-Saharan context.


id: cord-289017-vwye3pk9
title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010
author: Comach, Guillermo
date: 2012-09-11
txt: ./txt/cord-289017-vwye3pk9.txt
cache: ./cache/cord-289017-vwye3pk9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/22984519/
doi: 10.1371/journal.pone.0044511
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] .

abstract:
  BACKGROUND: Limited information exists on the epidemiology of acute febrile respiratory illnesses in tropical South American countries such as Venezuela. The objective of the present study was to examine the epidemiology of influenza-like illness (ILI) in two hospitals in Maracay, Venezuela. METHODOLOGY/PRINCIPAL FINDINGS: We performed a prospective surveillance study of persons with ILI who presented for care at two hospitals in Maracay, Venezuela, from October 2006 to December 2010. A respiratory specimen and clinical information were obtained from each participant. Viral isolation and identification with immunofluorescent antibodies and molecular methods were employed to detect respiratory viruses such as adenovirus, influenza A and B, parainfluenza, and respiratory sincytial virus, among others. There were 916 participants in the study (median age: 17 years; range: 1 month – 86 years). Viruses were identified in 143 (15.6%) subjects, and one participant was found to have a co-infection with more than one virus. Influenza viruses, including pandemic H1N1 2009, were the most frequently detected pathogens, accounting for 67.4% (97/144) of the viruses detected. Adenovirus (15/144), parainfluenza virus (13/144), and respiratory syncytial virus (11/144) were also important causes of ILI in this study. Pandemic H1N1 2009 virus became the most commonly isolated influenza virus during its initial appearance in 2009. Two waves of the pandemic were observed: the first which peaked in August 2009 and the second - higher than the preceding - that peaked in October 2009. In 2010, influenza A/H3N2 re-emerged as the most predominant respiratory virus detected. 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. Pandemic H1N1 2009 influenza virus did not completely replace other circulating influenza viruses during its initial appearance in 2009. Seasonal influenza A/H3N2 was the most common influenza virus in the post-pandemic phase.


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

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

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


id: cord-305460-wln758og
author: Alqahtani, Amani Salem
date: 2020-05-04
txt: ./txt/cord-305460-wln758og.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32375320/
doi: 10.3390/pharmacy8020078
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).

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

abstract:
  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. A prospective cohort study with data collection at three phases (before, during and after Hajj) was conducted among Australian pilgrims between August and December 2015. Baseline data were collected from 421 pilgrims before Hajj, with 391 providing follow-up data during Hajj and 300 after their home return. Most participants (78% [329/421]) received one or more recommended vaccines; travel agents’ advice was the main factor affecting vaccination uptake. Most participants (69% [270/391]) practiced hand hygiene with soap and sanitizers frequently, followed by disposable handkerchief use (36% [139/391]) and washing hands with water only (28% [111/391]). During Hajj 74% (288/391) of participants reported one or more illness symptoms, 86% (248/288) of these symptoms were respiratory. Cough was less often reported among pilgrims who received vaccinations, cleaned their hands with soap or alcoholic hand rubs, while a runny nose was less common among those who frequently washed their hands with plain water but was more common among those who used facemasks. This study reveals that most Australian Hajj pilgrims complied with key preventative measures, and that tour group operators’ advice played an important role in compliance. Pilgrims who were vaccinated and practiced hand hygiene were less likely to report infection symptoms.


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

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

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


id: cord-307674-4fb5xnil
title: Household‐level risk factors for secondary influenza‐like illness in a rural area of Bangladesh
author: Weaver, Anne M.
date: 2017-01-05
txt: ./txt/cord-307674-4fb5xnil.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27889937/
doi: 10.1111/tmi.12820
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.

abstract:
  OBJECTIVE: To describe household‐level risk factors for secondary influenza‐like illness (ILI), an important public health concern in the low‐income population of Bangladesh. METHODS: Secondary analysis of control participants in a randomised controlled trial evaluating the effect of handwashing to prevent household ILI transmission. We recruited index‐case patients with ILI – fever (<5 years); fever, cough or sore throat (≥5 years) – from health facilities, collected information on household factors and conducted syndromic surveillance among household contacts for 10 days after resolution of index‐case patients’ symptoms. We evaluated the associations between household factors at baseline and secondary ILI among household contacts using negative binomial regression, accounting for clustering by household. RESULTS: Our sample was 1491 household contacts of 184 index‐case patients. Seventy‐one percentage reported that smoking occurred in their home, 27% shared a latrine with one other household and 36% shared a latrine with >1 other household. A total of 114 household contacts (7.6%) had symptoms of ILI during follow‐up. Smoking in the home (RR (adj) 1.9, 95% CI: 1.2, 3.0) and sharing a latrine with one household (RR (adj) 2.1, 95% CI: 1.2, 3.6) or >1 household (RR (adj) 3.1, 95% CI: 1.8–5.2) were independently associated with increased risk of secondary ILI. CONCLUSION: Tobacco use in homes could increase respiratory illness in Bangladesh. The mechanism between use of shared latrines and household ILI transmission is not clear. It is possible that respiratory pathogens could be transmitted through faecal contact or contaminated fomites in shared latrines.


id: cord-309860-otx45b8x
title: Clinical Predictors of Influenza in Young Children: The Limitations of “Influenza-Like Illness”
author: Conway, Nicholas T.
date: 2012-09-03
url: https://www.ncbi.nlm.nih.gov/pubmed/26619439/
doi: 10.1093/jpids/pis081
abstract:
  BACKGROUND: Influenza-like illness (ILI) definitions have been infrequently studied in young children. Despite this, clinical definitions of ILI play an important role in influenza surveillance. This study aims to identify clinical predictors of influenza infection in children ≤5 years old from which age-specific ILI definitions are then constructed. METHODS: Children aged 6–59 months with a history of fever and acute respiratory symptoms were recruited in the Western Australia Influenza Vaccine Effectiveness (WAIVE) Study. Clinical data and per-nasal specimens were obtained from all children. Logistic regression identified significant predictors of influenza infection. Different ILI definitions were compared for diagnostic accuracy. RESULTS: Children were recruited from 2 winter influenza seasons (2008–2009; n = 944). Of 919 eligible children, 179 (19.5%) had laboratory-confirmed influenza infection. Predictors of infection included increasing age, lack of influenza vaccination, lower birth weight, fever, cough, and absence of wheeze. An ILI definition comprising fever ≥38°C, cough, and no wheeze had 58% sensitivity (95% confidence interval [CI], 50–66), 60% specificity (95% CI, 56–64), 26% positive predictive value (95% CI, 21–31), and 86% negative predictive value (95% CI, 82–89). The addition of other symptoms or higher fever thresholds to ILI definition had little impact. The Centers for Disease Control and Prevention definition of ILI (presence of fever [≥37.8°C] and cough and/or sore throat) was sensitive (92%; 95% CI, 86–95), yet lacked specificity (10%; 95% CI, 8–13) in this population. CONCLUSIONS: Influenza-like illness is a poor predictor of laboratory-confirmed influenza infection in young children but can be improved using age-specific data. Incorporating age-specific ILI definitions and/or diagnostic testing into influenza surveillance systems will improve the accuracy of epidemiological data.


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

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

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


id: cord-312493-wbhji81g
title: Exploring a Proposed WHO Method to Determine Thresholds for Seasonal Influenza Surveillance
author: Tay, Ee Laine
date: 2013-10-11
txt: ./txt/cord-312493-wbhji81g.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24146973/
doi: 10.1371/journal.pone.0077244
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.

abstract:
  INTRODUCTION: Health authorities find thresholds useful to gauge the start and severity of influenza seasons. We explored a method for deriving thresholds proposed in an influenza surveillance manual published by the World Health Organization (WHO). METHODS: For 2002-2011, we analysed two routine influenza-like-illness (ILI) datasets, general practice sentinel surveillance and a locum medical service sentinel surveillance, plus laboratory data and hospital admissions for influenza. For each sentinel dataset, we created two composite variables from the product of weekly ILI data and the relevant laboratory data, indicating the proportion of tested specimens that were positive. 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. From the thresholds, we compared the seasonal onset, end and intensity across all datasets from 2002-2011. Correlation between datasets was assessed using the mean correlation coefficient. RESULTS: The median week of peak activity was week 34 for all datasets, except hospital data (week 35). Means and medians were comparable and the 90% upper CIs were similar to the 95(th) 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. The composite variables improved the agreements between the ILI and other datasets. Datasets were well correlated, with mean correlation coefficients of >0.75 for a range of combinations. CONCLUSIONS: Thresholds for influenza surveillance are easily derived from historical surveillance and laboratory data using the approach proposed by WHO. Use of composite variables is helpful for describing influenza season characteristics.


id: cord-318856-f0m3wuyj
title: Can pollen explain the seasonality of flu-like illnesses in the Netherlands?
author: Hoogeveen, Martijn J.
date: 2020-10-22
url: https://www.sciencedirect.com/science/article/pii/S0048969720367127?v=s5
doi: 10.1016/j.scitotenv.2020.143182
abstract:
  Current models for flu-like epidemics insufficiently explain multi-cycle seasonality. Meteorological factors alone, including the associated behavior, do not predict seasonality, given substantial climate differences between countries that are subject to flu-like epidemics or COVID-19. Pollen is documented to be allergenic, it plays a role in immuno-activation and defense against respiratory viruses, and seems to create a bio-aerosol that lowers the reproduction number of flu-like viruses. Therefore, we hypothesize that pollen may explain the seasonality of flu-like epidemics, including COVID-19, in combination with meteorological variables. We have tested the Pollen-Flu Seasonality Theory for 2016-2020 flu-like seasons, including COVID-19, in the Netherlands, with its 17.4 million inhabitants. We combined changes in flu-like incidence per 100K/Dutch residents (code: ILI) with pollen concentrations and meteorological data. Finally, a predictive model was tested using pollen and meteorological threshold values, inversely correlated to flu-like incidence. We found a highly significant inverse correlation of r(224)= -0.41 (p < 0.001) between pollen and changes in flu-like incidence, corrected for the incubation period. The correlation was stronger after taking into account the incubation time. We found that our predictive model has the highest inverse correlation with changes in flu-like incidence of r(222) = -0.48 (p < 0.001) when average thresholds of 610 total pollen grains/m3, 120 allergenic pollen grains/m3, and a solar radiation of 510 J/cm2 are passed. The passing of at least the pollen thresholds, preludes the beginning and end of flu-like seasons. Solar radiation is a co-inhibitor of flu-like incidence, while temperature makes no difference. However, higher relative humidity increases with flu-like incidence. We conclude that pollen is a predictor of the inverse seasonality of flu-like epidemics, including COVID-19, and that solar radiation is a co-inhibitor, in the Netherlands.


id: cord-321704-jozrgcq3
author: Tan, Xin Quan
date: 2014-04-15
url: https://www.ncbi.nlm.nih.gov/pubmed/24735158/
doi: 10.1186/1471-2334-14-204
title:
  Respiratory viral pathogens among Singapore military servicemen 2009 – 2012: epidemiology and clinical characteristics

abstract:
  BACKGROUND: Few studies have comprehensively described tropical respiratory disease surveillance in military populations. There is also a lack of studies comparing clinical characteristics of the non-influenza pathogens with influenza and amongst themselves. METHODS: From May 2009 through October 2012, 7733 consenting cases of febrile respiratory illness (FRI) (temperature [greater than or equal to]37.5degreesC with cough or sorethroat) and controls in the Singapore military had clinical data and nasal washes collected prospectively. Nasal washes underwent multiplex PCR, and the analysis was limited to viral mono-infections. RESULTS: 49% of cases tested positive for at least one virus, of whom 10% had multiple infections. 53% of the FRI cases fulfilled the definition of influenza-like illness (ILI), of whom 52% were positive for at least one virus. The most frequent etiologies for mono-infections among FRI cases were Influenza A(H1N1)pdm09 (13%), Influenza B (13%) and coxsackevirus (9%). The sensitivity, specificity, positive predictive value and negative predictive value of ILI for influenza among FRI cases were 72%, 48%, 40% and 69% respectively. On logistic regression, there were marked differences in the prevalence of different symptoms and signs between viruses with fever more prevalent amongst influenza and adenovirus infections than other viruses. CONCLUSION: There are multiple viral etiologies for FRI and ILI with differing clinical symptoms in the Singapore military. Influenza and coxsackevirus were the most common etiology for FRI, while influenza and adenoviruses displayed the most febrile symptoms. Further studies should explore these differences and possible interventions.


id: cord-325794-lir8ht2i
title: Predicting individual risk for COVID19 complications using EMR data
author: Kinar, Y.
date: 2020-06-05
txt: ./txt/cord-325794-lir8ht2i.txt
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mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.06.03.20121574v1?rss=1
doi: 10.1101/2020.06.03.20121574
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).

abstract:
  Background: The global pandemic of COVID-19 has challenged healthcare organizations and caused numerous deaths and hospitalizations worldwide. The need for data-based decision support tools for many aspects of controlling and treating the disease is evident but has been hampered by the scarcity of real-world reliable data. Here we describe two approaches: a. 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. a preliminary model that is trained using existing real world COVID-19 data. Methods: We have utilized the computerized data of Maccabi Healthcare Services a 2.3 million member state-mandated health organization in Israel. The age and sex matched matrix used for training the XGBoost ILI-based model included, circa 690,000 rows and 900 features. 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. Findings: The AUC of our models and the priors on the 2137 COVID-19 patients for predicting moderate and severe complications as cases and all other as controls, the AUC for the ILI-based model was 0.852[0.824-0.879] for the COVID19-based model - 0.872[0.847-0.879].. Interpretation: These models can effectively identify patients at high-risk for complication, thus allowing optimization of resources and more focused follow up and early triage these patients if once symptoms worsen.


id: cord-334424-z7ygy25e
author: McCaw, James M
date: 2012-12-11
url: https://www.ncbi.nlm.nih.gov/pubmed/23231698/
doi: 10.1186/1471-2334-12-345
title:
  Household transmission of respiratory viruses – assessment of viral, individual and household characteristics in a population study of healthy Australian adults

abstract:
  BACKGROUND: Household transmission of influenza-like illness (ILI) may vary with viral and demographic characteristics. We examined the effect of these factors in a population-based sample of adults with ILI. METHODS: We conducted a prospective cohort study in community-dwelling Australian adults nested within an influenza vaccine effectiveness trial. On presentation with ILI, participants were swabbed for a range of respiratory viruses and asked to return a questionnaire collecting details of household members with or without similar symptoms. We used logistic and Poisson regression to assess the key characteristics of household transmission. RESULTS: 258 participants from multi-occupancy households experienced 279 ILI episodes and returned a questionnaire. Of these, 183 were the primary case in the household allowing assessment of factors associated with transmission. Transmission was significantly associated in univariate analyses with female sex (27% vs. 13%, risk ratio (RR) = 2.13 (1.08, 4.21)) and the presence of a child in the house (33% vs. 17%, RR = 1.90 (1.11, 3.26)). The secondary household attack proportion (SHAP) was 0.14, higher if influenza was isolated (RR = 2.1 (1.0, 4.5)). Vaccinated participants who nonetheless became infected with influenza had a higher SHAP (Incidence RR = 5.24 (2.17, 12.6)). CONCLUSIONS: The increased SHAP in households of vaccinated participants who nonetheless had confirmed influenza infection supports the hypothesis that in years of vaccine mismatch, not only is influenza vaccine less protective for the vaccine recipient, but that the population’s immunity is also lower.


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

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


id: cord-338674-tnnd1s57
title: Pilot study of influenza vaccine effectiveness in urban Australian children attending childcare
author: Yin, J Kevin
date: 2011-06-10
txt: ./txt/cord-338674-tnnd1s57.txt
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url: https://doi.org/10.1111/j.1440-1754.2011.02098.x
doi: 10.1111/j.1440-1754.2011.02098.x
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

abstract:
  Background: Influenza outbreaks in the childcare setting are a significant cause of excess winter morbidity. This study explored methods of follow up and sample collection for a proposed randomised controlled trial of influenza vaccination in children attending childcare. Methods: The study was conducted in four Sydney childcare centres during 2007. Healthy children aged 6–59 months eligible for vaccination were recruited in two centres, with another two acting as controls. Data on influenza‐like illness (ILI: ≥37.8°C plus at least one respiratory symptom) occurrence were collected weekly. In those children with an ILI, parents were asked to collect nasal swabs and send via surface mail for viral polymerase chain reaction. Vaccine efficacy (VE) for ILI was estimated overall and for subgroups aged 6–23 and 24–59 months using the formula VE = 1 − relative risk (RR). Results: Sixty‐three per cent (151/238) of eligible children had parents give consent. Sixty‐three children received influenza vaccine and 88 participated as controls. Of 26 specimens returned, a virus was detected in 18 (69%); none with influenza. Two symptomatic children had positive near‐patient influenza tests in general practice (one a vaccine failure). The RR with 95% confidence interval in all children and those aged 6–23 months were less than one, 0.56 (0.32–1.02) and 0.46 (0.15–1.45), respectively. Conclusions: This study demonstrated the feasibility and utility of parent‐collected and mailed respiratory specimens for VE research in the childcare setting. Two‐thirds of parent‐collected swabs proved positive for at least one virus. Finding ways to reduce reluctance of parents to submit samples could improve the representativeness of samples collected and the power of the study. No evidence was found for influenza VE, but point estimates were in the direction of protection.


id: cord-341260-vxsbv8t9
author: Loubet, P.
date: 2017-04-30
txt: ./txt/cord-341260-vxsbv8t9.txt
cache: ./cache/cord-341260-vxsbv8t9.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1198743X16305705
doi: 10.1016/j.cmi.2016.11.014
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.

title:
  Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France

abstract:
  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). Methods Patients hospitalized with ILI were included in this prospective, multicentre study carried out in six French hospitals during three consecutive influenza seasons (2012–2015). RSV and other respiratory viruses were detected by multiplex PCR in nasopharyngeal swabs. Risk factors for RSV infection were identified by backward stepwise logistic regression analysis. Results A total of 1452 patients hospitalized with ILI were included, of whom 59% (861/1452) were >65 years and 83% (1211/1452) had underlying chronic illnesses. RSV was detected in 4% (59/1452), and influenza virus in 39% (566/1452). Risk factors for RSV infection were cancer (adjusted OR 2.1, 95% CI 1.1–4.1, p 0.04), and immunosuppressive treatment (adjusted OR 2.0, 95% CI 1.1–3.8, p 0.03). Patients with RSV had a median length of stay of 9 days (6–25), and 57% of them (30/53) had complications, including pneumonia (23/53, 44%) and respiratory failure (15/53, 28%). Fifteen per cent (8/53) were admitted to an intensive care unit, and the in-hospital mortality rate was 8% (4/53). Pneumonia was more likely to occur in patients with RSV than in patients with RSV-negative ILI (44% (23/53) versus 26% (362/1393), p 0.006) or with influenza virus infection (44% versus 28% (157/560), p 0.02). Conclusion RSV is an infrequent cause of ILI during periods of influenza virus circulation but can cause severe complications in hospitalized adults. Risk factors for RSV detection in adults hospitalized with ILI include cancer and immunosuppressive treatment. Specific immunization and antiviral therapy might benefit patients at risk.


id: cord-344070-17oac3bg
author: Silverman, Justin D
date: 2020-04-03
url: https://doi.org/10.1101/2020.04.01.20050542
doi: 10.1101/2020.04.01.20050542
title:
  Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States

abstract:
  Detection of SARS-CoV-2 infections to date has relied on RT-PCR testing. However, a failure to identify early cases imported to a country, bottlenecks in RT-PCR testing, and the existence of infections which are asymptomatic, sub-clinical, or with an alternative presentation than the standard cough and fever have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how publicly available CDC influenza-like illness (ILI) outpatient surveillance data can be repurposed to estimate the detection rate of symptomatic SARS-CoV-2 infections. We find a surge of non-influenza ILI above the seasonal average and show that this surge is correlated with COVID case counts across states. By quantifying the number of excess ILI patients in March relative to previous years and comparing excess ILI to confirmed COVID case counts, we estimate the syndromic case detection rate of SARS-CoV-2 in the US to be less than 13%. If only 1/3 of patients infected with SARS-CoV-2 sought care, the ILI surge would correspond to more than 8.7 million new SARS-CoV-2 infections across the US during the three week period from March 8 to March 28. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to be doubling slower than every 4 days. Together these results suggest a conceptual model for the COVID epidemic in the US in which rapid spread across the US are combined with a large population of infected patients with presumably mild-to-moderate clinical symptoms. We emphasize the importance of testing these findings with seroprevalence data, and discuss the broader potential to use syndromic time series for early detection and understanding of emerging infectious diseases.


id: cord-345315-y3bdjnhg
author: Dai, Yaoyao
date: 2020-10-01
url: https://doi.org/10.1371/journal.pntd.0008758
doi: 10.1371/journal.pntd.0008758
title:
  Identifying the outbreak signal of COVID-19 before the response of the traditional disease monitoring system

abstract:
  New coronavirus cases and related deaths are continuing to occur worldwide. Early identification of the emergence of novel outbreaks of infectious diseases is critical to the generation of timely responses. We performed a comparative study to determine the feasibility of the early detection of the COVID-19 outbreak in China based on influenza surveillance data and the internet-based Baidu search index to evaluate the timelines of the alert signals compared with the traditional case reporting and response systems. An abnormal increase in the number of influenza-like illnesses (ILI) occurred at least one month earlier than the clinical reports of pneumonia with unknown causes and the conventional monitoring system. The peak of the search volume was 20 days earlier than the issuance of the massive official warning about the epidemic. The findings from this study suggest that monitoring abnormal surges of ILI and identifying peaks of online searches of key terms can provide early signals of novel disease outbreaks. We emphasize the importance of broadening the potential of syndromic surveillance, internet searches, and social media data together with the traditional disease surveillance system to enhance early detection and understanding of emerging infectious diseases. SYNOPSIS: Early identification of the emergence of an outbreak of a novel infectious disease is critical to generating a timely response. The traditional monitoring system is adequate for detecting the outbreak of common diseases; however, it is insufficient for the discovery of novel infectious diseases. In this study, we used COVID-19 as an example to compare the delay time of different tools for identifying disease outbreaks. The results showed that both the abnormal spike in influenza-like illnesses and the peak of online searches of key terms could provide early signals. We emphasize the importance of testing these findings and discussing the broader potential to use syndromic surveillance, internet searches, and social media data together with traditional disease surveillance systems for early detection and understanding of novel emerging infectious diseases.


id: cord-347079-1zbsbcdd
author: Silverman, Justin D.
date: 2020-06-22
url: https://www.ncbi.nlm.nih.gov/pubmed/32571980/
doi: 10.1126/scitranslmed.abc1126
title:
  Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States

abstract:
  Detection of SARS-CoV-2 infections to date has relied heavily on RT-PCR testing. However, limited test availability, high false-negative rates, and the existence of asymptomatic or sub-clinical infections have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how influenza-like illness (ILI) outpatient surveillance data can be used to estimate the prevalence of SARS-CoV-2. We found a surge of non-influenza ILI above the seasonal average in March 2020 and showed that this surge correlated with COVID-19 case counts across states. If 1/3 of patients infected with SARS-CoV-2 in the US sought care, this ILI surge would have corresponded to more than 8.7 million new SARS-CoV-2 infections across the US during the three-week period from March 8 to March 28, 2020. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to have been doubling slower than every 4 days. Together these results suggest a conceptual model for the COVID-19 epidemic in the US characterized by rapid spread across the US with over 80% infected patients remaining undetected. We emphasize the importance of testing these findings with seroprevalence data and discuss the broader potential to use syndromic surveillance for early detection and understanding of emerging infectious diseases.


id: cord-348061-ssjl2w7l
author: Chamberlain, Samuel D
date: 2020-04-10
txt: ./txt/cord-348061-ssjl2w7l.txt
cache: ./cache/cord-348061-ssjl2w7l.txt
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mime: text/plain
url: https://doi.org/10.1101/2020.04.06.20039909
doi: 10.1101/2020.04.06.20039909
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.

title:
  Real-time detection of COVID-19 epicenters within the United States using a network of smart thermometers

abstract:
  Containing outbreaks of infectious disease requires rapid identification of transmission hotspots, as the COVID-19 pandemic demonstrates. Focusing limited public health resources on transmission hotspots can contain spread, thus reducing morbidity and mortality, but rapid data on community-level disease dynamics is often unavailable. Here, we demonstrate an approach to identify anomalously elevated levels of influenza-like illness (ILI) in real-time, at the scale of US counties. 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. Anomalies are strongly correlated with COVID-19 case counts and may provide an early-warning system to locate outbreak epicenters.


id: cord-354143-p2ofapbd
author: Hellferscee, Orienka
date: 2017-07-06
txt: ./txt/cord-354143-p2ofapbd.txt
cache: ./cache/cord-354143-p2ofapbd.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1002/jmv.24869
doi: 10.1002/jmv.24869
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.

title:
  Enterovirus genotypes among patients with severe acute respiratory illness, influenza‐like illness, and asymptomatic individuals in South Africa, 2012‐2014

abstract:
  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 aimed to characterize and determine the prevalence of enterovirus genotypes among South African patients with respiratory illness and controls during June 2012 to July 2014. Syndromic SARI and influenza‐like illness (ILI) surveillance was performed at two sentinel sites. At each site nasopharyngeal/oropharyngeal specimens were collected from SARI and ILI patients as well as controls. Specimens were tested for enterovirus by real‐time PCR. Positive specimens were further genotyped by sequencing a region of the VP1 gene. The prevalence of enterovirus was 5.8% (87/1494), 3.4% (103/3079), and 3.4% (46/1367) among SARI, ILI, and controls, respectively (SARI/controls, P = 0.002 and ILI/control, P = 0.973). Among the 101/236 (42.8%) enterovirus‐positive specimens that could be genotyped, we observed a high diversity of circulating enterovirus genotypes (a total of 33 genotypes) from all four human enterovirus species with high prevalence of Enterovirus‐B (60.4%; 61/101) and Enterovirus‐A (21.8%; 22/101) compared to Enterovirus‐C (10.9%; 11/101) and Enterovirus‐D (6.9%; 7/101) (P = 0.477). Of the enterovirus genotypes identified, Echovirus 30 (9.9%, 10/101), Coxsackie virus B5 (7.9%, 8/101) and Enterovirus‐D68 (6.9%, 7/101) were most prevalent. There was no difference in disease severity (SARI or ILI compared to controls) between the different enterovirus species (P = 0.167). 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.


