Dataset Information

Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms.

ABSTRACT: Seasonal influenza surveillance is usually carried out by sentinel general practitioners (GPs) who compile weekly reports based on the number of influenza-like illness (ILI) clinical cases observed among visited patients. This traditional practice for surveillance generally presents several issues, such as a delay of one week or more in releasing reports, population biases in the health-seeking behaviour, and the lack of a common definition of ILI case. On the other hand, the availability of novel data streams has recently led to the emergence of non-traditional approaches for disease surveillance that can alleviate these issues. In Europe, a participatory web-based surveillance system called Influenzanet represents a powerful tool for monitoring seasonal influenza epidemics thanks to aid of self-selected volunteers from the general population who monitor and report their health status through Internet-based surveys, thus allowing a real-time estimate of the level of influenza circulating in the population. In this work, we propose an unsupervised probabilistic framework that combines time series analysis of self-reported symptoms collected by the Influenzanet platforms and performs an algorithmic detection of groups of symptoms, called syndromes. The aim of this study is to show that participatory web-based surveillance systems are capable of detecting the temporal trends of influenza-like illness even without relying on a specific case definition. The methodology was applied to data collected by Influenzanet platforms over the course of six influenza seasons, from 2011-2012 to 2016-2017, with an average of 34,000 participants per season. Results show that our framework is capable of selecting temporal trends of syndromes that closely follow the ILI incidence rates reported by the traditional surveillance systems in the various countries (Pearson correlations ranging from 0.69 for Italy to 0.88 for the Netherlands, with the sole exception of Ireland with a correlation of 0.38). The proposed framework was able to forecast quite accurately the ILI trend of the forthcoming influenza season (2016-2017) based only on the available information of the previous years (2011-2016). Furthermore, to broaden the scope of our approach, we applied it both in a forecasting fashion to predict the ILI trend of the 2016-2017 influenza season (Pearson correlations ranging from 0.60 for Ireland and UK, and 0.85 for the Netherlands) and also to detect gastrointestinal syndrome in France (Pearson correlation of 0.66). The final result is a near-real-time flexible surveillance framework not constrained by any specific case definition and capable of capturing the heterogeneity in symptoms circulation during influenza epidemics in the various European countries.

SUBMITTER: Kalimeri K

PROVIDER: S-EPMC6472822 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms.

Kalimeri Kyriaki K Delfino Matteo M Cattuto Ciro C Perrotta Daniela D Colizza Vittoria V Guerrisi Caroline C Turbelin Clement C Duggan Jim J Edmunds John J Obi Chinelo C Pebody Richard R Franco Ana O AO Moreno Yamir Y Meloni Sandro S Koppeschaar Carl C Kjelsø Charlotte C Mexia Ricardo R Paolotti Daniela D

PLoS computational biology 20190408 4

Seasonal influenza surveillance is usually carried out by sentinel general practitioners (GPs) who compile weekly reports based on the number of influenza-like illness (ILI) clinical cases observed among visited patients. This traditional practice for surveillance generally presents several issues, such as a delay of one week or more in releasing reports, population biases in the health-seeking behaviour, and the lack of a common definition of ILI case. On the other hand, the availability of nov ...[more]

PMID: 30958817

Similar Datasets

Project description:BACKGROUND:Effective surveillance of influenza requires a broad network of health care providers actively reporting cases of influenza-like illnesses and positive laboratory results. Not only is this traditional surveillance system costly to establish and maintain but there is also a time lag between a change in influenza activity and its detection. A new surveillance system that is both reliable and timely will help public health officials to effectively control an epidemic and mitigate the burden of the disease. OBJECTIVE:This study aimed to evaluate the use of parent-reported data of febrile illnesses in children submitted through the Fever Coach app in real-time surveillance of influenza activities. METHODS:Fever Coach is a mobile app designed to help parents and caregivers manage fever in young children, currently mainly serviced in South Korea. The app analyzes data entered by a caregiver and provides tailored information for care of the child based on the child's age, sex, body weight, body temperature, and accompanying symptoms. Using the data submitted to the app during the 2016-2017 influenza season, we built a regression model that monitors influenza incidence for the 2017-2018 season and validated the model by comparing the predictions with the public influenza surveillance data from the Korea Centers for Disease Control and Prevention (KCDC). RESULTS:During the 2-year study period, 70,203 diagnosis data, including 7702 influenza reports, were submitted. There was a significant correlation between the influenza activity predicted by Fever Coach and that reported by KCDC (Spearman ?=0.878; P<.001). Using this model, the influenza epidemic in the 2017-2018 season was detected 10 days before the epidemic alert announced by KCDC. CONCLUSIONS:The Fever Coach app successfully collected data from 7.73% (207,699/2,686,580) of the target population by providing care instruction for febrile children. These data were used to develop a model that accurately estimated influenza activity measured by the central government agency using reports from sentinel facilities in the national surveillance network.

Project description:BackgroundSelf-reported symptoms during the COVID-19 pandemic have been used to train artificial intelligence models to identify possible infection foci. To date, these models have only considered the culmination or peak of symptoms, which is not suitable for the early detection of infection. We aimed to estimate the probability of an individual being infected with SARS-CoV-2 on the basis of early self-reported symptoms to enable timely self-isolation and urgent testing.MethodsIn this large-scale, prospective, epidemiological surveillance study, we used prospective, observational, longitudinal, self-reported data from participants in the UK on 19 symptoms over 3 days after symptoms onset and COVID-19 PCR test results extracted from the COVID-19 Symptom Study mobile phone app. We divided the study population into a training set (those who reported symptoms between April 29, 2020, and Oct 15, 2020) and a test set (those who reported symptoms between Oct 16, 2020, and Nov 30, 2020), and used three models to analyse the self-reported symptoms: the UK's National Health Service (NHS) algorithm, logistic regression, and the hierarchical Gaussian process model we designed to account for several important variables (eg, specific COVID-19 symptoms, comorbidities, and clinical information). Model performance to predict COVID-19 positivity was compared in terms of sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) in the test set. For the hierarchical Gaussian process model, we also evaluated the relevance of symptoms in the early detection of COVID-19 in population subgroups stratified according to occupation, sex, age, and body-mass index.FindingsThe training set comprised 182 991 participants and the test set comprised 15 049 participants. When trained on 3 days of self-reported symptoms, the hierarchical Gaussian process model had a higher prediction AUC (0·80 [95% CI 0·80-0·81]) than did the logistic regression model (0·74 [0·74-0·75]) and the NHS algorithm (0·67 [0·67-0·67]). AUCs for all models increased with the number of days of self-reported symptoms, but were still high for the hierarchical Gaussian process model at day 1 (0·73 [95% CI 0·73-0·74]) and day 2 (0·79 [0·78-0·79]). At day 3, the hierarchical Gaussian process model also had a significantly higher sensitivity, but a non-statistically lower specificity, than did the two other models. The hierarchical Gaussian process model also identified different sets of relevant features to detect COVID-19 between younger and older subgroups, and between health-care workers and non-health-care workers. When used during different pandemic periods, the model was robust to changes in populations.InterpretationEarly detection of SARS-CoV-2 infection is feasible with our model. Such early detection is crucial to contain the spread of COVID-19 and efficiently allocate medical resources.FundingZOE, the UK Government Department of Health and Social Care, the Wellcome Trust, the UK Engineering and Physical Sciences Research Council, the UK National Institute for Health Research, the UK Medical Research Council, the British Heart Foundation, the Alzheimer's Society, the Chronic Disease Research Foundation, and the Massachusetts Consortium on Pathogen Readiness.

Project description:BackgroundThe Internet is becoming more commonly used as a tool for disease surveillance. Similarly to other surveillance systems and to studies using online data collection, Internet-based surveillance will have biases in participation, affecting the generalizability of the results. Here we quantify the participation biases of Influenzanet, an ongoing European-wide network of Internet-based participatory surveillance systems for influenza-like-illness.MethodsIn 2011/2012 Influenzanet launched a standardized common framework for data collection applied to seven European countries. Influenzanet participants were compared to the general population of the participating countries to assess the representativeness of the sample in terms of a set of demographic, geographic, socio-economic and health indicators.ResultsMore than 30,000 European residents registered to the system in the 2011/2012 season, and a subset of 25,481 participants were selected for this study. All age classes (10 years brackets) were represented in the cohort, including under 10 and over 70 years old. The Influenzanet population was not representative of the general population in terms of age distribution, underrepresenting the youngest and oldest age classes. The gender imbalance differed between countries. A counterbalance between gender-specific information-seeking behavior (more prominent in women) and Internet usage (with higher rates in male populations) may be at the origin of this difference. Once adjusted by demographic indicators, a similar propensity to commute was observed for each country, and the same top three transportation modes were used for six countries out of seven. Smokers were underrepresented in the majority of countries, as were individuals with diabetes; the representativeness of asthma prevalence and vaccination coverage for 65+ individuals in two successive seasons (2010/2011 and 2011/2012) varied between countries.ConclusionsExisting demographic and national datasets allowed the quantification of the participation biases of a large cohort for influenza-like-illness surveillance in the general population. Significant differences were found between Influenzanet participants and the general population. The quantified biases need to be taken into account in the analysis of Influenzanet epidemiological studies and provide indications on populations groups that should be targeted in recruitment efforts.

Dataset Information

Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms.

Publications

Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets