Dataset Information

Detecting COVID-19 infection hotspots in England using large-scale self-reported data from a mobile application: a prospective, observational study.

ABSTRACT:

Background

As many countries seek to slow the spread of COVID-19 without reimposing national restrictions, it has become important to track the disease at a local level to identify areas in need of targeted intervention.

Methods

In this prospective, observational study, we did modelling using longitudinal, self-reported data from users of the COVID Symptom Study app in England between March 24, and Sept 29, 2020. Beginning on April 28, in England, the Department of Health and Social Care allocated RT-PCR tests for COVID-19 to app users who logged themselves as healthy at least once in 9 days and then reported any symptom. We calculated incidence of COVID-19 using the invited swab (RT-PCR) tests reported in the app, and we estimated prevalence using a symptom-based method (using logistic regression) and a method based on both symptoms and swab test results. We used incidence rates to estimate the effective reproduction number, R(t), modelling the system as a Poisson process and using Markov Chain Monte-Carlo. We used three datasets to validate our models: the Office for National Statistics (ONS) Community Infection Survey, the Real-time Assessment of Community Transmission (REACT-1) study, and UK Government testing data. We used geographically granular estimates to highlight regions with rapidly increasing case numbers, or hotspots.

Findings

From March 24 to Sept 29, 2020, a total of 2 873 726 users living in England signed up to use the app, of whom 2 842 732 (98·9%) provided valid age information and daily assessments. These users provided a total of 120 192 306 daily reports of their symptoms, and recorded the results of 169 682 invited swab tests. On a national level, our estimates of incidence and prevalence showed a similar sensitivity to changes to those reported in the ONS and REACT-1 studies. On Sept 28, 2020, we estimated an incidence of 15 841 (95% CI 14 023-17 885) daily cases, a prevalence of 0·53% (0·45-0·60), and R(t) of 1·17 (1·15-1·19) in England. On a geographically granular level, on Sept 28, 2020, we detected 15 (75%) of the 20 regions with highest incidence according to government test data.

Interpretation

Our method could help to detect rapid case increases in regions where government testing provision is lower. Self-reported data from mobile applications can provide an agile resource to inform policy makers during a quickly moving pandemic, serving as a complementary resource to more traditional instruments for disease surveillance.

Funding

Zoe Global, UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK National Institute for Health Research, UK Medical Research Council and British Heart Foundation, Alzheimer's Society, Chronic Disease Research Foundation.

SUBMITTER: Varsavsky T

PROVIDER: S-EPMC7785969 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundMobile health apps (MHA) have the potential to improve health care. The commercial MHA market is rapidly growing, but the content and quality of available MHA are unknown. Instruments for the assessment of the quality and content of MHA are highly needed. The Mobile Application Rating Scale (MARS) is one of the most widely used tools to evaluate the quality of MHA. Only few validation studies investigated its metric quality. No study has evaluated the construct validity and concurrent validity.ObjectiveThis study evaluates the construct validity, concurrent validity, reliability, and objectivity, of the MARS.MethodsData was pooled from 15 international app quality reviews to evaluate the metric properties of the MARS. The MARS measures app quality across four dimensions: engagement, functionality, aesthetics and information quality. Construct validity was evaluated by assessing related competing confirmatory models by confirmatory factor analysis (CFA). Non-centrality (RMSEA), incremental (CFI, TLI) and residual (SRMR) fit indices were used to evaluate the goodness of fit. As a measure of concurrent validity, the correlations to another quality assessment tool (ENLIGHT) were investigated. Reliability was determined using Omega. Objectivity was assessed by intra-class correlation.ResultsIn total, MARS ratings from 1,299 MHA covering 15 different health domains were included. Confirmatory factor analysis confirmed a bifactor model with a general factor and a factor for each dimension (RMSEA = 0.074, TLI = 0.922, CFI = 0.940, SRMR = 0.059). Reliability was good to excellent (Omega 0.79 to 0.93). Objectivity was high (ICC = 0.82). MARS correlated with ENLIGHT (ps<.05).ConclusionThe metric evaluation of the MARS demonstrated its suitability for the quality assessment. As such, the MARS could be used to make the quality of MHA transparent to health care stakeholders and patients. Future studies could extend the present findings by investigating the re-test reliability and predictive validity of the MARS.

Project description:Under the current policy decision making paradigm we make or evaluate a policy decision by intervening different socio-economic parameters and analyzing the impact of those interventions. This process involves identifying the causal relation between interventions and outcomes. Matching method is one of the popular techniques to identify such causal relations. However, in one-to-one matching, when a treatment or control unit has multiple pair assignment options with similar match quality, different matching algorithms often assign different pairs. Since all the matching algorithms assign pairs without considering the outcomes, it is possible that with the same data and same hypothesis, different experimenters can reach different conclusions creating an uncertainty in policy decision making. This problem becomes more prominent in the case of large-scale observational studies as there are more pair assignment options. Recently, a robust approach has been proposed to tackle the uncertainty that uses an integer programming model to explore all possible assignments. Though the proposed integer programming model is very efficient in making robust causal inference, it is not scalable to big data observational studies. With the current approach, an observational study with 50,000 samples will generate hundreds of thousands binary variables. Solving such integer programming problem is computationally expensive and becomes even worse with the increase of sample size. In this work, we consider causal inference testing with binary outcomes and propose computationally efficient algorithms that are adaptable for large-scale observational studies. By leveraging the structure of the optimization model, we propose a robustness condition that further reduces the computational burden. We validate the efficiency of the proposed algorithms by testing the causal relation between the Medicare Hospital Readmission Reduction Program (HRRP) and non-index readmissions (i.e., readmission to a hospital that is different from the hospital that discharged the patient) from the State of California Patient Discharge Database from 2010 to 2014. Our result shows that HRRP has a causal relation with the increase in non-index readmissions. The proposed algorithms proved to be highly scalable in testing causal relations from large-scale observational studies.

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.