Efficient real-time monitoring of an emerging influenza pandemic: how feasible?

DOI10.1214/19-AOAS1278zbMATH Open1439.62216arXiv1608.05292OpenAlexW3017166785MaRDI QIDQ2179944FDOQ2179944

Authors: Paul J. Birrell, Lorenz Wernisch, Brian D. M. Tom, Leonhard Held, Gareth O. Roberts, Richard G. Pebody, Daniela De Angelis 

Publication date: 13 May 2020

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: A prompt public health response to a new epidemic relies on the ability to monitor and predict its evolution in real time as data accumulate. The 2009 A/H1N1 outbreak in the UK revealed pandemic data as noisy, contaminated, potentially biased, and originating from multiple sources. This seriously challenges the capacity for real-time monitoring. Here we assess the feasibility of real-time inference based on such data by constructing an analytic tool combining an age-stratified SEIR transmission model with various observation models describing the data generation mechanisms. As batches of data become available, a sequential Monte Carlo (SMC) algorithm is developed to synthesise multiple imperfect data streams, iterate epidemic inferences and assess model adequacy amidst a rapidly evolving epidemic environment, substantially reducing computation time in comparison to standard MCMC, to ensure timely delivery of real-time epidemic assessments. In application to simulated data designed to mimic the 2009 A/H1N1 epidemic, SMC is shown to have additional benefits in terms of assessing predictive performance and coping with parameter non-identifiability.

Full work available at URL: https://arxiv.org/abs/1608.05292

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zbMATH Keywords

sequential Monte Carlopandemic influenzareal-time inferenceresample-moveSEIR transmission model

Mathematics Subject Classification ID

Time series, auto-correlation, regression, etc. in statistics (GARCH) (62M10) Applications of statistics to biology and medical sciences; meta analysis (62P10) Monte Carlo methods (65C05) Sequential estimation (62L12)

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Cited In (9)

• Joining and splitting models with Markov melding
• When did coronavirus arrive in Europe?
• Efficient real-time monitoring of an emerging influenza pandemic: how feasible?
• Accelerating Bayesian inference for stochastic epidemic models using incidence data
• Tracking epidemics with google flu trends data and a state-space SEIR model
• Synthesising evidence to estimate pandemic (2009) A/H1N1 influenza severity in 2009--2011
• Efficient empirical likelihood inference for recovery rate of COVID19 under double-censoring
• Joint quantification of transmission dynamics and diagnostic accuracy applied to influenza
• Evidence synthesis for stochastic epidemic models

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