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

Published version
Peer-reviewed

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Authors

Birrell, Paul J 
Wernisch, Lorenz 
Tom, Brian DM 
Held, Leonhard 
Roberts, Gareth O 

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.

Description

Keywords

stat.CO, stat.CO, stat.AP

Journal Title

Annals of Applied Statistics

Conference Name

Journal ISSN

1932-6157
1941-7330

Volume Title

14

Publisher

Institute of Mathematical Statistics

Rights

All rights reserved
Sponsorship
MRC (unknown)
Engineering and Physical Sciences Research Council (EP/R018561/1)
Engineering and Physical Sciences Research Council (EP/R034710/1)
MRC, NIHR