title: Avoidable errors in the modelling of outbreaks of emerging pathogens, with special reference to Ebola.
abstract: As an emergent infectious disease outbreak unfolds, public health response is reliant on information on key epidemiological quantities, such as transmission potential and serial interval. Increasingly, transmission models fit to incidence data are used to estimate these parameters and guide policy. Some widely used modelling practices lead to potentially large errors in parameter estimates and, consequently, errors in model-based forecasts. Even more worryingly, in such situations, confidence in parameter estimates and forecasts can itself be far overestimated, leading to the potential for large errors that mask their own presence. Fortunately, straightforward and computationally inexpensive alternatives exist that avoid these problems. Here, we first use a simulation study to demonstrate potential pitfalls of the standard practice of fitting deterministic models to cumulative incidence data. Next, we demonstrate an alternative based on stochastic models fit to raw data from an early phase of 2014 West Africa Ebola virus disease outbreak. We show not only that bias is thereby reduced, but that uncertainty in estimates and forecasts is better quantified and that, critically, lack of model fit is more readily diagnosed. We conclude with a short list of principles to guide the modelling response to future infectious disease outbreaks.
authors.affiliation: Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI 48109, USA Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA kingaa@umich.edu.
authors.forename: Aaron A
authors.initials: AA
authors.lastname: King
authors.affiliation: Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Domenech de Cellès
authors.affiliation: Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Felicia M G
authors.initials: FM
authors.lastname: Magpantay
authors.affiliation: Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI 48109, USA Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Pejman
authors.initials: P
authors.lastname: Rohani
mesh_terms: D000354:Africa, Western / Q000453:epidemiology; D015982:Bias; D021821:Communicable Diseases, Emerging / Q000453:epidemiology* / Q000821:virology; D004196:Disease Outbreaks; D029043:Ebolavirus / Q000502:physiology*; D019142:Hemorrhagic Fever, Ebola / Q000453:epidemiology* / Q000821:virology; D006801:Humans; D008962:Models, Theoretical
keywords: Ebola virus disease; emerging infectious disease; forecast
references.citation: Proc Biol Sci. 2001 May 7;268(1470):985-93
references.pmid: 11370974
references.citation: J Theor Biol. 2003 Dec 21;225(4):419-30
references.pmid: 14615200
references.citation: BMC Med. 2014;12:196
references.pmid: 25300956
references.citation: Epidemiology. 2012 Jul;23(4):523-30
references.pmid: 22659546
references.citation: Science. 2009 Jun 19;324(5934):1557-61
references.pmid: 19433588
references.citation: Bull Math Biol. 2014 Jan;76(1):245-60
references.pmid: 24272389
references.citation: Science. 2003 Jun 20;300(5627):1966-70
references.pmid: 12766207
references.citation: PLoS Curr. 2014 Sep 18;6:null
references.pmid: 25642357
references.citation: Lancet. 2013 Aug 24;382(9893):694-9
references.pmid: 23831141
references.citation: PLoS Curr. 2014 Sep 02;6:null
references.pmid: 25642360
references.citation: Nature. 2001 Oct 4;413(6855):542-8
references.pmid: 11586365
references.citation: Science. 2001 Oct 26;294(5543):813-7
references.pmid: 11679661
references.citation: J R Soc Interface. 2010 Feb 6;7(43):271-83
references.pmid: 19535416
references.citation: PLoS Med. 2005 Jul;2(7):e174
references.pmid: 16013892
references.citation: PLoS Curr. 2014 Sep 08;6:null
references.pmid: 25642358
references.citation: Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):719-24
references.pmid: 25568084
references.citation: Nature. 1996 Aug 29;382(6594):779-88
references.pmid: 8752271
references.citation: Ann Intern Med. 2011 May 3;154(9):593-601
references.pmid: 21383314