A simple approach to measure transmissibility and forecast incidence

被引:40
作者
Nouvellet, Pierre [1 ,2 ]
Cori, Anne [1 ]
Garske, Tini [1 ]
Blake, Isobel M. [1 ]
Dorigatti, Ilaria [1 ]
Hinsley, Wes [1 ]
Jombart, Thibaut [1 ,2 ]
Mills, Harriet L. [1 ]
Nedjati-Gilani, Gemma [1 ]
Van Kerkhove, Maria D. [1 ,3 ]
Fraser, Christophe [1 ,2 ]
Donnelly, Christl A. [1 ,2 ]
Ferguson, Neil M. [1 ,2 ]
Riley, Steven [1 ,2 ]
机构
[1] Imperial Coll London, MRC Ctr Outbreak Anal & Modelling, Fac Med, London, England
[2] Imperial Coll London, Natl Inst Hlth Res, Fac Med, Hlth Protect Res Unit Modelling Methodol, London, England
[3] Inst Pasteur, Ctr Global Hlth, Paris, France
基金
英国医学研究理事会; 英国惠康基金; 美国国家卫生研究院;
关键词
Forecasting; Rapid response; Branching process; Renewal equation; MCMC; EBOLA-VIRUS DISEASE; WEST-AFRICA; EPIDEMICS; OUTBREAKS; NUMBERS;
D O I
10.1016/j.epidem.2017.02.012
中图分类号
R51 [传染病];
学科分类号
100401 ;
摘要
Outbreaks of novel pathogens such as SARS, pandemic influenza and Ebola require substantial investments in reactive interventions, with consequent implementation plans sometimes revised on a weekly basis. Therefore, short-term forecasts of incidence are often of high priority. In light of the recent Ebola epidemic in West Africa, a forecasting exercise was convened by a network of infectious disease modellers. The challenge was to forecast unseen "future" simulated data for four different scenarios at five different time points. In a similar method to that used during the recent Ebola epidemic, we estimated current levels of transmissibility, over variable time-windows chosen in an ad hoc way. Current estimated transmissibility was then used to forecast near-future incidence. We performed well within the challenge and often produced accurate forecasts. A retrospective analysis showed that our subjective method for deciding on the window of time with which to estimate transmissibility often resulted in the optimal choice. However, when near-future trends deviated substantially from exponential patterns, the accuracy of our forecasts was reduced. This exercise highlights the urgent need for infectious disease modellers to develop more robust descriptions of processes - other than the widespread depletion of susceptible individuals - that produce non-exponential patterns of incidence. (c) 2017 The Authors. Published by Elsevier B.V.
引用
收藏
页码:29 / 35
页数:7
相关论文
共 23 条
[1]   Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study [J].
Agua-Agum, Junerlyn ;
Ariyarajah, Archchun ;
Aylward, Bruce ;
Bawo, Luke ;
Bilivogui, Pepe ;
Blake, Isobel M. ;
Brennan, Richard J. ;
Cawthorne, Amy ;
Cleary, Eilish ;
Clement, Peter ;
Conteh, Roland ;
Cori, Anne ;
Dafae, Foday ;
Dahl, Benjamin ;
Dangou, Jean-Marie ;
Diallo, Boubacar ;
Donnelly, Christl A. ;
Dorigatti, Ilaria ;
Dye, Christopher ;
Eckmanns, Tim ;
Fallah, Mosoka ;
Ferguson, Neil M. ;
Fiebig, Lena ;
Fraser, Christophe ;
Garske, Tini ;
Gonzalez, Lice ;
Hamblion, Esther ;
Hamid, Nuha ;
Hersey, Sara ;
Hinsley, Wes ;
Jambei, Amara ;
Jombart, Thibaut ;
Kargbo, David ;
Keita, Sakoba ;
Kinzer, Michael ;
George, Fred Kuti ;
Godefroy, Beatrice ;
Gutierrez, Giovanna ;
Kannangarage, Niluka ;
Mills, Harriet L. ;
Moller, Thomas ;
Meijers, Sascha ;
Mohamed, Yasmine ;
Morgan, Oliver ;
Nedjati-Gilani, Gemma ;
Newton, Emily ;
Nouvellet, Pierre ;
Nyenswah, Tolbert ;
Perea, William ;
Perkins, Devin .
PLOS MEDICINE, 2016, 13 (11)
[2]   Ebola Virus Disease among Male and Female Persons in West Africa [J].
Agua-Agum, Junerlyn ;
Ariyarajah, Archchun ;
Blake, Isobel M. ;
Cori, Anne ;
Donnelly, Christl A. ;
Dorigatti, Ilaria ;
Dye, Christopher ;
Eck-Manns, Tim ;
Ferguson, Neil M. ;
Fraser, Christophe ;
Garske, Tini ;
Hinsley, Wes ;
Jombart, Thibaut ;
Mills, Harriet L. ;
Nedjati-Gilani, Gemma ;
Newton, Emily ;
Nouvellet, Pierre ;
Perkins, Devin ;
Riley, Steven ;
Schumacher, Dirk ;
Shah, Anita ;
Thomas, Lisa J. ;
Van Kerkhove, Maria D. .
NEW ENGLAND JOURNAL OF MEDICINE, 2016, 374 (01) :96-98
[3]   Ebola Virus Disease among Children in West Africa [J].
Agua-Agum, Junerlyn ;
Ariyarajah, Archchun ;
Blake, Isobel M. ;
Cori, Anne ;
Donnelly, Christl A. ;
Dorigatti, Ilaria ;
Dye, Christopher ;
Eckmanns, Tim ;
Ferguson, Neil M. ;
Fowler, Robert A. ;
Fraser, Christophe ;
Garske, Tini ;
Hinsley, Wes ;
Jombart, Thibaut ;
Mills, Harriet L. ;
Murthy, Srinivas ;
Nedjati-Gilani, Gemma ;
Nouvellet, Pierre ;
Pelletier, Louise ;
Riley, Steven ;
Schumacher, Dirk ;
Shah, Anita ;
Van Kerkhove, Maria D. .
NEW ENGLAND JOURNAL OF MEDICINE, 2015, 372 (13) :1274-1277
[4]   Ebola Virus Disease in West Africa - The First 9 Months of the Epidemic and Forward Projections [J].
Aylward, Bruce ;
Barboza, Philippe ;
Bawo, Luke ;
Bertherat, Eric ;
Bilivogui, Pepe ;
Blake, Isobel ;
Brennan, Rick ;
Briand, Sylvie ;
Chakauya, Jethro Magwati ;
Chitala, Kennedy ;
Conteh, Roland M. ;
Cori, Anne ;
Croisier, Alice ;
Dangou, Jean-Marie ;
Diallo, Boubacar ;
Donnelly, Christl A. ;
Dye, Christopher ;
Eckmanns, Tim ;
Ferguson, Neil M. ;
Formenty, Pierre ;
Fuhrer, Caroline ;
Fukuda, Keiji ;
Garske, Tini ;
Gasasira, Alex ;
Gbanyan, Stephen ;
Graaff, Peter ;
Heleze, Emmanuel ;
Jambai, Amara ;
Jombart, Thibaut ;
Kasolo, Francis ;
Kadiobo, Albert Mbule ;
Keita, Sakoba ;
Kertesz, Daniel ;
Kone, Moussa ;
Lane, Chris ;
Markoff, Jered ;
Massaquoi, Moses ;
Mills, Harriet ;
Mulba, John Mike ;
Musa, Emmanuel ;
Myhre, Joel ;
Nasidi, Abdusalam ;
Nilles, Eric ;
Nouvellet, Pierre ;
Nshimirimana, Deo ;
Nuttall, Isabelle ;
Nyenswah, Tolbert ;
Olu, Olushayo ;
Pendergast, Scott ;
Perea, William .
NEW ENGLAND JOURNAL OF MEDICINE, 2014, 371 (16) :1481-1495
[5]   Investigating heterogeneity in pneumococcal transmission:: A Bayesian-MCMC approach applied to a follow-up of schools [J].
Cauchemez, Simon ;
Temime, Laura ;
Guillemot, Didier ;
Varon, Emmanuelle ;
Valleron, Alain-Jacques ;
Thomas, Guy ;
Boelle, Perre-Yves .
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 2006, 101 (475) :946-958
[6]   Mathematical modeling of the West Africa Ebola epidemic [J].
Chretien, Jean-Paul ;
Riley, Steven ;
George, Dylan B. .
ELIFE, 2015, 4
[7]  
Cori A., 2017, PHILOS T B IN PRESS
[8]   A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics [J].
Cori, Anne ;
Ferguson, Neil M. ;
Fraser, Christophe ;
Cauchemez, Simon .
AMERICAN JOURNAL OF EPIDEMIOLOGY, 2013, 178 (09) :1505-1512
[9]   Estimating Individual and Household Reproduction Numbers in an Emerging Epidemic [J].
Fraser, Christophe .
PLOS ONE, 2007, 2 (08)
[10]   Predicting the Epidemic Sizes of Influenza A/H1N1, A/H3N2, and B: A Statistical Method [J].
Goldstein, Edward ;
Cobey, Sarah ;
Takahashi, Saki ;
Miller, Joel C. ;
Lipsitch, Marc .
PLOS MEDICINE, 2011, 8 (07)