Journal article
Reconstructing foot-and-mouth disease outbreaks: a methods comparison of transmission network models
SM Firestone, Y Hayama, R Bradhurst, T Yamamoto, T Tsutsui, MA Stevenson
Scientific Reports | NATURE PORTFOLIO | Published : 2019
Abstract
A number of transmission network models are available that combine genomic and epidemiological data to reconstruct networks of who infected whom during infectious disease outbreaks. For such models to reliably inform decision-making they must be transparently validated, robust, and capable of producing accurate predictions within the short data collection and inference timeframes typical of outbreak responses. A lack of transparent multi-model comparisons reduces confidence in the accuracy of transmission network model outputs, negatively impacting on their more widespread use as decision-support tools. We undertook a formal comparison of the performance of nine published transmission networ..
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Awarded by Australian Research Council
Funding Acknowledgements
This research was supported by an Australian Research Council Discovery Early Career Researcher Award (project number DE160100477). Components of this research were undertaken on the Melbourne Bioinformatics High Performance Cluster (grant number VR0277) and the Spartan HPC-Cloud Chimera (project 0549). The AADIS model was initially developed by the Australian Government Department of Agriculture and Water Resources in collaboration with the University of New England and has kindly been made available to support this research. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. The authors would also like to acknowledge helpful comments on the research provided by colleagues in the National Institute of Animal Health (NIAH), Japan and the Asia-Pacific Centre for Animal Health (The University of Melbourne); Graeme Garner (DAWR, Canberra); Sebastian Duchene (Bio21 Institute, The University of Melbourne), the authors of models compared in this study, especially those consulted during the study and comments from the reviewers that improved the manuscript.