論文

査読有り 国際誌
2019年3月18日

Reconstructing foot-and-mouth disease outbreaks: a methods comparison of transmission network models.

Scientific reports
  • Simon M Firestone
  • ,
  • Yoko Hayama
  • ,
  • Richard Bradhurst
  • ,
  • Takehisa Yamamoto
  • ,
  • Toshiyuki Tsutsui
  • ,
  • Mark A Stevenson

9
1
開始ページ
4809
終了ページ
4809
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1038/s41598-019-41103-6

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 network models based on a set of foot-and-mouth disease outbreaks simulated in a previously free country, with corresponding simulated phylogenies and genomic samples from animals on infected premises. Of the transmission network models tested, Lau's systematic Bayesian integration framework was found to be the most accurate for inferring the transmission network and timing of exposures, correctly identifying the source of 73% of the infected premises (with 91% accuracy for sources with model support >0.80). The Structured COalescent Transmission Tree Inference provided the most accurate inference of molecular clock rates. This validation study points to which models might be reliably used to reconstruct similar future outbreaks and how to interpret the outputs to inform control. Further research could involve extending the best-performing models to explicitly represent within-host diversity so they can handle next-generation sequencing data, incorporating additional animal and farm-level covariates and combining predictions using Ensemble methods and other approaches.

リンク情報
DOI
https://doi.org/10.1038/s41598-019-41103-6
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/30886211
PubMed Central
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423326
ID情報
  • DOI : 10.1038/s41598-019-41103-6
  • PubMed ID : 30886211
  • PubMed Central 記事ID : PMC6423326

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