Outbreak analytics: a developing data science for informing the response to emerging pathogens

Jonathan A. Polonsky, Amrish Baidjoe, Zhian N. Kamvar, Anne Cori, Kara Durski, W. John Edmunds, Rosalind M. Eggo, Sebastian Funk, Laurent Kaiser, Patrick Keating, Olivier le Polain de Waroux, Michael Marks, Paula Moraga, Oliver Morgan, Pierre Nouvellet, Ruwan Ratnayake, Chrissy H. Roberts, Jimmy Whitworth, Thibaut Jombart

Research output: Contribution to journalReview article

4 Citations (Scopus)

Abstract

Despite continued efforts to improve health systems worldwide, emerging pathogen epidemics remain a major public health concern. Effective response to such outbreaks relies on timely intervention, ideally informed by all available sources of data. The collection, visualization and analysis of outbreak data are becoming increasingly complex, owing to the diversity in types of data, questions and available methods to address them. Recent advances have led to the rise of outbreak analytics, an emerging data science focused on the technological and methodological aspects of the outbreak data pipeline, from collection to analysis, modelling and reporting to inform outbreak response. In this article, we assess the current state of the field. After laying out the context of outbreak response, we critically review the most common analytics components, their inter-dependencies, data requirements and the type of information they can provide to inform operations in real time. We discuss some challenges and opportunities and conclude on the potential role of outbreak analytics for improving our understanding of, and response to outbreaks of emerging pathogens. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.

Original languageEnglish
Article number20180276
Pages (from-to)1-11
Number of pages11
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Volume374
Issue number1776
Early online date20 May 2019
DOIs
Publication statusPublished - 1 Jul 2019

Keywords

  • Epidemics
  • Infectious
  • Methods
  • Pipeline
  • Software
  • Tools

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Polonsky, J. A., Baidjoe, A., Kamvar, Z. N., Cori, A., Durski, K., Edmunds, W. J., ... Jombart, T. (2019). Outbreak analytics: a developing data science for informing the response to emerging pathogens. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1776), 1-11. [20180276]. https://doi.org/10.1098/rstb.2018.0276

Outbreak analytics: a developing data science for informing the response to emerging pathogens. / Polonsky, Jonathan A.; Baidjoe, Amrish; Kamvar, Zhian N.; Cori, Anne; Durski, Kara; Edmunds, W. John; Eggo, Rosalind M.; Funk, Sebastian; Kaiser, Laurent; Keating, Patrick; le Polain de Waroux, Olivier; Marks, Michael; Moraga, Paula; Morgan, Oliver; Nouvellet, Pierre; Ratnayake, Ruwan; Roberts, Chrissy H.; Whitworth, Jimmy; Jombart, Thibaut.

In: Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 374, No. 1776, 20180276, 01.07.2019, p. 1-11.

Research output: Contribution to journalReview article

Polonsky, JA, Baidjoe, A, Kamvar, ZN, Cori, A, Durski, K, Edmunds, WJ, Eggo, RM, Funk, S, Kaiser, L, Keating, P, le Polain de Waroux, O, Marks, M, Moraga, P, Morgan, O, Nouvellet, P, Ratnayake, R, Roberts, CH, Whitworth, J & Jombart, T 2019, 'Outbreak analytics: a developing data science for informing the response to emerging pathogens', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 374, no. 1776, 20180276, pp. 1-11. https://doi.org/10.1098/rstb.2018.0276
Polonsky, Jonathan A. ; Baidjoe, Amrish ; Kamvar, Zhian N. ; Cori, Anne ; Durski, Kara ; Edmunds, W. John ; Eggo, Rosalind M. ; Funk, Sebastian ; Kaiser, Laurent ; Keating, Patrick ; le Polain de Waroux, Olivier ; Marks, Michael ; Moraga, Paula ; Morgan, Oliver ; Nouvellet, Pierre ; Ratnayake, Ruwan ; Roberts, Chrissy H. ; Whitworth, Jimmy ; Jombart, Thibaut. / Outbreak analytics: a developing data science for informing the response to emerging pathogens. In: Philosophical Transactions of the Royal Society B: Biological Sciences. 2019 ; Vol. 374, No. 1776. pp. 1-11.
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