This document discusses investigating the spatial epidemiology of zoonotic viral haemorrhagic fevers such as Ebola. It examines using species distribution models to spatially assess the potential for animal transmission of diseases like Ebola to humans. It also examines using these models to spatially assess how diseases spread through human populations after initial transmission. The document outlines how boosted regression trees can be used to model disease suitability based on environmental correlates and make predictions about potential risk areas. It concludes by discussing the need to better understand disease dynamics in animal reservoirs and human exposure risk to predict spillover events.

1. Investigating the spatial
epidemiology of zoonotic viral
haemorrhagic fevers
David Pigott; pigottdm@uw.edu
Thursday, 17th March 2016

2. Hypothetical outbreak progression
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3. Suspected life-cycle of Ebolavirus
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4. Considering Ebola spatially
• Zoonotic transmission of Ebola
o Spatial consideration of potential for animals to spread
EVD
o Identify risk areas for “spillover” infections
.V.
• Secondary human-to-human transmission of Ebola
o Spatial assessment of how disease propagates
through human populations
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5. Species distribution models
• Consider a species
oThree factors influence
where it can be found
─ Biotic
─ Abiotic
─ Movement
• How can we leverage
covariate information to
characterise the niche
of a disease?
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B A
Picture: Freya Shearer (based upon Peterson et al. 2008)

6. Species distribution models
• Using models to interpret variation in reported occurrences within
environmental space
o Extract environmental correlates at case/control locations
o Model suitability as a non-linear function of environmental
correlates
o Make predictions for all other cells
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Picture: Nick Golding

7. How BRTs work
• Combine regression trees with boosting
Boosting: apply shrinkage and iteratively improve
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Elith et al. (2008). J Anim Ecol, 77: 802-813.

8. How BRTs work
• Bootstrapping to estimate prediction uncertainty
Ebola:
200-times shrinkage;
10-fold cross-validation; Area under the curve validation
500 bootstrap submodels
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9. Ebola
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Ebola index cases Background samples Covariates

10. Zoonotic risk of EVD
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11. Next steps?
• What is the true nature of
risk?
o Dynamics in reservoirs?
o Spillover exposure?
o Human element of risk?
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Plowright et al. (2015) Ecological dynamics of
emerging bat virus spillover Proc Roy Soc B
Dynamics of Hendra virus
infection

12. Next steps
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13. Acknowledgements
• Multiple members of the Spatial Ecology and Epidemiology
Group, Oxford as well as collaborators internationally
• Mapping reference
o Pigott, Golding et al. (2014) Mapping the zoonotic niche of Ebola
virus disease eLife
• Some SDM resources
o Elith et al. (2008) A working guide to boosted regression trees J.
Anim. Ecol.
o Peterson et al. (2011) Ecological Niches and Geographic
Distributions
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