Investigating the spatial
epidemiology of zoonotic viral
haemorrhagic fevers
David Pigott; [email protected]
Thursday, 17th March 2016
Hypothetical outbreak progression
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Suspected life-cycle of Ebolavirus
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Considering Ebola spatially
• Zoonotic transmission of Ebola
oSpatial consideration of potential for animals to spread
EVD
o Identify risk areas for “spillover” infections
.V.
• Secondary human-to-human transmission of Ebola
oSpatial assessment of how disease propagates
through human populations
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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)
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
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.
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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Ebola
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Ebola index cases Background samples Covariates
Zoonotic risk of EVD
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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
Next steps
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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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