Population-level differences in disease transmission: a Bayesian analysis of multiple smallpox epidemics

Epidemics. 2013 Sep;5(3):146-56. doi: 10.1016/j.epidem.2013.07.001. Epub 2013 Jul 25.


Estimates of a disease's basic reproductive rate R0 play a central role in understanding outbreaks and planning intervention strategies. In many calculations of R0, a simplifying assumption is that different host populations have effectively identical transmission rates. This assumption can lead to an underestimate of the overall uncertainty associated with R0, which, due to the non-linearity of epidemic processes, may result in a mis-estimate of epidemic intensity and miscalculated expenditures associated with public-health interventions. In this paper, we utilize a Bayesian method for quantifying the overall uncertainty arising from differences in population-specific basic reproductive rates. Using this method, we fit spatial and non-spatial susceptible-exposed-infected-recovered (SEIR) models to a series of 13 smallpox outbreaks. Five outbreaks occurred in populations that had been previously exposed to smallpox, while the remaining eight occurred in Native-American populations that were naïve to the disease at the time. The Native-American outbreaks were close in a spatial and temporal sense. Using Bayesian Information Criterion (BIC), we show that the best model includes population-specific R0 values. These differences in R0 values may, in part, be due to differences in genetic background, social structure, or food and water availability. As a result of these inter-population differences, the overall uncertainty associated with the "population average" value of smallpox R0 is larger, a finding that can have important consequences for controlling epidemics. In general, Bayesian hierarchical models are able to properly account for the uncertainty associated with multiple epidemics, provide a clearer understanding of variability in epidemic dynamics, and yield a better assessment of the range of potential risks and consequences that decision makers face.

Keywords: Bayesian hierarchical models; Markov chain Monte Carlo (MCMC); Smallpox Variola major; Spatial epidemic dynamics; Uncertainty.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Africa / epidemiology
  • Bayes Theorem
  • Epidemics / statistics & numerical data*
  • Europe / epidemiology
  • Humans
  • Models, Biological*
  • Smallpox / epidemiology
  • Smallpox / transmission*
  • Uncertainty
  • United States / epidemiology