Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

Nuno Rodrigues Faria, Marc A. Suchard, Andrew Rambaut, Daniel G. Streicker, Philippe Lemey

Research output: Contribution to journalArticlepeer-review


The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens, despite being central for the development of predictive models and assessing the efficacy of prevention strategies. Here, we describe a flexible Bayesian statistical framework to reconstruct virus transmission between different host species based on viral gene sequences, while simultaneously testing and estimating the contribution of several potential predictors of cross-species transmission. Specifically, we use a generalized linear model extension of phylogenetic diffusion to perform Bayesian model averaging over candidate predictors. By further extending this model with branch partitioning, we allow for distinct host transition processes on external and internal branches, thus discriminating between recent cross-species transmissions, many of which are likely to result in dead-end infections, and host shifts that reflect successful onwards transmission in the new host species. Our approach corroborates genetic distance between hosts as a key determinant of both host shifts and cross-species transmissions of rabies virus in North American bats. Furthermore, our results indicate that geographical range overlap is a modest predictor for cross-species transmission, but not for host shifts. Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes.

Original languageEnglish
Article number20120196
Pages (from-to)-
Number of pages9
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Issue number1614
Publication statusPublished - 19 Mar 2013


  • Bayesian diffusion models
  • branch partitioning
  • cross-species transmission
  • rabies virus

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