Molecular evolution of viruses of the family Filoviridae based on 97 whole-genome sequences

Abstract

Viruses in the Ebolavirus and Marburgvirus genera (family Filoviridae) have been associated with large outbreaks of hemorrhagic fever in human and nonhuman primates. The first documented cases occurred in primates over 45 years ago, but the amount of virus genetic diversity detected within bat populations, which have recently been identified as potential reservoir hosts, suggests that the filoviruses are much older. Here, detailed Bayesian coalescent phylogenetic analyses are performed on 97 whole-genome sequences, 55 of which are newly reported, to comprehensively examine molecular evolutionary rates and estimate dates of common ancestry for viruses within the family Filoviridae. Molecular evolutionary rates for viruses belonging to different species range from 0.46 × 10(-4) nucleotide substitutions/site/year for Sudan ebolavirus to 8.21 × 10(-4) nucleotide substitutions/site/year for Reston ebolavirus. Most recent common ancestry can be traced back only within the last 50 years for Reston ebolavirus and Zaire ebolavirus species and suggests that viruses within these species may have undergone recent genetic bottlenecks. Viruses within Marburg marburgvirus and Sudan ebolavirus species can be traced back further and share most recent common ancestors approximately 700 and 850 years before the present, respectively. Examination of the whole family suggests that members of the Filoviridae, including the recently described Lloviu virus, shared a most recent common ancestor approximately 10,000 years ago. These data will be valuable for understanding the evolution of filoviruses in the context of natural history as new reservoir hosts are identified and, further, for determining mechanisms of emergence, pathogenicity, and the ongoing threat to public health.

Fig 1

Bayesian coalescent analysis of Ebola virus. The maximum clade credibility tree is shown with the MRCA, in years before 2008, at each node. Posterior probability values are shown beneath MRCA estimates. Scale is in substitutions/site.

Fig 2

Bayesian coalescent analysis of Sudan virus. The maximum clade credibility tree is shown with the MRCA, in years before 2011, at each node. Posterior probability values are shown beneath MRCA estimates. Scale is in substitutions/site.

Fig 3

Bayesian coalescent analysis of Reston virus. The maximum clade credibility tree is shown with the MRCA, in years before 2009, at each node. Posterior probability values are shown beneath MRCA estimates. Scale is in substitutions/site.

Fig 4

Bayesian coalescent analysis of viruses of the species Marburg marburgvirus. The maximum clade credibility tree is shown with the MRCA, in years before 2009, at each node. Posterior probability values are shown beneath MRCA estimates. Scale is in substitutions/site.

Fig 5

Bayesian coalescent analysis of viruses of the family Filoviridae. The maximum clade credibility tree is shown with the MRCA, in years before 2007, at each node. Posterior probability values are shown beneath MRCA estimates. Scale is in substitutions/site.