Phylogenetic insights into Ebola dynamics in the unobserved reservoir


JT McCrone
Fred Hutch Cancer Center
May 23, 2024
VIDD retreat
St. Edward State Park

Ebola virus

  • (-) sense RNA virus ~18 Kb genome
  • 17 independent spillover events from a poorly characterized reservoir
  • Wide-spread mortality observed among great apes in Gabon and the Republic of Congo during the 1990s
  • Anti-Ebola antibodies and viral RNA have been detected in multiple bat species

Ebola evolution in humans

Keita, A. K, et al., 2021

Rate heterogeneity between outbreaks follows a similar pattern

A latent branch-rate model

evolutionary rate = 0| μ

latent $ \overset{\mbox{$\lambda$}}{\Leftrightarrow}$ replicating

Latent branches date back to initial epidemic wave

Geographic implications of 'slow-down' events

Simulations suggest more latent lineages exist

Hypothesis: Ebola dynamics in the reservoir

  • Active transmission from 1970-2014 seeding latent infections
  • Recent outbreaks (2014-present) stem from reactivated infections
  • Long-lived reservoir host
  • Dynamic spill-over threat
  • Unknown mechanism for latency

Thank you

University of Edinburgh

  • Andrew Rambaut
  • Ifeayni Omah
  • Verity Hill
  • Ben Jackson
  • Áine O'Toole
  • Rachel Colquhoun
  • Emily Scher
  • Shawn Yu
  • Guy Baele -KU Leuven

McCrone lab

  • Conner Copeland
  • Cristian Ovadiuc

Bedford lab

  • Nicola Muller

Matsen Group

  • Eric Matsen
  • Joseph Brew