Viruses, evolution and epidemiology
Trevor Bedford (@trvrb)
Sequence pathogen genomes to reconstruct epidemic spread
Epidemic process
Sample some individuals
Sequence and determine phylogeny
Sequence and determine phylogeny
Outline
- Ebola spread in West Africa
- Zika spread in the Americas
Ebola
Ebola epidemic in West Africa
Virus genomes reveal factors that spread and sustained the Ebola epidemic
with 
Gytis Dudas, Andrew Rambaut, Luiz Carvalho, Marc Suchard, Philippe Lemey,
and many others
Sequencing of 1610 Ebola virus genomes collected during the 2013-2016 West African epidemic
Phylogenetic reconstruction of evolution and spread
Tracking migration events
Factors influencing migration rates
Spatial structure at the country level
Substantial mixing at the regional level
Regional outbreaks due to multiple introductions
Zika
Zika's arrival and spread in the Americas
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
with Nuno Faria, Nick Loman, Oli Pybus, Luiz Alcantara, Ester Sabino, Josh Quick,
Alli Black,
Ingra Morales, Julien Thézé, Marcio Nunes, Jacqueline de Jesus,
Marta Giovanetti, Moritz Kraemer, Sarah Hill and many others
Road trip through northeast Brazil to collect samples and sequence
Case reports and diagnostics suggest initiation in northeast Brazil
Phylogeny infers an origin in northeast Brazil
Important analyses, let's make them more rapid and more automated
nextstrain
Project to conduct real-time molecular epidemiology and evolutionary analysis of emerging epidemics
with
Richard Neher,
James Hadfield,
Colin Megill,
Sidney Bell,
Charlton Callender,
Barney Potter,
and 
John Huddleston
nextstrain.org
Acknowledgements
Bedford Lab:
Alli Black,
Sidney Bell,
Gytis Dudas,
John Huddleston,
Barney Potter,
James Hadfield,
Louise Moncla
Influenza: WHO Global Influenza Surveillance Network, GISAID, Richard Neher, Colin Russell, Andrew Rambaut, Marc Suchard, Philippe Lemey, Steven Riley
Ebola: Gytis Dudas, Andrew Rambaut, Luiz Carvalho, Philippe Lemey, Marc Suchard, Andrew Tatem
Zika: Nick Loman, Nuno Faria, Oli Pybus, Josh Quick, Kristian Andersen, Nathan Grubaugh, Jason Ladner, Gustavo Palacios, Sharon Isern, Gytis Dudas, Alli Black, Barney Potter, Esther Ellis
Nextstrain: Richard Neher, James Hadfield, Colin Megill, Sidney Bell, Charlton Callender, Barney Potter, John Huddleston
