Real-time tracking of virus evolution

Trevor Bedford (@trvrb)
7 Mar 2017
Pew Annual Meeting
Santa Barbara, CA

Spread of plague in 14th century

Spread of swine flu in 2009

Sequencing to reconstruct epidemic spread

Epidemic process

Sample some individuals

Sequence and determine phylogeny

Sequence and determine phylogeny

Phylogenetic tracking has the capacity to revolutionize epidemiology

Tracking geographic spread of the Ebola epidemic

with Gytis Dudas, Luiz Carvalho, Marc Suchard, Philippe Lemey, Andrew Rambaut
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

Spatial structure at the country level

Substantial mixing at the regional level

Regional outbreaks due to multiple introductions

However, this has mostly been done in a retrospective manner

(with some notable exceptions, ala Kristian's recent Zika work)

nextstrain

Project to conduct real-time molecular epidemiology and evolutionary analysis of emerging epidemics

Richard Neher, Colin Megill, James Hadfield,
Charlton Callender, Sidney Bell, Barney Potter,
Sarah Murata,

nextstrain.org

Rapid on-the-ground sequencing by Ian Goodfellow, Matt Cotten and colleagues

Now with the Zika epidemic, we have the possibility of doing this in a closer to real-time fashion

Zika's arrival and spread in the Americas

Acknowledgements

Ebola: data producers, Gytis Dudas, Andrew Rambaut, Luiz Carvalho, Philippe Lemey, Marc Suchard, Andrew Tatem, Nick Loman, Ian Goodfellow, Matt Cotten, Paul Kellam, Kristian Andersen, Pardis Sabeti, many others

Zika: data producers, Kristian Andersen, Nathan Grubaugh, Nick Loman, Nuno Faria, Oliver Pybus, Josh Quick, Allison Black, Gytis Dudas, many others

Nextstrain: Richard Neher, Colin Megill, James Hadfield, Charlton Callender, Sarah Murata, Sidney Bell, Barney Potter