Viral phylodynamics


Trevor Bedford, Allison Black and James Hadfield
18 Apr 2017
Comp Bio Symposium
Fred Hutch

Viral phylodynamics

Pybus and Rambaut. 2009.

Broad scale patterns

Global spread of influenza

Bedford et al 2015

Spread of Ebola in West Africa

 
Dudas et al 2017

Fine scale patterns

Outbreak of locally-acquired infections focused in Miami-Dade county

Grubaugh et al. 2017

Phylogeny shows local transmission rather than repeated introductions

Grubaugh et al. 2017

How can we generate genomic data quickly during global outbreaks?

Tracking origins of the Zika epidemic in Brazil

with Nuno Faria, Nick Loman, Oli Pybus, Luiz Alcantara, Ester Sabino, Josh Quick, Ingra Morales, Julien Thézé, Marcio Nunes, Jacqueline de Jesus, Marta Giovanetti, Moritz Kraemer, Sarah Hill and many others

Faria et al. 2017. bioRxiv.

Case reports and diagnostics suggest initiation in northeast Brazil

Faria et al. 2017

Road trip through northeast Brazil to collect samples and sequence

Phylogeny also supports outbreak origin in northeast Brazil

Faria et al. 2017

Genomic epidemiology of Zika in the US Virgin Islands

with Esther Ellis, Brett Ellis, Barney Potter, Leora Feldstein, and others





Preliminary analysis shows multiple introductions of Zika to USVI

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


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

Nextstrain architecture

Ebola









Ian Goodfellow, Matt Cotten et al

Zika













Avian influenza H7N9


nextstrain.org

Acknowledgements

Zika in Florida: Kristian Andersen, Nathan Grubaugh, Jason Ladner, Gustavo Palacios, Sharon Isern, Oli Pybus, Moritz Kraemer, Gytis Dudas, Amanda Tan, Karthik Gangavarapu, Michael Wiley, Stephen White, Julien Thézé, Scott Michael, many others

Zika in Brazil: Nuno Faria, Nick Loman, Oli Pybus, Luiz Alcantara, Ester Sabino, Josh Quick, Ingra Morales, Julien Thézé, Marcio Nunes, Jacqueline de Jesus, Marta Giovanetti, Moritz Kraemer, Sarah Hill, many others

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