Real-time genomic surveillance of pathogen evolution and spread
Trevor Bedford (@trvrb)
19 Jun 2017
Viral Pathogenesis Symposium
Fred Hutch
Spread of plague in 14th century
Spread of swine flu in 2009
Sequencing to reconstruct pathogen spread
Epidemic process
Sample some individuals
Sequence and determine phylogeny
Sequence and determine phylogeny
Localized Middle Eastern MERS-CoV phylogeny
Regional West African Ebola phylogeny
Global influenza phylogeny
Phylogenetic tracking has the capacity to revolutionize epidemiology
Outline
- Ebola spread in West Africa
- Zika spread in the Americas
- "Real-time" analyses
Ebola
Tracking geographic spread of 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
Effect of borders on migration rates
Spatial structure at the country level
Substantial mixing at the regional level
Regional outbreaks due to multiple introductions
Ebola spread in West Africa followed a gravity model with moderate slowing by international borders, in which spread is driven by short-lived migratory clusters
Zika
Zika's arrival and spread in the Americas
Tracking origins of the Zika epidemic
with Nuno Faria, Nick Loman, Oli Pybus, Luiz Alcantara, Ester Sabino, Josh Quick, Allison 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
Local spread of Zika in Florida
with Nathan Grubaugh, Kristian Andersen, Jason Ladner, Gustavo Palacios, Sharon Isern, Oli Pybus, Moritz Kraemer, Gytis Dudas, Amanda Tan, Karthik Gangavarapu, Michael Wiley, Stephen White, Julien Thézé, Scott Michael, Leah Gillis, Pardis Sabeti, and many others
Outbreak of locally-acquired infections focused in Miami-Dade county
Phylogeny shows a surprising degree of clustering
Genomic epidemiology of Zika in the US Virgin Islands
with Allison Black, Barney Potter, Esther Ellis, Brett Ellis, Kristian Andersen,
Nathan Grubaugh, Leora Feldstein, and others
Preliminary analysis of 20 genomes shows multiple introductions to USVI
Important analyses, let's make them more rapid and more automated
Key challenges
- Timely analysis and sharing of results critical
- Dissemination must be scalable
- Integrate many data sources
- Results must be easily interpretable and queryable
nextstrain
Project to conduct real-time molecular epidemiology and evolutionary analysis of emerging epidemics
Richard Neher,
Trevor Bedford,
James Hadfield,
Colin Megill,
Sidney Bell,
Charlton Callender,
Barney Potter,
Sarah Murata,
Nextstrain architecture
All code open source at github.com/nextstrain
nextstrain.org
Rapid on-the-ground sequencing by Ian Goodfellow, Matt Cotten and colleagues
Desired analytics are pathogen specific and tied to response measures
Acknowledgements
Ebola: 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: Nick Loman, Nuno Faria, Oliver Pybus, Josh Quick, Kristian Andersen, Nathan Grubaugh, Jason Ladner, Gustavo Palacios, Sharon Isern, Gytis Dudas, Allison Black, Barney Potter, Esther Ellis, many others
Nextstrain: Richard Neher, James Hadfield, Colin Megill, Sidney Bell, Charlton Callender, Barney Potter, Sarah Murata
