Real-time tracking of virus evolution

Trevor Bedford (@trvrb)
23 May 2018
AMD Seminar Series
CDC

We work at the interface of virology, evolution and epidemiology

Sequencing to reconstruct pathogen evolution and 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

• Influenza circulation and antigenic drift
• Ebola spread in West Africa
• Zika spread in the Americas
• "Real-time" analyses

Influenza

Influenza virion

Population turnover is extremely rapid

Clades emerge, die out and take over

Clades show rapid turnover

Dynamics driven by antigenic drift

Drift necessitates vaccine updates

H3N2 vaccine updates occur every ~2 years

Vaccine strain selection by WHO

Problem of applied evolutionary biology

Every paper in the field...

• "These observations have implications for influenza surveillance and vaccine formulation" (Wolf et al 2006)
• "Our results have implications for the design of vaccines to combat rapidly mutating viral diseases" (Gupta et al 2006)
• "These results may have important implications for influenza vaccine and antiviral research" (Bhatt et al 2011)
• "Needless to say, these results have important implications for the updating of vaccines against influenza" (Zinder et al 2013)

Disconnect between evolutionary studies and information needed by WHO

• WHO needs specific advice, ie this strain is likely to take off, this strain is likely to die out
• Problems of generality and timeliness

2014 workshop on microbial evolution at the Kavli Institute for Theoretical Physics

Decided to tackle this head on and build something that

1. Charts behavior of specific strains
2. Can be kept continually up to date

Nextflu

Project to provide a real-time view of the evolving influenza population

Nextflu

Project to provide a real-time view of the evolving influenza population

All in collaboration with Richard Neher

Nextflu pipeline

1. Download all recent HA sequences from GISAID
2. Filter to remove outliers
3. Subsample across time and space
4. Align sequences
5. Build tree
6. Estimate clade frequencies
7. Infer antigenic phenotypes
8. Export for visualization

Up-to-date analysis publicly available at:

Nextflu.org

Current H3N2 diversity

Current H3N2 diversity

Two clades have been growing rapidly

Clade A2 more recently increasing

Reassortment event appears to drive success of clade A2

Reassortment event appears to drive success of clade A2

Further methods to integrate serological data and forecast future strain turnover

Ebola

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

Sequenced genomes were representative of spatiotemporal diversity

Phylogenetic reconstruction of epidemic

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

Each introduction results in a minor outbreak

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

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

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 introductions from the Caribbean and a surprising degree of clustering

Flow of infected travelers greatest from Caribbean

Clustering suggests fewer, longer transmission chains and higher R₀

Genomic epidemiology of Zika in the US Virgin Islands

with Alli Black, Barney Potter, Gytis Dudas, Esther Ellis, Brett Ellis,
Kristian Andersen, Nathan Grubaugh, Leora Feldstein, and others
(and special thanks to Adam Geballe)

Preliminary analysis of 31 genomes shows multiple introductions to USVI

Actionable inferences

Genomic analyses were mostly done in a retrospective manner

Key challenges to making genomic epidemiology actionable

• 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

with Richard Neher, James Hadfield, Colin Megill,
Sidney Bell, John Huddleston, Barney Potter,
Charlton Callender, Emma Hodcroft

Nextstrain architecture

All code open source at github.com/nextstrain

Fauna

Rethink database of virus and titer data

• Harmonizes data from different sources
• Integrates different types of data (serology, sequences, case details)
• Provides an interface for downstream analysis

Augur

Build scripts to align sequences, build trees and annotate

• Flexible build scripts to incorporate different viruses and analyses
• Constructs time-resolved phylogenies
• Annotates with geographic transitions and mutation events

Example augur pipeline for 1600 Ebola genomes

• Align with MAFFT (34 min)
• Build ML tree with RAxML (54 min)
• Temporally resolve tree and geographic ancestry with TreeTime (16 min)
• Total pipeline (1 hr 46 min)

Auspice

Web visualization of resulting trees

• Interactive data exploration and filtering
• Framework through React / D3
• Connects phylogeny, geography and genotypes

nextstrain.org

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

Build out pipelines for different pathogens, improve databasing and lower
bioinformatics bar

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, Barney Potter, John Huddleston, Dave Wentworth, Becky Garten, Jackie Katz, Vivien Dugan, Xiyan Xu, Elizabeth Neuhaus, Sujatha Seenu

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, Alli Black, Jason Ladner, Gustavo Palacios, Sharon Isern, Gytis Dudas, Barney Potter, Esther Ellis

Nextstrain: Richard Neher, James Hadfield, Colin Megill, Sidney Bell, Charlton Callender, Barney Potter, John Huddleston, Emma Hodcroft