Real-time evolutionary tracking for pathogen surveillance and epidemiological investigation

Trevor Bedford (@trvrb) and Richard Neher (@richardneher)
1 Dec 2016
BD2K Open Data Science Symposium
Bethesda, MD

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

Phylogenetic tracking has the capacity to revolutionize epidemiology

Detailed understanding of Ebola spread from sequence data

However, this has mostly been done in a retrospective manner


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

Key challenges

  • Timely analysis and sharing of results critical
  • Dissemination must be scalable
  • Integrate many data sources
  • Results must be easily interpretable and queryable

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 truly real-time fashion

Zika's arrival and spread in the Americas

Nextstrain working as an open science resource

  • Data from individual contributors become more interpretable
  • Nextstrain provides incentives for data sharing
  • Virtuous cycle maximizing public health benefits

Nextstrain development

  • Rapidly deployable platform for outbreak tracking
  • Efficient pipeline with automated updates
  • Comprehensive state of the art analysis
  • Intuitive yet powerful visualization

Nextstrain development team

Richard Neher, Trevor Bedford, Colin Megill,
Charlton Callender, Sarah Murata, Sidney Bell

Nextstrain architecture

New visualization at


Ebola: data producers, Gytis Dudas, Andrew Rambaut, Nick Loman, Ian Goodfellow, Paul Kellam, Danny Park, Kristian Andersen, Pardis Sabeti

Zika: data producers, Nick Loman, Kristian Andersen, Gytis Dudas, Nuno Faria, Andrew Rambaut, Oliver Pybus, Allison Black, Luiz Alcantara and the rest of the ZiBRA team

Nextstrain: Colin Megill, Charlton Callender, Sarah Murata, Sidney Bell