Real-time tracking of pathogen evolution and spread

Richard Neher
Biozentrum & SIB, University of Basel

slides at neherlab.org/201907_ECDC.html

Frequent mutations imply...

• most viruses in an outbreak differ from each other
• transmission chains are can be inferred
• transmission can be ruled out!
• geographic spread can be reconstructed
• phenotypic changes can be inferred (for some pathogens)

GISRS and GISAID -- Influenza virus surveillance

• comprehensive coverage of the world
• timely sharing of data -- often within 2-3 weeks of sampling
• hundreds of sequences per week (in peak months)

→ requires continuous analysis and easy dissemination

→ interpretable and intuitive visualization

Visualization features of nextstrain

• Regular and time scaled phylogenies
• Mutations are mapped to the tree
• Filtering to time interval, region, country, authors, ...
• Zoom into clades
• Information on specific viruses
• Color by amino acid or nucleotide
• Frequency trajectories of clades and mutations
• Color by antigenic advance, predictive scores, etc

Phylodynamic analysis with nextstrain

• input: metadata (csv table) + sequences
• composable snakemake pipeline
  • filtering (select relevant strains)
  • alignment
  • tree building (optionally time scaled trees)
  • ancestral state reconstruction and phylogeography
  • additional pathogen specific steps
• export to visualization
• runs in minutes to 1h

Web visualization with nextstrain

• fairly easy to set-up
  
• can be run locally (localhost)
  
• or be deployed on your own servers
• work in progress:
  • flexible branding
  • drag and drop features
  • (better docs...)