Tracking SARS-Cov-2 using viral genomes and projecting its spread

Richard Neher
Biozentrum, University of Basel

slides at

Tracking diversity and spread in nextstrain

  • We have 2500 full genomes now
  • Provides structure to the outbreak → resolves transmission chains and clusters
  • About one change every 2 weeks → limit to resolution
  • heavily affected by sampling and sequencing efforts
  • This isn't big data: nothing is iid

Predictions and scenarios

  • Substantial uncertainties in parameters
  • Uncertainties in how well interventions work, continuously changing policies and behavior
  • heterogeneity will become important as soon as you reach local saturation
  • transport and contact networks could be used to inform all of this.