Tracking SARS-Cov-2 using viral genomes and projecting its spread
Richard Neher
Biozentrum, University of Basel
slides at neherlab.org/202004_Ellis.html
- 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
- 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.