Recent progress in predictive modeling

Richard Neher & Trevor Bedford
Biozentrum, University of Basel & Fred Hutch Seattle

slides at

Tools and models

  • Tools ( /
    • Flexible display/analysis to HI/FRA data via nextflu
    • medium term: move to nextstrain with map
  • prediction
    • Spotting growing clades: Local branching index
    • Spotting growing clades: Frequency trajectories
    • Spotting growing clades: antigenic data



Useful additions?

  • host age?
  • flagging of recurrent mutations?
  • glycosylation
  • NA, other segments, ...

Prediction: Local Branching Index

  • Single time point
  • agnostic/ignorant of biology
  • Similar to Luksza/Laessig's phylogenetic component

Prediction: Frequencies

  • With time resolved data, more accurate extrapolation should be possible
  • Nextflu estimates smoothed frequency trajectories
  • Region specific frequencies could use all available data
  • Concerns regarding oversampling of certains regions/cities

Prediction: antigenic data

  • Antigenic advance is associated with success
  • Small advanced clades nevertheless die out


  • Combining different signals requires parameters
  • We have only about 20y to train models on
  • Overfitting is a serious concern
  • Generate more data: Sequence 200 viruses per year from 1970 - 1995??