Tracking and predicting the spread of infectious disease

Richard Neher
Biozentrum, University of Basel

slides at

Human seasonal influenza viruses

slide by Trevor Bedford

Sequences record the spread of pathogens

images by Trevor Bedford

Real-time analysis with nextstrain

Prediction of the dominating H3N2 influenza strain

  • no influenza specific input
  • how can the model be improved? (see model by Luksza & Laessig)
  • what other context might this apply?
RN, Russell, Shraiman, eLife, 2014

Enterovirus D68 -- with Jan Albert and Robert Dyrdak

  • Non-polio enterovirus
  • Large outbreak in 2014 with severe neurological symptoms in young children
    (acute flaccid myelitis)
  • Another outbreak in 2016
  • Outbreaks tend to start in late summer/fall
  • Several reports of EV-D68 outbreaks in the past 6 weeks
    (255 (suspected) AFM cases in the US as of this week)

joint project with Trevor Bedford & his lab

Campylobacter Jejeuni in the Basel area (Reist, Seth-Smith et al)

Campylobacter Jejeuni in the Basel area (Reist, Seth-Smith et al)

Species trees and gene trees

Phenotype associations with acquired genes

Plasmid phylogenies


  • Trevor Bedford
  • Colin Megill
  • Pavel Sagulenko
  • Sidney Bell
  • James Hadfield
  • Wei Ding
  • Emma Hodcroft
  • Sanda Dejanic


  • Robert Dyrdak
  • Jan Albert
  • Lina Thebo
  • Emma Hodcroft