Tracking and predicting the spread of infectious disease


Richard Neher
Biozentrum, University of Basel


slides at neherlab.org/201811_Novartis_visit.html

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)

nextstrain.org

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

Acknowledgments

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

Acknowledgments

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