Outlook: Surveillance with Nextstrain

Richard Neher
Biozentrum, University of Basel

slides at neherlab.org/201810_NRP72_site_visit.html

GISRS and GISAID -- Influenza virus surveillance

  • comprehensive coverage of the world
  • timely sharing of data -- often within 2-3weeks of sampling
  • hundreds of sequences per week (in peak months)
→ requires continuous analysis and easy dissemination
→ interpretable and intuitive visualization

Real-time analysis with nextstrain

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

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

Ciprofloxacin resistance (Reist, Seth-Smith et al)

Species trees and gene trees

Phenotype associations with acquired genes

Plasmid phylogenies

Enterovirus D68 -- Collaboration 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
    (127 AFM cases in the US as of yesterday)

Whole genome deep sequencing

  • Geographic spread and phylogenetic patterns?
  • Immune escape?
  • Within host diversity?
  • Transmission bottlenecks/multiplicity of infection?


joint work with Jan Albert & his lab

Phylodynamic analysis

  • EV-D68 outbreaks come from distinct clades.
  • The evolutionary rate is very high -- a lot of power to study transmission chains
  • Most variation is synonymous
Dyrdak et al, biorxiv


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


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