Real-time phylogenetic analysis of emerging pathogens

Richard Neher
Biozentrum, University of Basel

slides at

Human seasonal influenza viruses

slide by Trevor Bedford

  • Influenza viruses evolve to avoid human immunity
  • Vaccines need frequent updates

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

joint work with Trevor Bedford & his lab

joint project with Trevor Bedford & his lab

Using nextstrain -- phylodynamics analysis

  • input: metadata (csv table) + sequences (fasta or vcf)
  • snakemake pipeline
    • filtering
    • alignment
    • tree building (+time scaled trees)
    • ancestral state reconstruction and phylogeography
  • export to visualization
  • runs in minutes to 1h

Using nextstrain -- web visualization

  • can be run locally (localhost)
  • share your own builds through nextstrain/community
  • deploy nextstrain on your own servers
  • work in progress:
    • flexible branding
    • drag and drop features
    • (better docs...)

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

Global evolutionary patterns

  • Specific diversity clusters in VP3 and VP1
  • Coincide with homologous epitopes in other enteroviruses
  • But little evidence of escape between subclades
Dyrdak et al, biorxiv

Whole genome deep sequencing of Enterovirus D68

  • Amplified in 4 overlapping segments
  • Illumina sequenced to high coverage
Dyrdak et al, biorxiv

iSNV frequency accuracy and sequencing errors

  • iSNV frequencies reproducible above 1%
  • background at around 1/1000
Dyrdak et al, biorxiv

With-in host diversity

  • Above 0.5%, iSNVs are biological
  • Most samples have few iSNVs, three had more than 20
Dyrdak et al, biorxiv

Dual infections

  • A set of iSNVs at very similar frequencies in full linkage
  • Suggest infection with two related variants
  • 3 out of 50 samples: Implies high prevalence
Dyrdak et al, biorxiv


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


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