Ist die Evolution von Grippeviren vorhersehbar?

Richard Neher
Biozentrum, University of Basel

slides at


tobacco mosaic virus (Thomas Splettstoesser, wikipedia)

bacteria phage (adenosine, wikipedia)

influenza virus wikipedia

human immunodeficiency virus (HIV) wikipedia
  • Viren benötigen Wirtszellen zur Replikation
  • sind wenig mehr als Genom + Kapsid
  • ihr Genom ist 5-200Tsd Basen lang (+Ausnahmen)
  • zahlenmäßig dominierenden Organismen $\sim 10^{31}$

Influenza virus

  • Surface proteins hemagglutinin (HA) and neuraminidase (NA)
  • Influenza A virus
    • Common in birds and mammals
    • Many different subtypes defined by surface proteins
    • H3N2, H1N1, H7N9, H5N1
  • Influenza B virus
    • infects mainly humans
    • two lineages that split 30-40y ago
    • B/Victoria vs B/Yamagata

Human Influenza A viruses

slide by Trevor Bedford

Weekly numbers of positive influenza tests in the US by subtype

Data by the US CDC

Tracking virus spread and evolution by sequencing




... thousands of sequences...

Phylogenetic analysis of viral sequences

RNA viruses have a high mutation rate. New mutations arise every few weeks.

  • Influenza virus evolves to avoid human immunity
  • Vaccines need frequent updates

joint work with Trevor Bedford & his lab

Can we predicting influenza virus evolution?

  • Extrapolate current trends
  • Predict based on historical patterns
  • Use the branching pattern to predict success
  • Measure antigenic properties of circulating viruses
RN, Russell, Shraiman, eLife, 2014

Fitness inference from trees

$$P(\mathbf{x}|T) = \frac{1}{Z(T)} p_0(x_0) \prod_{i=0}^{n_{int}} g(x_{i_1}, t_{i_1}| x_i, t_i)g(x_{i_2}, t_{i_2}| x_i, t_i)$$
RN, Russell, Shraiman, eLife, 2014

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

joint work with Trevor Bedford & his lab


  • RNA viruses evolve fast
  • Viral lineages pick up mutations every few weeks
  • Genomic sequences can be used to track viral spread
  • Algorithms can predict future influenza virus variants
  • Automated real-time analysis can help fight the spread of disease

Joint work with....

  • Boris Shraiman
  • Colin Russell
  • Trevor Bedford

  • Trevor Bedford
  • Colin Megill
  • Pavel Sagulenko
  • Sidney Bell
  • James Hadfield
  • Wei Ding