Virus evolution and the predictability of next year's flu


Richard Neher
Biozentrum, University of Basel


slides at neherlab.org/201711_dinosaurs.html

Human seasonal influenza viruses

slide by Trevor Bedford


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

nextflu.org

joint work with Trevor Bedford & his lab

Beyond tracking: can we predict?

Clonal interference and traveling waves

RN, Annual Reviews, 2013; Desai & Fisher; Brunet & Derrida; Kessler & Levine

Predicting evolution

Given the branching pattern:

  • can we predict fitness?
  • pick the closest relative of the future?
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

Hemagglutination Inhibition assays

Slide by Trevor Bedford

HI data sets

  • Long list of distances between sera and viruses
  • Tables are sparse, only close by pairs
  • Structure of space is not immediately clear
  • MDS in 2 or 3 dimensions
Smith et al, Science 2002
Slide by Trevor Bedford

Integrating antigenic and molecular evolution

  • $H_{a\beta} = v_a + p_\beta + \sum_{i\in (a,b)} d_i$
  • each branch contributes $d_i$ to antigenic distance
  • sparse solution for $d_i$ through $l_1$ regularization
  • related model where $d_i$ are associated with substitutions
RN et al, PNAS, 2016

HI distances on the phylogenetic tree

nextstrain.org

joint work with Trevor Bedford & his lab

Summary

  • RNA virus evolution can be observed directly
  • Rapidly adapting population require new population genetic models
  • Those model can be used to infer fit clades
  • Future influenza population can be anticipated
  • Automated real-time analysis can help fight the spread of disease

Influenza and Theory acknowledgments

  • Boris Shraiman
  • Colin Russell
  • Trevor Bedford
  • Oskar Hallatschek

nextstrain.org

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