Evolution of RNA viruses

Richard Neher
Biozentrum, University of Basel

slides at neherlab.org/201802_swissnex.html

HIV-1 evolution within infected individuals

  • The HIV population is initially homogeneous
  • HIV changes and diversifies to evade the immune system
silouhette: clipartfest.com, Zanini at al, 2015. Collaboration with Jan Albert and his group

The evolving global population of influenza A/H3N2 viruses

  • Influenza viruses evolve to avoid human immunity
  • Grey crosses indicated past vaccine viruses
  • Vaccines need frequent updates

Positions in influenza haemaglutinin associated with escape from human immunity.

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