HIV1 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